Krypton in PDB 8rxj: Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
Enzymatic activity of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
All present enzymatic activity of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton:
1.12.7.2;
Protein crystallography data
The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton, PDB code: 8rxj
was solved by
K.Bikbaev,
T.Harand,
L.Scheuenstuhl,
P.Carpentier,
I.Span,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.50 /
1.51
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.376,
86.931,
88.889,
90,
90,
90
|
R / Rfree (%)
|
15.8 /
18.6
|
Other elements in 8rxj:
The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton also contains other interesting chemical elements:
Krypton Binding Sites:
The binding sites of Krypton atom in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
(pdb code 8rxj). This binding sites where shown within
5.0 Angstroms radius around Krypton atom.
In total 10 binding sites of Krypton where determined in the
Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton, PDB code: 8rxj:
Jump to Krypton binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Krypton binding site 1 out
of 10 in 8rxj
Go back to
Krypton Binding Sites List in 8rxj
Krypton binding site 1 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 1 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr501
b:24.1
occ:0.40
|
HB3
|
A:GLU156
|
3.0
|
18.6
|
1.0
|
HZ
|
A:PHE372
|
3.0
|
27.5
|
1.0
|
HD13
|
A:ILE153
|
3.1
|
15.9
|
1.0
|
HG11
|
A:VAL302
|
3.1
|
18.5
|
1.0
|
HB1
|
A:ALA306
|
3.1
|
18.4
|
1.0
|
HG2
|
A:GLU156
|
3.2
|
21.1
|
1.0
|
HG12
|
A:VAL302
|
3.2
|
18.5
|
1.0
|
CD
|
A:GLU156
|
3.3
|
24.6
|
1.0
|
OE1
|
A:GLU156
|
3.3
|
24.0
|
1.0
|
CG1
|
A:VAL302
|
3.5
|
18.7
|
1.0
|
CG
|
A:GLU156
|
3.5
|
20.9
|
1.0
|
HG13
|
A:VAL302
|
3.6
|
18.5
|
1.0
|
CB
|
A:GLU156
|
3.7
|
18.4
|
1.0
|
OE2
|
A:GLU156
|
3.7
|
22.6
|
1.0
|
CD1
|
A:ILE153
|
3.7
|
16.0
|
1.0
|
HD11
|
A:ILE153
|
3.8
|
15.9
|
1.0
|
HD12
|
A:ILE153
|
3.8
|
15.9
|
1.0
|
CZ
|
A:PHE372
|
3.9
|
27.5
|
1.0
|
HG23
|
A:THR176
|
3.9
|
17.4
|
1.0
|
HE2
|
A:PHE372
|
3.9
|
28.3
|
1.0
|
KR
|
A:KR508
|
3.9
|
24.2
|
0.1
|
CB
|
A:ALA306
|
4.0
|
19.0
|
1.0
|
HB3
|
A:ALA306
|
4.1
|
18.4
|
1.0
|
HA
|
A:ILE153
|
4.1
|
16.5
|
1.0
|
HG23
|
A:THR152
|
4.2
|
17.1
|
1.0
|
HB2
|
A:GLU156
|
4.2
|
18.6
|
1.0
|
CE2
|
A:PHE372
|
4.3
|
28.9
|
1.0
|
HB2
|
A:ALA306
|
4.5
|
18.4
|
1.0
|
O
|
A:HOH705
|
4.5
|
26.3
|
1.0
|
HG3
|
A:GLU156
|
4.5
|
21.1
|
1.0
|
O
|
A:VAL302
|
4.5
|
17.6
|
1.0
|
HZ
|
A:PHE296
|
4.7
|
15.6
|
1.0
|
H
|
A:GLY157
|
4.7
|
21.4
|
1.0
|
O
|
A:HOH621
|
4.8
|
17.1
|
1.0
|
CG2
|
A:THR176
|
4.8
|
17.6
|
1.0
|
C
|
A:GLU156
