Krypton in PDB 6z8o: Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
Enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
All present enzymatic activity of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr:
1.12.7.2;
Protein crystallography data
The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr, PDB code: 6z8o
was solved by
S.Zacarias,
A.Temporao,
P.Carpentier,
P.Van Der Linden,
I.A.C.Pereira,
P.M.Matias,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.12 /
2.20
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.716,
97.022,
121.318,
90.00,
104.66,
90.00
|
|
R / Rfree (%)
|
22.6 /
27.5
|
Other elements in 6z8o:
The structure of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr also contains other interesting chemical elements:
Krypton Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Binding sites:
The binding sites of Krypton atom in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
(pdb code 6z8o). This binding sites where shown within
5.0 Angstroms radius around Krypton atom.
In total 20 binding sites of Krypton where determined in the
Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr, PDB code: 6z8o:
Jump to Krypton binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Krypton binding site 1 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 1 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 1 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr305
b:57.0
occ:0.76
|
HZ
|
B:PHE139
|
2.9
|
68.7
|
1.0
|
|
HD11
|
A:LEU38
|
3.1
|
61.3
|
1.0
|
|
HA
|
A:ALA34
|
3.3
|
60.2
|
1.0
|
|
HD21
|
A:LEU38
|
3.4
|
66.2
|
1.0
|
|
HE1
|
B:TYR162
|
3.4
|
57.4
|
1.0
|
|
HE2
|
B:PHE139
|
3.4
|
73.4
|
1.0
|
|
HD12
|
A:LEU37
|
3.5
|
52.0
|
1.0
|
|
HG
|
A:LEU38
|
3.5
|
62.6
|
1.0
|
|
CZ
|
B:PHE139
|
3.7
|
56.1
|
1.0
|
|
HB2
|
A:LEU37
|
3.7
|
54.8
|
1.0
|
|
HB1
|
A:ALA34
|
3.8
|
58.4
|
1.0
|
|
CD1
|
A:LEU38
|
3.8
|
49.9
|
1.0
|
|
HD11
|
B:LEU166
|
3.9
|
57.7
|
1.0
|
|
CE2
|
B:PHE139
|
3.9
|
60.0
|
1.0
|
|
CG
|
A:LEU38
|
4.0
|
51.0
|
1.0
|
|
CD2
|
A:LEU38
|
4.1
|
54.0
|
1.0
|
|
HD12
|
A:LEU38
|
4.1
|
61.3
|
1.0
|
|
CA
|
A:ALA34
|
4.1
|
49.0
|
1.0
|
|
HB2
|
A:ALA34
|
4.1
|
58.4
|
1.0
|
|
CB
|
A:ALA34
|
4.2
|
47.5
|
1.0
|
|
HH
|
B:TYR162
|
4.2
|
55.9
|
1.0
|
|
CE1
|
B:TYR162
|
4.3
|
46.7
|
1.0
|
|
HD23
|
A:LEU38
|
4.3
|
66.2
|
1.0
|
|
CD1
|
A:LEU37
|
4.3
|
42.1
|
1.0
|
|
HB3
|
A:LEU37
|
4.3
|
54.8
|
1.0
|
|
O
|
A:ALA34
|
4.4
|
50.4
|
1.0
|
|
CB
|
A:LEU37
|
4.4
|
44.5
|
1.0
|
|
HD13
|
A:LEU37
|
4.4
|
52.0
|
1.0
|
|
CD1
|
B:LEU166
|
4.5
|
46.9
|
1.0
|
|
HD13
|
B:LEU166
|
4.5
|
57.7
|
1.0
|
|
HD12
|
B:LEU166
|
4.6
|
57.7
|
1.0
|
|
HG12
|
B:ILE163
|
4.6
|
60.8
|
1.0
|
|
HD13
|
A:LEU38
|
4.6
|
61.3
|
1.0
|
|
C
|
A:ALA34
|
4.8
|
48.9
|
1.0
|
|
CE1
|
B:PHE139
|
4.9
|
54.0
|
1.0
|
|
OH
|
B:TYR162
|
4.9
|
45.4
|
1.0
|
|
HD22
|
A:LEU38
|
4.9
|
66.2
|
1.0
|
|
CG
|
A:LEU37
|
4.9
|
42.2
|
1.0
|
|
HD1
|
B:TYR162
|
5.0
|
59.6
|
1.0
|
|
Krypton binding site 2 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 2 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 2 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr306
b:58.1
occ:0.71
|
HA
|
A:VAL170
|
3.1
|
60.6
|
1.0
|
|
HD11
|
A:LEU116
|
3.1
|
42.4
|
1.0
|
|
HG22
|
A:VAL170
|
3.1
|
58.1
|
1.0
|
|
CE1
|
A:PHE73
|
3.3
|
46.1
|
1.0
|
|
HB3
|
A:ALA173
|
3.3
|
64.4
|
1.0
|
|
CD1
|
A:PHE73
|
3.3
|
39.5
|
1.0
|
|
HE1
|
A:PHE73
|
3.3
|
56.8
|
1.0
|
|
HD1
|
A:PHE73
|
3.3
|
48.9
|
1.0
|
|
HG13
|
A:VAL170
|
3.5
|
51.1
|
1.0
|
|
HG
|
A:LEU174
|
3.6
|
54.4
|
1.0
|
|
O
|
A:VAL170
|
3.8
|
49.0
|
1.0
|
|
HD23
|
A:LEU174
|
3.8
|
53.5
|
1.0
|
|
HD21
|
A:LEU174
|
3.8
|
53.5
|
1.0
|
|
CA
|
A:VAL170
|
3.9
|
49.3
|
1.0
|
|
CZ
|
A:PHE73
|
3.9
|
45.5
|
1.0
|
|
CG
|
A:PHE73
|
4.0
|
40.4
|
1.0
|
|
KR
|
A:KR309
|
4.0
|
46.9
|
0.4
|
|
CG2
|
A:VAL170
|
4.0
|
47.2
|
1.0
|
|
CD1
|
A:LEU116
|
4.0
|
34.2
|
1.0
|
|
HB1
|
A:ALA173
|
4.1
|
64.4
|
1.0
|
|
CB
|
A:ALA173
|
4.1
|
52.5
|
1.0
|
|
HD12
|
A:LEU116
|
4.2
|
42.4
|
1.0
|
|
CD2
|
A:LEU174
|
4.2
|
43.4
|
1.0
|
|
C
|
A:VAL170
|
4.3
|
43.5
|
1.0
|
|
CG1
|
A:VAL170
|
4.3
|