|
4.8
|
20.1
|
1.0
|
HA
|
A:ALA306
|
4.8
|
17.3
|
1.0
|
N
|
A:GLY157
|
4.9
|
21.6
|
1.0
|
CA
|
A:GLU156
|
4.9
|
17.0
|
1.0
|
HG21
|
A:THR176
|
4.9
|
17.4
|
1.0
|
CB
|
A:VAL302
|
5.0
|
18.1
|
1.0
|
O
|
A:THR152
|
5.0
|
16.0
|
1.0
|
CE1
|
A:PHE372
|
5.0
|
26.4
|
1.0
|
|
Krypton binding site 2 out
of 10 in 8rxj
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Krypton Binding Sites List in 8rxj
Krypton binding site 2 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 2 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr502
b:26.1
occ:0.77
|
HD21
|
A:LEU307
|
2.9
|
22.5
|
1.0
|
HD2
|
A:PHE372
|
3.1
|
27.4
|
1.0
|
HB3
|
A:ALA306
|
3.3
|
18.4
|
1.0
|
HD2
|
A:PHE160
|
3.3
|
25.1
|
1.0
|
HE2
|
A:PHE160
|
3.3
|
24.6
|
1.0
|
HA
|
A:LEU307
|
3.4
|
18.2
|
1.0
|
HB1
|
A:ALA310
|
3.4
|
23.2
|
1.0
|
HE2
|
A:PHE372
|
3.6
|
28.3
|
1.0
|
HB2
|
A:ALA310
|
3.6
|
23.2
|
1.0
|
HB2
|
A:ALA306
|
3.6
|
18.4
|
1.0
|
HG
|
A:LEU307
|
3.7
|
21.0
|
1.0
|
CD2
|
A:LEU307
|
3.7
|
23.2
|
1.0
|
HD23
|
A:LEU307
|
3.7
|
22.5
|
1.0
|
CD2
|
A:PHE160
|
3.7
|
26.5
|
1.0
|
CE2
|
A:PHE160
|
3.8
|
23.9
|
1.0
|
C
|
A:ALA306
|
3.8
|
17.1
|
1.0
|
CB
|
A:ALA306
|
3.9
|
19.0
|
1.0
|
O
|
A:ALA306
|
3.9
|
18.0
|
1.0
|
CD2
|
A:PHE372
|
3.9
|
28.2
|
1.0
|
CB
|
A:ALA310
|
3.9
|
23.9
|
1.0
|
N
|
A:LEU307
|
4.0
|
16.0
|
1.0
|
HB3
|
A:ALA310
|
4.1
|
23.3
|
1.0
|
CA
|
A:LEU307
|
4.1
|
18.8
|
1.0
|
CE2
|
A:PHE372
|
4.1
|
28.9
|
1.0
|
CG
|
A:LEU307
|
4.2
|
20.9
|
1.0
|
KR
|
A:KR508
|
4.2
|
24.2
|
0.1
|
H
|
A:LEU307
|
4.3
|
16.9
|
1.0
|
HG13
|
A:VAL345
|
4.4
|
32.2
|
1.0
|
HG13
|
A:VAL347
|
4.4
|
23.4
|
1.0
|
CA
|
A:ALA306
|
4.5
|
17.0
|
1.0
|
HD22
|
A:LEU307
|
4.5
|
22.6
|
1.0
|
KR
|
A:KR503
|
4.6
|
37.9
|
0.6
|
SD
|
A:MET303
|
4.6
|
22.6
|
1.0
|
HB1
|
A:ALA306
|
4.7
|
18.4
|
1.0
|
CB
|
A:LEU307
|
4.7
|
19.5
|
1.0
|
O
|
A:MET303
|
4.8
|
17.0
|
1.0
|
CG
|
A:PHE160
|
4.9
|
23.8
|
1.0
|
CZ
|
A:PHE160
|
4.9
|
24.8
|
1.0
|
H
|
A:ALA310
|
4.9
|
19.8
|
1.0
|
|
Krypton binding site 3 out
of 10 in 8rxj
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Krypton Binding Sites List in 8rxj
Krypton binding site 3 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 3 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr503
b:37.9
occ:0.57
|
HB3
|
A:ALA310
|
2.9
|
23.3
|
1.0
|
HG21
|
A:VAL345
|
3.0
|
32.0
|
1.0
|
HE2
|
A:PHE160
|
3.2
|
24.6
|
1.0
|
HD11
|
A:LEU164
|
3.2
|
49.8
|
1.0
|
HG21
|
A:VAL340
|
3.3
|
49.2
|
1.0
|
HG13
|
A:VAL340
|
3.4
|
46.4
|
1.0
|
HG23
|
A:VAL161
|
3.5
|
27.7
|
1.0
|
HG21
|
A:VAL314
|
3.5
|
28.1
|
1.0
|
HG13
|
A:VAL345
|
3.7
|
32.2
|
1.0
|
HD13
|
A:LEU164
|
3.8
|
49.8
|
1.0
|
CB
|
A:ALA310
|
3.8
|
23.9
|
1.0
|
CD1
|
A:LEU164
|
3.8
|
51.5
|
1.0
|