41.4
|
1.0
|
|
CB
|
A:VAL170
|
4.3
|
42.5
|
1.0
|
|
HZ
|
A:PHE73
|
4.3
|
56.0
|
1.0
|
|
HB3
|
A:PHE73
|
4.4
|
53.7
|
1.0
|
|
CG
|
A:LEU174
|
4.4
|
44.1
|
1.0
|
|
HG23
|
A:VAL170
|
4.4
|
58.1
|
1.0
|
|
HD13
|
A:LEU116
|
4.5
|
42.4
|
1.0
|
|
CE2
|
A:PHE73
|
4.5
|
45.5
|
1.0
|
|
CD2
|
A:PHE73
|
4.5
|
40.9
|
1.0
|
|
H
|
A:LEU174
|
4.5
|
61.4
|
1.0
|
|
HB2
|
A:ALA173
|
4.5
|
64.4
|
1.0
|
|
HD21
|
A:LEU116
|
4.5
|
51.5
|
1.0
|
|
HG21
|
A:VAL170
|
4.6
|
58.1
|
1.0
|
|
CB
|
A:PHE73
|
4.7
|
43.6
|
1.0
|
|
HG11
|
A:VAL170
|
4.7
|
51.1
|
1.0
|
|
HD11
|
A:LEU174
|
4.8
|
51.7
|
1.0
|
|
HG
|
A:LEU116
|
4.9
|
42.2
|
1.0
|
|
N
|
A:LEU174
|
4.9
|
50.0
|
1.0
|
|
HB2
|
A:PHE73
|
4.9
|
53.7
|
1.0
|
|
HG12
|
A:VAL170
|
5.0
|
51.1
|
1.0
|
|
O
|
A:THR169
|
5.0
|
50.3
|
1.0
|
|
CG
|
A:LEU116
|
5.0
|
34.0
|
1.0
|
|
Krypton binding site 3 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 3 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 3 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr307
b:45.1
occ:0.57
|
HG21
|
A:VAL170
|
2.7
|
58.1
|
1.0
|
|
HG11
|
A:VAL36
|
3.3
|
56.3
|
1.0
|
|
HD13
|
A:ILE41
|
3.3
|
55.6
|
1.0
|
|
HD21
|
A:LEU25
|
3.5
|
48.4
|
1.0
|
|
CG2
|
A:VAL170
|
3.6
|
47.2
|
1.0
|
|
HG22
|
A:ILE166
|
3.6
|
48.5
|
1.0
|
|
HG23
|
A:VAL170
|
3.8
|
58.1
|
1.0
|
|
HD11
|
A:LEU25
|
3.8
|
49.4
|
1.0
|
|
HG13
|
A:VAL36
|
3.8
|
56.3
|
1.0
|
|
HA
|
A:VAL167
|
3.9
|
49.9
|
1.0
|
|
CG1
|
A:VAL36
|
3.9
|
45.8
|
1.0
|
|
HG11
|
A:VAL170
|
3.9
|
51.1
|
1.0
|
|
HB
|
A:VAL170
|
3.9
|
52.4
|
1.0
|
|
HG12
|
A:VAL36
|
4.0
|
56.3
|
1.0
|
|
HG22
|
A:VAL167
|
4.1
|
47.0
|
1.0
|
|
HD22
|
A:LEU25
|
4.1
|
48.4
|
1.0
|
|
CD1
|
A:ILE41
|
4.2
|
45.1
|
1.0
|
|
CB
|
A:VAL170
|
4.2
|
42.5
|
1.0
|
|
HG22
|
A:VAL170
|
4.3
|
58.1
|
1.0
|
|
HD11
|
A:ILE41
|
4.3
|
55.6
|
1.0
|
|
CD2
|
A:LEU25
|
4.3
|
39.1
|
1.0
|
|
HD13
|
A:LEU25
|
4.3
|
49.4
|
1.0
|
|
HZ3
|
A:TRP12
|
4.3
|
49.2
|
1.0
|
|
HG21
|
A:ILE41
|
4.3
|
51.9
|
1.0
|
|
HG21
|
A:ILE166
|
4.3
|
48.5
|
1.0
|
|
CG2
|
A:ILE166
|
4.4
|
39.2
|
1.0
|
|
CD1
|
A:LEU25
|
4.5
|
40.0
|
1.0
|
|
CG1
|
A:VAL170
|
4.6
|
41.4
|
1.0
|
|
HD12
|
A:ILE41
|
4.7
|
55.6
|
1.0
|
|
HG12
|
A:ILE41
|
4.7
|
54.3
|
1.0
|
|
CA
|
A:VAL167
|
4.7
|
40.4
|
1.0
|
|
HG23
|
A:ILE166
|
4.8
|
48.5
|
1.0
|
|
HG23
|
A:ILE41
|
4.8
|
51.9
|
1.0
|
|
HG23
|
A:VAL167
|
4.9
|
47.0
|
1.0
|
|
CG2
|
A:VAL167
|
4.9
|
38.0
|
1.0
|
|
N
|
A:VAL167
|
4.9
|
37.8
|
1.0
|
|
HD23
|
A:LEU25
|
5.0
|
48.4
|
1.0
|
|
Krypton binding site 4 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 4 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 4 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr308
b:52.4
occ:0.87
|
HD21
|
A:LEU26
|
3.2
|
51.9
|
1.0
|
|
HG11
|
A:VAL49
|
3.3
|
39.9
|
1.0
|
|
HD23
|
A:LEU25
|
3.5
|
48.4
|
1.0
|
|
HE2
|
A:HIS46
|
3.6
|
35.8
|
1.0
|
|
HD23
|
A:LEU26
|
3.6
|
51.9
|
1.0
|
|
NE2
|
A:HIS46
|
3.8
|
28.6
|
1.0
|
|
HD2
|
A:HIS46
|
3.8
|
32.8
|
1.0
|
|
HB3
|
A:SER22
|
3.9
|
50.5
|
1.0
|
|
CD2
|
A:LEU26
|
3.9
|
42.0
|
1.0
|
|
CD2
|
A:HIS46
|
3.9
|
26.1
|
1.0
|
|
HD11
|
A:ILE33
|
4.0
|
51.6
|
1.0
|
|
HD21
|
A:LEU43
|
4.1
|
52.5
|
1.0
|
|
HG13
|
A:VAL49
|
4.1
|
39.9
|
1.0
|
|
HG21
|
A:VAL49
|
4.1
|
37.3
|
1.0
|
|
CG1
|
A:VAL49
|
4.2
|
32.1
|
1.0
|
|
HG12
|
A:ILE33
|
4.2
|
56.3
|
1.0
|
|
HD21
|
A:LEU37
|
4.3
|
53.4
|
1.0
|
|
HG
|
A:LEU26
|
4.3
|
46.6
|
1.0
|
|
CD2
|
A:LEU25
|
4.4
|
39.1
|
1.0
|
|
HA
|
A:SER22
|
4.4
|
56.0
|
1.0
|
|
HD11
|
A:LEU37
|
4.4
|
52.0
|
1.0
|
|
HD22
|
A:LEU43
|
4.4
|
52.5
|
1.0
|
|
HB3
|
A:LEU25
|
4.5
|
50.9
|
1.0
|
|
O
|
A:SER22
|
4.5
|
42.6
|
1.0
|
|
CE1
|
A:HIS46
|
4.6
|
28.0
|
1.0
|
|
HD21
|
A:LEU25
|
4.6
|
48.4
|
1.0
|
|
HD22
|
A:LEU26
|
4.6
|
51.9
|
1.0
|
|
CD2
|
A:LEU43
|
4.6
|
42.6
|
1.0
|
|
CG
|
A:LEU26
|
4.7
|
37.6
|
1.0
|
|
HG
|
A:LEU25
|
4.7
|
48.0
|
1.0
|
|
CB
|
A:SER22
|
4.7
|
40.9
|
1.0
|
|
HG12
|
A:VAL49
|
4.7
|
39.9
|
1.0
|
|
CG
|
A:HIS46
|
4.8
|
28.5
|
1.0
|
|
CD1
|
A:ILE33
|
4.8
|
41.8
|
1.0
|
|
HD11
|
A:LEU26
|
4.8
|
36.3
|
1.0
|
|
HG22
|
A:VAL49
|
4.8
|
37.3
|
1.0
|
|
CG2
|
A:VAL49
|
4.8
|
29.9
|
1.0
|
|
HD23
|
A:LEU43
|
4.8
|
52.5