HD12
|
A:LEU164
|
3.8
|
49.7
|
1.0
|
CE2
|
A:PHE160
|
3.9
|
23.9
|
1.0
|
CG2
|
A:VAL345
|
3.9
|
32.2
|
1.0
|
HD2
|
A:PHE160
|
4.0
|
25.1
|
1.0
|
HB2
|
A:ALA310
|
4.0
|
23.2
|
1.0
|
HB
|
A:VAL340
|
4.0
|
47.2
|
1.0
|
HB1
|
A:ALA310
|
4.1
|
23.2
|
1.0
|
HG23
|
A:VAL345
|
4.1
|
32.0
|
1.0
|
CG2
|
A:VAL340
|
4.1
|
50.6
|
1.0
|
CG1
|
A:VAL340
|
4.2
|
46.6
|
1.0
|
CD2
|
A:PHE160
|
4.3
|
26.5
|
1.0
|
HG22
|
A:VAL314
|
4.3
|
28.1
|
1.0
|
CG2
|
A:VAL314
|
4.3
|
27.9
|
1.0
|
CG2
|
A:VAL161
|
4.4
|
28.2
|
1.0
|
CB
|
A:VAL340
|
4.4
|
46.4
|
1.0
|
HG22
|
A:VAL161
|
4.4
|
27.7
|
1.0
|
HG22
|
A:VAL345
|
4.4
|
32.0
|
1.0
|
CG1
|
A:VAL345
|
4.5
|
32.4
|
1.0
|
HG22
|
A:VAL340
|
4.6
|
49.3
|
1.0
|
KR
|
A:KR502
|
4.6
|
26.1
|
0.8
|
KR
|
A:KR510
|
4.7
|
43.5
|
0.3
|
HG12
|
A:VAL340
|
4.7
|
46.3
|
1.0
|
HG11
|
A:VAL345
|
4.7
|
32.2
|
1.0
|
CB
|
A:VAL345
|
4.7
|
31.6
|
1.0
|
HG21
|
A:VAL161
|
4.7
|
27.7
|
1.0
|
HA
|
A:VAL161
|
4.8
|
25.9
|
1.0
|
HG23
|
A:VAL340
|
4.8
|
49.2
|
1.0
|
CZ
|
A:PHE160
|
4.8
|
24.8
|
1.0
|
HG23
|
A:VAL314
|
4.8
|
28.1
|
1.0
|
HB
|
A:VAL345
|
4.9
|
31.7
|
1.0
|
HG11
|
A:VAL340
|
4.9
|
46.2
|
1.0
|
CA
|
A:ALA310
|
4.9
|
21.9
|
1.0
|
O
|
A:ALA310
|
4.9
|
22.3
|
1.0
|
HZ
|
A:PHE160
|
5.0
|
24.1
|
1.0
|
|
Krypton binding site 4 out
of 10 in 8rxj
Go back to
Krypton Binding Sites List in 8rxj
Krypton binding site 4 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 4 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr504
b:41.1
occ:0.60
|
HB3
|
B:GLN63
|
3.0
|
20.7
|
1.0
|
HB1
|
A:ALA313
|
3.2
|
27.1
|
1.0
|
HB3
|
A:GLU312
|
3.3
|
24.5
|
1.0
|
H
|
A:ALA313
|
3.3
|
25.9
|
1.0
|
HA
|
A:ALA313
|
3.4
|
27.3
|
1.0
|
HG2
|
A:GLU312
|
3.4
|
26.6
|
1.0
|
N
|
A:ALA313
|
3.4
|
25.3
|
1.0
|
O
|
A:PHE309
|
3.5
|
18.7
|
1.0
|
HG3
|
B:GLN63
|
3.6
|
21.5
|
1.0
|
CB
|
B:GLN63
|
3.7
|
20.8
|
1.0
|
HB2
|
B:GLN63
|
3.7
|
20.6
|
1.0
|
CA
|
A:ALA313
|
3.7
|
27.7
|
1.0
|
CE2
|
A:PHE309
|
3.8
|
19.7
|
1.0
|
CG
|
B:GLN63
|
3.9
|
21.4
|
1.0
|
CB
|
A:ALA313
|
3.9
|
26.8
|
1.0
|
CD
|
B:GLN63
|
3.9
|
22.2
|
1.0
|
C
|
A:GLU312
|
4.0
|
25.8
|
1.0
|
CD2
|
A:PHE309
|
4.0
|
18.4
|
1.0
|
CB
|
A:GLU312
|
4.0
|
24.7
|
1.0
|
CG
|
A:GLU312
|
4.0
|
26.5
|
1.0
|
HE2
|
A:PHE309
|
4.0
|
20.0
|
1.0
|
HA
|
A:PHE309
|
4.0
|
17.6
|
1.0
|
NE2
|
B:GLN63
|
4.1
|
21.1
|
1.0
|
HE22
|
B:GLN63
|
4.1
|
21.4
|
1.0
|
CZ
|
A:PHE309
|
4.1
|
22.4
|
1.0
|
HD2
|
A:PHE309
|
4.2
|
18.4
|
1.0
|
CG
|
A:PHE309
|
4.3
|
17.1
|
1.0
|
C
|
A:PHE309
|
4.4
|
19.0
|
1.0
|
CE1
|
A:PHE309
|
4.4
|
22.8
|
1.0
|
CD
|
A:GLU312
|
4.4
|
28.9
|
1.0
|
HZ
|
A:PHE309
|
4.4
|
21.8
|
1.0
|
OE1
|
B:GLN63
|
4.5
|
19.5
|
1.0
|
HE21
|
B:GLN63
|
4.5
|
21.4
|
1.0
|
HB3
|
A:ALA313
|
4.5
|
27.1
|
1.0
|
CA
|