|
1.0
|
|
CG1
|
A:ILE33
|
4.9
|
45.8
|
1.0
|
|
CA
|
A:SER22
|
4.9
|
45.5
|
1.0
|
|
HD13
|
A:ILE33
|
4.9
|
51.6
|
1.0
|
|
HE1
|
A:HIS46
|
5.0
|
35.1
|
1.0
|
|
Krypton binding site 5 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 5 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 5 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr309
b:46.9
occ:0.44
|
HD21
|
A:LEU116
|
3.0
|
51.5
|
1.0
|
|
HB3
|
A:ALA114
|
3.1
|
49.6
|
1.0
|
|
HE1
|
A:PHE73
|
3.1
|
56.8
|
1.0
|
|
HB1
|
A:ALA173
|
3.2
|
64.4
|
1.0
|
|
HG11
|
A:VAL189
|
3.4
|
68.2
|
1.0
|
|
HB1
|
A:ALA114
|
3.4
|
49.6
|
1.0
|
|
HG21
|
A:VAL154
|
3.4
|
53.6
|
1.0
|
|
CB
|
A:ALA114
|
3.5
|
40.1
|
1.0
|
|
HB2
|
A:ALA173
|
3.6
|
64.4
|
1.0
|
|
HB2
|
A:ALA114
|
3.6
|
49.6
|
1.0
|
|
CB
|
A:ALA173
|
3.7
|
52.5
|
1.0
|
|
HD1
|
A:PHE73
|
3.8
|
48.9
|
1.0
|
|
HD23
|
A:LEU116
|
3.8
|
51.5
|
1.0
|
|
HB3
|
A:ALA173
|
3.8
|
64.4
|
1.0
|
|
CD2
|
A:LEU116
|
3.8
|
41.7
|
1.0
|
|
HD22
|
A:LEU186
|
3.8
|
69.1
|
1.0
|
|
CE1
|
A:PHE73
|
3.9
|
46.1
|
1.0
|
|
HG23
|
A:VAL154
|
4.0
|
53.6
|
1.0
|
|
KR
|
A:KR306
|
4.0
|
58.1
|
0.7
|
|
HD11
|
A:LEU116
|
4.0
|
42.4
|
1.0
|
|
HG21
|
A:VAL189
|
4.0
|
66.0
|
1.0
|
|
CG2
|
A:VAL154
|
4.1
|
43.5
|
1.0
|
|
CD1
|
A:PHE73
|
4.2
|
39.5
|
1.0
|
|
CG1
|
A:VAL189
|
4.3
|
55.7
|
1.0
|
|
HD21
|
A:LEU186
|
4.3
|
69.1
|
1.0
|
|
HG
|
A:LEU116
|
4.4
|
42.2
|
1.0
|
|
CD2
|
A:LEU186
|
4.5
|
56.4
|
1.0
|
|
HD22
|
A:LEU116
|
4.5
|
51.5
|
1.0
|
|
HB
|
A:VAL154
|
4.5
|
46.6
|
1.0
|
|
CG
|
A:LEU116
|
4.5
|
34.0
|
1.0
|
|
HG12
|
A:VAL189
|
4.7
|
68.2
|
1.0
|
|
CD1
|
A:LEU116
|
4.7
|
34.2
|
1.0
|
|
HG13
|
A:VAL189
|
4.8
|
68.2
|
1.0
|
|
HD11
|
A:ILE177
|
4.8
|
62.9
|
1.0
|
|
HD23
|
A:LEU186
|
4.8
|
69.1
|
1.0
|
|
HG22
|
A:VAL154
|
4.9
|
53.6
|
1.0
|
|
CG2
|
A:VAL189
|
4.9
|
53.8
|
1.0
|
|
CB
|
A:VAL154
|
4.9
|
37.6
|
1.0
|
|
Krypton binding site 6 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 6 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 6 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr310
b:36.5