A:GLU312
|
4.5
|
22.4
|
1.0
|
O
|
A:GLU312
|
4.5
|
24.2
|
1.0
|
HB2
|
A:ALA313
|
4.5
|
27.1
|
1.0
|
CD1
|
A:PHE309
|
4.6
|
18.8
|
1.0
|
CA
|
A:PHE309
|
4.7
|
17.1
|
1.0
|
OE1
|
A:GLU312
|
4.7
|
23.7
|
1.0
|
H
|
A:GLU312
|
4.8
|
22.1
|
1.0
|
HB2
|
A:GLU312
|
4.8
|
24.5
|
1.0
|
HG2
|
B:GLN63
|
4.9
|
21.5
|
1.0
|
HG3
|
A:GLU312
|
4.9
|
26.6
|
1.0
|
HE1
|
A:PHE309
|
5.0
|
21.6
|
1.0
|
|
Krypton binding site 5 out
of 10 in 8rxj
Go back to
Krypton Binding Sites List in 8rxj
Krypton binding site 5 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 5 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr505
b:21.2
occ:0.10
|
HD11
|
A:ILE254
|
2.2
|
20.0
|
1.0
|
HD13
|
A:ILE254
|
2.4
|
20.0
|
1.0
|
CD1
|
A:ILE254
|
2.5
|
20.4
|
1.0
|
HD12
|
A:ILE254
|
2.6
|
20.0
|
1.0
|
HG22
|
A:ILE204
|
2.7
|
15.1
|
1.0
|
HG2
|
A:GLU240
|
2.8
|
14.9
|
1.0
|
HD13
|
A:LEU246
|
2.9
|
20.4
|
1.0
|
HA2
|
A:GLY241
|
2.9
|
14.1
|
1.0
|
HD11
|
A:LEU246
|
3.2
|
20.4
|
1.0
|
HB3
|
A:GLU240
|
3.3
|
14.6
|
1.0
|
CD1
|
A:LEU246
|
3.4
|
20.1
|
1.0
|
CG
|
A:GLU240
|
3.4
|
14.6
|
1.0
|
HD12
|
A:LEU246
|
3.5
|
20.4
|
1.0
|
CG2
|
A:ILE204
|
3.5
|
15.4
|
1.0
|
CD
|
A:GLU240
|
3.6
|
15.7
|
1.0
|
HG21
|
A:ILE204
|
3.6
|
15.1
|
1.0
|
HA2
|
A:GLY205
|
3.6
|
14.2
|
1.0
|
N
|
A:GLY241
|
3.6
|
14.0
|
1.0
|
CA
|
A:GLY241
|
3.7
|
13.9
|
1.0
|
C
|
A:GLU240
|
3.7
|
14.3
|
1.0
|
O
|
A:GLU240
|
3.7
|
14.1
|
1.0
|
CB
|
A:GLU240
|
3.8
|
14.8
|
1.0
|
OE2
|
A:GLU240
|
3.9
|
15.3
|
1.0
|
HG23
|
A:ILE204
|
3.9
|
15.1
|
1.0
|
HG
|
A:SER202
|
4.0
|
16.0
|
0.0
|
CG1
|
A:ILE254
|
4.0
|
19.1
|
1.0
|
H
|
A:GLY241
|
4.0
|
14.0
|
1.0
|
OE1
|
A:GLU240
|
4.0
|
16.8
|
1.0
|
H
|
A:GLY205
|
4.0
|
13.3
|
1.0
|
N
|
A:GLY205
|
4.0
|
13.1
|
1.0
|
HA3
|
A:GLY241
|
4.1
|
14.0
|
1.0
|
HG13
|
A:ILE204
|
4.1
|
14.1
|
1.0
|
CA
|
A:GLY205
|
4.1
|
14.4
|
1.0
|
HA3
|
A:GLY205
|
4.1
|
14.2
|
1.0
|
O
|
A:HOH672
|
4.3
|
15.6
|
1.0
|
HG3
|
A:GLU240
|
4.3
|
14.9
|
1.0
|
HB
|
A:ILE254
|
4.3
|
17.1
|
1.0
|
CA
|
A:GLU240
|
4.4
|
14.2
|
1.0
|
OG
|
A:SER202
|
4.4
|
16.0
|
1.0
|
HG13
|
A:ILE254
|
4.4
|
18.7
|
1.0
|
HG21
|
A:ILE254
|
4.5
|
17.1
|
1.0
|
HG12
|
A:ILE254
|
4.5
|
18.8
|
1.0
|
C
|
A:ILE204
|
4.5
|
12.7
|
1.0
|
CB
|
A:ILE204
|
4.6
|
14.3
|
1.0
|
HB2
|
A:GLU240
|
4.7
|
14.6
|
1.0
|
CB
|
A:ILE254
|
4.7
|
16.5
|
1.0
|
CG1
|
A:ILE204
|
4.7
|
14.1
|
1.0
|
HB3
|
A:LEU246
|
4.8
|
20.3
|
1.0
|
HG12
|
A:ILE204
|
4.8
|
14.0
|
1.0
|
CG
|
A:LEU246
|
4.8
|
21.5
|
1.0
|
O
|
A:HOH645
|
4.8
|
22.4
|
1.0
|
HD3
|
A:LYS237
|
4.9
|
13.9
|
1.0
|
C
|
A:GLY241
|
4.9
|
14.3
|
1.0
|
HA
|
A:GLU240
|
4.9
|
14.3
|
1.0
|
O
|
A:ILE204
|
5.0
|
14.7
|
1.0
|
O
|
A:LYS237
|
5.0
|
12.9
|
1.0
|
|
Krypton binding site 6 out
of 10 in 8rxj
Go back to
Krypton Binding Sites List in 8rxj
Krypton binding site 6 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 6 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr506
b:23.4
occ:0.37
|
HG23
|
A:ILE67
|
2.8
|
15.9
|
1.0
|
HE2
|
A:TYR189
|
2.8
|
20.4
|
1.0
|
HG21
|
A:THR188
|
3.1
|
16.9
|
1.0
|
HG22
|
A:ILE67
|
3.1
|
15.9
|
1.0
|
HG2
|
A:LYS184
|
3.1
|
15.9
|
1.0
|
O
|
A:GLU64
|
3.1
|
16.6
|
1.0
|
HE2
|
A:LYS184
|
3.3
|
16.4
|
1.0
|
CG2
|
A:ILE67
|
3.4
|
16.1
|
1.0
|
HA
|
A:ALA65
|
3.4
|
15.3
|
1.0
|
HB
|
A:THR188
|
3.4
|
15.6
|
1.0
|
OG1
|
A:THR188
|
3.5
|
14.5
|
1.0
|
CE2
|
A:TYR189
|
3.6
|
20.9
|
1.0
|
HA
|
A:TYR185
|
3.6
|
13.7
|
1.0
|
C
|
A:ALA65
|
3.7
|
14.6
|
1.0
|
O
|
A:ALA65
|
3.8
|
16.8
|
1.0
|
CB
|
A:THR188
|
3.8
|
14.8
|
1.0
|
HD3
|
A:LYS184
|
3.8
|
16.1
|
1.0
|
CG2
|
A:THR188
|
3.8
|
17.9
|
1.0
|
HH
|
A:TYR189
|
3.8
|
21.1
|
0.0
|
HG21
|
A:ILE67
|
3.9
|
15.9
|
1.0
|
CG
|
A:LYS184
|
3.9
|
16.1
|
1.0
|
CA
|
A:ALA65
|
4.0
|
14.7
|
1.0
|
HG21
|
A:THR47
|
4.0
|
20.0
|
1.0
|
O
|
A:CYS66
|
4.0
|
15.3
|
1.0
|
O
|
A:LYS184
|
4.0
|
14.5
|
1.0
|
C
|
A:GLU64
|
4.0
|
15.4
|
1.0
|
O
|
A:HOH626
|
4.1
|
15.9
|
1.0
|
HA
|
A:ILE67
|
4.1
|
15.1
|
1.0
|
CE
|
A:LYS184
|
4.1
|
16.6
|
1.0
|
CD
|
A:LYS184
|
4.1
|
15.9
|
1.0
|
OH
|
A:TYR189
|
4.1
|
21.0
|
1.0
|
N
|
A:CYS66
|
4.2
|
14.9
|
1.0
|
C
|
A:CYS66
|
4.2
|
16.0
|
1.0
|
HG1
|
A:THR188
|
4.2
|
14.6
|
0.0
|
CZ
|
A:TYR189
|
4.3
|
20.6
|
1.0
|
HD2
|
A:TYR189
|
4.3
|
19.2
|
1.0
|
C
|
A:LYS184
|
4.3
|
14.7
|
1.0
|
CD2
|
A:TYR189
|
4.3
|
19.2
|
1.0
|
HG23
|
A:THR188
|
4.3
|
16.9
|
1.0
|
H
|
A:CYS66
|
4.4
|
14.8
|
1.0
|
N
|
A:ILE67
|
4.4
|
15.4
|
1.0
|
HB3
|
A:LYS184
|
4.4
|
15.2
|
1.0
|
N
|
A:ALA65
|
4.5
|
16.3
|
1.0
|
CA
|
A:TYR185
|
4.5
|
14.0
|
1.0
|
HG22
|
A:THR188
|
4.5
|
16.9
|
1.0
|
HZ1
|
A:LYS184
|
4.5
|
16.6
|
1.0
|
N
|
A:TYR185
|
4.5
|
13.5
|
1.0
|
CB
|
A:ILE67
|
4.6
|
15.4
|
1.0
|
HG3
|
A:LYS184
|
4.6
|
15.9
|
1.0
|
CA
|
A:ILE67
|
4.6
|
15.4
|
1.0
|
CB
|
A:LYS184
|
4.7
|
15.2
|
1.0
|
CA
|
A:CYS66
|
4.8
|
14.6
|
1.0
|
HE3
|
A:LYS184
|
4.8
|
16.4
|
1.0
|
NZ
|
A:LYS184
|
4.9
|
16.6
|
1.0
|
H
|
A:ILE67
|
4.9
|
15.5
|
1.0
|
CG2
|
A:THR47
|
4.9
|
20.4
|
1.0
|
HG13
|
B:VAL99
|
5.0
|
17.8
|
1.0
|
HB
|
A:ILE67
|
5.0
|
15.5
|
1.0
|
|
Krypton binding site 7 out
of 10 in 8rxj
Go back to
Krypton Binding Sites List in 8rxj
Krypton binding site 7 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 7 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr507
b:29.9
occ:0.50
|
O
|
A:HOH667
|
2.4
|
29.4
|
1.0
|
HA
|
A:GLN135
|
3.1
|
18.0
|
1.0
|
HB2
|
A:PHE139
|
3.3
|
15.4
|
1.0
|
H
|
A:CYS142
|
3.4
|
16.1
|
1.0
|
HB2
|
A:CYS142
|
3.5
|
16.8
|
1.0
|
O
|
A:PHE139
|
3.5
|
17.5