occ:0.46
|
HD11
|
A:LEU26
|
2.9
|
36.3
|
1.0
|
|
HG21
|
A:THR48
|
2.9
|
49.2
|
1.0
|
|
HG23
|
A:VAL23
|
3.3
|
42.0
|
1.0
|
|
HG22
|
A:VAL23
|
3.3
|
42.0
|
1.0
|
|
HB2
|
A:SER22
|
3.5
|
50.5
|
1.0
|
|
HD12
|
A:LEU26
|
3.6
|
36.3
|
1.0
|
|
HB3
|
A:SER22
|
3.6
|
50.5
|
1.0
|
|
HG22
|
A:THR19
|
3.6
|
48.1
|
1.0
|
|
CD1
|
A:LEU26
|
3.7
|
29.0
|
1.0
|
|
CG2
|
A:THR48
|
3.8
|
39.8
|
1.0
|
|
CG2
|
A:VAL23
|
3.8
|
33.8
|
1.0
|
|
HG22
|
A:THR48
|
3.8
|
49.2
|
1.0
|
|
HG21
|
A:THR19
|
3.8
|
48.1
|
1.0
|
|
HD11
|
B:LEU120
|
3.9
|
46.8
|
1.0
|
|
HG23
|
A:THR19
|
4.0
|
48.1
|
1.0
|
|
HA
|
A:VAL23
|
4.0
|
46.1
|
1.0
|
|
CB
|
A:SER22
|
4.0
|
40.9
|
1.0
|
|
CG2
|
A:THR19
|
4.0
|
38.9
|
1.0
|
|
HB
|
A:THR48
|
4.2
|
36.6
|
1.0
|
|
HD13
|
A:LEU26
|
4.2
|
36.3
|
1.0
|
|
HD21
|
B:LEU120
|
4.3
|
35.9
|
1.0
|
|
HG21
|
A:VAL23
|
4.4
|
42.0
|
1.0
|
|
HG12
|
A:VAL49
|
4.4
|
39.9
|
1.0
|
|
HG23
|
A:THR48
|
4.4
|
49.2
|
1.0
|
|
HG
|
A:LEU26
|
4.5
|
46.6
|
1.0
|
|
N
|
A:VAL23
|
4.5
|
50.0
|
1.0
|
|
CB
|
A:THR48
|
4.5
|
29.4
|
1.0
|
|
HG13
|
A:VAL49
|
4.6
|
39.9
|
1.0
|
|
C
|
A:SER22
|
4.6
|
45.5
|
1.0
|
|
CA
|
A:VAL23
|
4.6
|
37.2
|
1.0
|
|
HG22
|
B:VAL77
|
4.7
|
39.4
|
1.0
|
|
CG
|
A:LEU26
|
4.7
|
37.6
|
1.0
|
|
HG1
|
A:THR48
|
4.7
|
35.7
|
1.0
|
|
H
|
A:VAL23
|
4.7
|
61.4
|
1.0
|
|
HD21
|
A:LEU26
|
4.8
|
51.9
|
1.0
|
|
HD21
|
B:LEU125
|
4.8
|
49.8
|
1.0
|
|
CD1
|
B:LEU120
|
4.8
|
37.8
|
1.0
|
|
CB
|
A:VAL23
|
4.8
|
36.7
|
1.0
|
|
CG1
|
A:VAL49
|
4.9
|
32.1
|
1.0
|
|
O
|
A:SER22
|
4.9
|
42.6
|
1.0
|
|
HE1
|
A:HIS46
|
5.0
|
35.1
|
1.0
|
|
HG11
|
A:VAL49
|
5.0
|
39.9
|
1.0
|
|
HD13
|
B:LEU120
|
5.0
|
46.8
|
1.0
|
|
CA
|
A:SER22
|
5.0
|
45.5
|
1.0
|
|
Krypton binding site 7 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 7 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 7 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Kr506
b:44.0
occ:0.52
|
HA2
|
B:GLY158
|
3.0
|
74.5
|
1.0
|
|
HE2
|
B:PHE122
|
3.0
|
58.4
|
1.0
|
|
HB1
|
B:ALA127
|
3.1
|
59.4
|
1.0
|
|
HG21
|
B:VAL131
|
3.2
|
67.9
|
1.0
|
|
HD11
|