|
1.0
|
N
|
A:CYS142
|
3.5
|
15.9
|
1.0
|
HA
|
A:HIS141
|
3.6
|
16.1
|
1.0
|
HB2
|
A:GLN135
|
3.6
|
20.5
|
1.0
|
C
|
A:HIS141
|
3.7
|
16.1
|
1.0
|
N
|
A:GLN135
|
3.7
|
16.6
|
1.0
|
CA
|
A:GLN135
|
3.8
|
18.0
|
1.0
|
HB3
|
A:LEU134
|
3.8
|
15.8
|
1.0
|
HB3
|
A:PHE139
|
3.8
|
15.4
|
1.0
|
HB2
|
A:LEU134
|
3.9
|
15.8
|
1.0
|
O
|
A:HOH708
|
3.9
|
19.1
|
1.0
|
C
|
A:LEU134
|
4.0
|
15.3
|
1.0
|
CB
|
A:PHE139
|
4.0
|
15.9
|
1.0
|
H
|
A:GLN135
|
4.0
|
16.6
|
1.0
|
CA
|
A:HIS141
|
4.0
|
15.9
|
1.0
|
O
|
A:HIS141
|
4.1
|
15.7
|
1.0
|
CB
|
A:GLN135
|
4.1
|
20.1
|
1.0
|
CB
|
A:CYS142
|
4.1
|
16.3
|
1.0
|
O
|
A:LEU134
|
4.1
|
16.2
|
1.0
|
HB3
|
A:CYS142
|
4.1
|
16.8
|
1.0
|
C
|
A:PHE139
|
4.1
|
17.2
|
1.0
|
N
|
A:HIS141
|
4.2
|
15.9
|
1.0
|
HG2
|
A:GLN135
|
4.2
|
24.4
|
1.0
|
CB
|
A:LEU134
|
4.3
|
15.8
|
1.0
|
O
|
A:HOH684
|
4.3
|
26.6
|
1.0
|
CA
|
A:CYS142
|
4.4
|
16.4
|
1.0
|
C
|
A:ALA140
|
4.5
|
17.1
|
1.0
|
H
|
A:HIS141
|
4.5
|
16.2
|
1.0
|
CA
|
A:PHE139
|
4.6
|
15.9
|
1.0
|
O
|
A:ALA140
|
4.6
|
18.4
|
1.0
|
HA
|
A:CYS142
|
4.6
|
16.2
|
1.0
|
CG
|
A:GLN135
|
4.7
|
24.7
|
1.0
|
O
|
A:LEU131
|
4.7
|
19.0
|
1.0
|
CA
|
A:LEU134
|
4.7
|
15.3
|
1.0
|
HB2
|
A:ALA104
|
4.8
|
15.4
|
1.0
|
H
|
A:PHE139
|
4.9
|
16.5
|
1.0
|
HB3
|
A:GLN135
|
5.0
|
20.6
|
1.0
|
|
Krypton binding site 8 out
of 10 in 8rxj
Go back to
Krypton Binding Sites List in 8rxj
Krypton binding site 8 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 8 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr508
b:24.2
occ:0.10
|
HE2
|
A:PHE372
|
2.2
|
28.3
|
1.0
|
CE2
|
A:PHE372
|
2.7
|
28.9
|
1.0
|
HA2
|
A:GLY157
|
2.8
|
22.5
|
1.0
|
HB2
|
A:PHE160
|
2.8
|
22.3
|
1.0
|
HB3
|
A:PHE160
|
2.9
|
22.4
|
1.0
|
HZ
|
A:PHE372
|
3.0
|
27.5
|
1.0
|
HB3
|
A:ALA306
|
3.0
|
18.4
|
1.0
|
CZ
|
A:PHE372
|
3.1
|
27.5
|
1.0
|
HG2
|
A:GLU156
|
3.2
|
21.1
|
1.0
|
CB
|
A:PHE160
|
3.2
|
22.6
|
1.0
|
O
|
A:GLU156
|
3.3
|
19.8
|
1.0
|
HD2
|
A:PHE160
|
3.5
|
25.1
|
1.0
|
CD2
|
A:PHE372
|
3.5
|
28.2
|
1.0
|
CA
|
A:GLY157
|
3.6
|
22.8
|
1.0
|
C
|
A:GLU156
|
3.7
|
20.1
|
1.0
|
CG
|
A:PHE160
|
3.8
|
23.8
|
1.0
|
HD2
|
A:PHE372
|
3.8
|
27.4
|
1.0
|
N
|
A:GLY157
|
3.8
|
21.6
|
1.0
|
HB1
|
A:ALA306
|
3.8
|
18.4
|
1.0
|
CB
|
A:ALA306
|
3.9
|
19.0
|
1.0
|
CD2
|
A:PHE160
|
3.9
|
26.5
|
1.0
|
KR
|
A:KR501
|
3.9
|
24.1
|
0.4
|
CG
|
A:GLU156
|
4.1
|
20.9
|
1.0
|
CE1
|
A:PHE372
|
4.2
|
26.4
|
1.0
|
KR
|
A:KR502
|
4.2
|
26.1
|
0.8
|
HA3
|
A:GLY157
|
4.2
|
22.5
|
1.0
|
H
|
A:PHE160
|
4.3
|
20.4
|
1.0
|
HB2
|
A:ALA306
|
4.3
|
18.4
|
1.0
|
OE1
|
A:GLN174
|
4.4
|
25.0
|
1.0
|
H
|
A:GLY157
|
4.4
|
21.4
|
1.0
|
HB3
|
A:GLU156
|
4.5
|
18.6
|
1.0
|
O
|
A:GLY157
|
4.5
|
24.4
|
1.0
|
C
|
A:GLY157
|
4.6
|
23.0
|
1.0
|
CG
|
A:PHE372
|
4.6
|
24.5
|
1.0
|
HG3
|
A:GLU156
|
4.6
|
21.1
|
1.0
|
CA
|
A:PHE160
|
4.6
|
20.1
|
1.0
|
CB
|
A:GLU156
|
4.7
|
18.4
|
1.0
|
HE1
|
A:PHE372
|
4.8
|
26.3
|
1.0
|
CD1
|
A:PHE372
|
4.8
|
24.8
|
1.0
|
N
|
A:PHE160
|
4.8
|
20.5
|
1.0
|
CA
|
A:GLU156
|
4.8
|
17.0
|
1.0
|
CD1
|
A:PHE160
|
4.8
|
22.6
|
1.0
|
CD
|
A:GLU156
|
4.9
|
24.6
|
1.0
|
HA
|
A:ALA306
|
4.9
|
17.3
|
1.0
|
OE2
|
A:GLU156
|
4.9
|
22.6
|
1.0
|
CE2
|
A:PHE160
|
5.0
|
23.9
|
1.0
|
CA
|
A:ALA306
|
5.0
|
17.0
|
1.0
|
|
Krypton binding site 9 out
of 10 in 8rxj
Go back to
Krypton Binding Sites List in 8rxj
Krypton binding site 9 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 9 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr509
b:17.4
occ:0.10
|
HG12
|
A:VAL327
|
2.3
|
23.5
|
1.0
|
HG22
|
A:VAL349
|
3.0
|
19.3
|
1.0
|
HG22
|
A:VAL347
|
3.0
|
23.6
|
1.0
|
O
|
A:LYS334
|
3.0
|
30.5
|
1.0
|
HA
|
A:GLU335
|
3.0
|
33.7
|
1.0
|
HA
|
A:VAL327
|
3.1
|
23.6
|
1.0
|
C
|
A:LYS334
|
3.2
|
29.7
|
1.0
|
CG1
|
A:VAL327
|
3.3
|
23.6
|
1.0
|
HA
|
A:ALA348
|
3.3
|
22.5
|
1.0
|
C
|
A:GLU335
|
3.4
|
34.0
|
1.0
|
H
|
A:ALA336
|
3.4
|
31.1
|
1.0
|
CA
|
A:GLU335
|
3.4
|
32.7
|
1.0
|
N
|
A:GLU335
|
3.4
|
33.7
|
1.0
|
HB2
|
A:LYS334
|
3.4
|
24.7
|
1.0
|
N
|
A:ALA336
|
3.4
|
29.7
|
1.0
|
HB
|
A:VAL349
|
3.5
|
19.1
|
1.0
|
HB3
|
A:LYS334
|
3.5
|
24.7
|
1.0
|
H
|
A:VAL349
|
3.5
|
19.6
|
1.0
|
HB1
|
A:ALA336
|
3.5
|
30.7
|
1.0
|
HB2
|
A:ALA336
|
3.5
|
30.7
|
1.0
|
CG2
|
A:VAL349
|
3.7
|
19.5
|
1.0
|
O
|
A:VAL347
|
3.8
|
26.2
|
1.0
|
HG21
|
A:VAL349
|
3.8
|
19.3
|
1.0
|
HG11
|
A:VAL327
|
3.8
|
23.5
|
1.0
|
HB
|
A:VAL327
|
3.8
|
23.6
|
1.0
|
HG13
|
A:VAL327
|
3.8
|
23.5
|
1.0
|
CB
|
A:LYS334
|
3.8
|
24.9
|
1.0
|
N
|
A:VAL349
|
3.8
|
19.5
|
1.0
|
CG2
|
A:VAL347
|
3.9
|
23.6
|
1.0
|
CB
|
A:VAL327
|
3.9
|
23.5
|
1.0
|
CB
|
A:ALA336
|
3.9
|
30.4
|
1.0
|
O
|
A:GLU335
|
3.9
|
32.1
|
1.0
|
CA
|
A:VAL327
|
3.9
|
23.2
|
1.0
|
H
|
A:GLU335
|
4.0
|
32.4
|
1.0
|
CA
|
A:ALA348
|
4.0
|
22.5
|
1.0
|
CB
|
A:VAL349
|
4.1
|
18.9
|
1.0
|
HG23
|
A:VAL347
|
4.1
|
23.6
|
1.0
|
CA
|
A:LYS334
|
4.1
|
27.7
|
1.0
|
C
|
A:ALA348
|
4.1
|
20.4
|
1.0
|
C
|
A:VAL347
|
4.2
|
24.8
|
1.0
|
HG21
|
A:VAL347
|
4.2
|
23.6
|
1.0
|
CA
|
A:ALA336
|
4.3
|
31.5
|
1.0
|
N
|
A:ALA348
|
4.4
|
22.0
|
1.0
|
O
|
A:ALA326
|
4.4
|
31.8
|
1.0
|
HG2
|
A:MET303
|
4.5
|
19.9
|
1.0
|
HG23
|
A:VAL349
|
4.5
|
19.3
|
1.0
|
CA
|
A:VAL349
|
4.6
|
18.9
|
1.0
|
N
|
A:VAL327
|
4.7
|
24.6
|
1.0
|
HA
|
A:LYS334
|
4.8
|
27.0
|
1.0
|
HB3
|
A:ALA336
|
4.8
|
30.7
|
1.0
|
C
|
A:ALA326
|
4.8
|
31.4
|
1.0
|
H
|
A:LYS334
|
4.9
|
25.9
|
1.0
|
O
|
A:ALA348
|
4.9
|
19.7
|
1.0
|
CB
|
A:GLU335
|
4.9
|
37.4
|
1.0
|
HE3
|
A:LYS334
|
4.9
|
20.9
|
1.0
|
HA
|
A:ALA336
|
4.9
|
31.0
|
1.0
|
CB
|
A:VAL347
|
5.0
|
23.5
|
1.0
|
|
Krypton binding site 10 out
of 10 in 8rxj
Go back to
Krypton Binding Sites List in 8rxj
Krypton binding site 10 out
of 10 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton
 Mono view
 Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 10 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase C178A Mutant in Hinact- Like State Derivatized with Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr510
b:43.5
occ:0.30
|
HG23
|
A:VAL340
|
2.4
|
49.2
|
1.0
|
HG21
|
A:VAL340
|
2.6
|
49.2
|
1.0
|
CG2
|
A:VAL340
|
2.9
|
50.6
|
1.0
|
HD22
|
A:LEU307
|
3.1
|
22.6
|
1.0
|
HB2
|
A:TYR311
|
3.1
|
25.8
|
1.0
|
HG11
|
A:VAL340
|
3.1
|
46.2
|
1.0
|
HD21
|
A:LEU307
|
3.2
|
22.5
|
1.0
|
HG13
|
A:VAL340
|
3.3
|
46.4
|
1.0
|
HB2
|
A:ALA310
|
3.3
|
23.2
|
1.0
|
HA
|
A:TYR311
|
3.3
|
23.5
|
1.0
|
HG13
|
A:VAL338
|
3.3
|
39.6
|
1.0
|
HG12
|
A:VAL338
|
3.4
|
39.7
|
1.0
|
HA
|
A:LEU307
|
3.5
|
18.2
|
1.0
|
CG1
|
A:VAL340
|
3.5
|
46.6
|
1.0
|
CD2
|
A:LEU307
|
3.6
|
23.2
|
1.0
|
H
|
A:TYR311
|
3.6
|
21.4
|
1.0
|
O
|
A:LEU307
|
3.6
|
16.8
|
1.0
|
HG22
|
A:VAL340
|
3.6
|
49.3
|
1.0
|
HD2
|
A:TYR311
|
3.6
|
31.5
|
1.0
|
N
|
A:TYR311
|
3.7
|
20.7
|
1.0
|
CA
|
A:TYR311
|
3.8
|
23.4
|
1.0
|
CB
|
A:VAL340
|
3.8
|
46.4
|
1.0
|
HB3
|
A:LEU307
|
3.8
|
19.6
|
1.0
|
CB
|
A:TYR311
|
3.8
|
25.8
|
1.0
|
CG1
|
A:VAL338
|
3.9
|
40.7
|
1.0
|
HB3
|
A:ALA310
|
4.0
|
23.3
|
1.0
|
CB
|
A:ALA310
|
4.1
|
23.9
|
1.0
|
CA
|
A:LEU307
|
4.2
|
18.8
|
1.0
|
C
|
A:ALA310
|
4.2
|
21.4
|
1.0
|
HD23
|
A:LEU307
|
4.3
|
22.5
|
1.0
|
C
|
A:LEU307
|
4.3
|
17.7
|
1.0
|
CB
|
A:LEU307
|
4.3
|
19.5
|
1.0
|
CD2
|
A:TYR311
|
4.4
|
31.8
|
1.0
|
HG12
|
A:VAL340
|
4.5
|
46.3
|
1.0
|
HB
|
A:VAL340
|
4.5
|
47.2
|
1.0
|
HE2
|
A:PHE324
|
4.5
|
20.2
|
1.0
|
HZ
|
A:PHE324
|
4.5
|
20.0
|
1.0
|
HG11
|
A:VAL338
|
4.5
|
39.7
|
1.0
|
HB
|
A:VAL338
|
4.5
|
36.9
|
1.0
|
HB3
|
A:TYR311
|
4.6
|
25.7
|
1.0
|
HA
|
A:VAL340
|
4.6
|
46.7
|
1.0
|
CG
|
A:LEU307
|
4.6
|
20.9
|
1.0
|
CG
|
A:TYR311
|
4.6
|
28.2
|
1.0
|
KR
|
A:KR503
|
4.7
|
37.9
|
0.6
|
CA
|
A:VAL340
|
4.7
|
46.8
|
1.0
|
CA
|
A:ALA310
|
4.8
|
21.9
|
1.0
|
O
|
A:ALA310
|
4.8
|
22.3
|
1.0
|
HB1
|
A:ALA310
|
4.8
|
23.2
|
1.0
|
CB
|
A:VAL338
|
4.8
|
37.7
|
1.0
|
CE2
|
A:PHE324
|
4.9
|
19.8
|
1.0
|
CZ
|
A:PHE324
|
4.9
|
20.4
|
1.0
|
O
|
A:ASN339
|
4.9
|
45.2
|
1.0
|
HG21
|
A:VAL345
|
4.9
|
32.0
|
1.0
|
|
Reference:
K.Bikbaev,
T.Harand,
L.Scheuenstuhl,
P.Carpentier,
M.A.Martini,
J.A.Birrell,
I.Span.
Krypton Derivatization of [Fefe] Hydrogenase From Desulfovibrio Desulfuricans Reveals Its Gas Channel To Be Published.
Page generated: Tue Feb 25 10:21:25 2025
|