B:ILE228
|
3.2
|
69.6
|
1.0
|
|
O
|
B:GLY158
|
3.4
|
55.5
|
1.0
|
|
HA3
|
B:GLY158
|
3.5
|
74.5
|
1.0
|
|
CA
|
B:GLY158
|
3.6
|
60.9
|
1.0
|
|
HG21
|
B:VAL224
|
3.6
|
68.7
|
1.0
|
|
HE1
|
B:TYR123
|
3.6
|
59.1
|
1.0
|
|
CE2
|
B:PHE122
|
3.7
|
47.5
|
1.0
|
|
HD12
|
B:ILE228
|
3.7
|
69.6
|
1.0
|
|
HB2
|
B:ALA127
|
3.7
|
59.4
|
1.0
|
|
HD1
|
B:TYR123
|
3.8
|
56.8
|
1.0
|
|
CD1
|
B:ILE228
|
3.8
|
56.8
|
1.0
|
|
CB
|
B:ALA127
|
3.9
|
48.3
|
1.0
|
|
C
|
B:GLY158
|
3.9
|
57.0
|
1.0
|
|
HZ
|
B:PHE122
|
4.0
|
63.1
|
1.0
|
|
HD13
|
B:ILE228
|
4.0
|
69.6
|
1.0
|
|
CE1
|
B:TYR123
|
4.1
|
48.1
|
1.0
|
|
HG22
|
B:VAL224
|
4.1
|
68.7
|
1.0
|
|
CG2
|
B:VAL131
|
4.1
|
55.4
|
1.0
|
|
HG11
|
B:VAL224
|
4.1
|
67.7
|
1.0
|
|
CD1
|
B:TYR123
|
4.2
|
46.2
|
1.0
|
|
CZ
|
B:PHE122
|
4.2
|
51.4
|
1.0
|
|
HB3
|
B:ALA127
|
4.3
|
59.4
|
1.0
|
|
CG2
|
B:VAL224
|
4.3
|
56.1
|
1.0
|
|
HG23
|
B:VAL131
|
4.4
|
67.9
|
1.0
|
|
HB2
|
B:GLN161
|
4.4
|
65.4
|
1.0
|
|
HG13
|
B:VAL224
|
4.4
|
67.7
|
1.0
|
|
HG22
|
B:VAL131
|
4.5
|
67.9
|
1.0
|
|
HA
|
B:TYR123
|
4.6
|
47.0
|
1.0
|
|
CD2
|
B:PHE122
|
4.6
|
46.5
|
1.0
|
|
HG11
|
B:VAL131
|
4.6
|
73.4
|
1.0
|
|
H
|
B:TYR162
|
4.7
|
65.0
|
1.0
|
|
HD2
|
B:PHE122
|
4.7
|
57.2
|
1.0
|
|
CG1
|
B:VAL224
|
4.7
|
55.2
|
1.0
|
|
HB2
|
B:TYR162
|
4.8
|
59.0
|
1.0
|
|
OE1
|
B:GLN161
|
4.9
|
55.1
|
1.0
|
|
N
|
B:GLY158
|
4.9
|
62.9
|
1.0
|
|
HG23
|
B:VAL224
|
5.0
|
68.7
|
1.0
|
|
HH
|
B:TYR123
|
5.0
|
67.3
|
1.0
|
|
Krypton binding site 8 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 8 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 8 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Kr507
b:40.7
occ:0.52
|
KR
|
B:KR508
|
2.0
|
36.3
|
0.2
|
|
HD11
|
A:LEU37
|
3.2
|
52.0
|
1.0
|
|
HD21
|
B:LEU166
|
3.3
|
53.6
|
1.0
|
|
OH
|
B:TYR162
|
3.3
|
45.4
|
1.0
|
|
HH
|
B:TYR162
|
3.4
|
55.9
|
1.0
|
|
HD12
|
A:LEU37
|
3.4
|
52.0
|
1.0
|
|
HD22
|
A:LEU26
|
3.6
|
51.9
|
1.0
|
|
HD21
|
A:LEU26
|
3.7
|
51.9
|
1.0
|
|
CD1
|
A:LEU37
|
3.7
|
42.1
|
1.0
|
|
HG11
|
A:VAL49
|
3.7
|
39.9
|
1.0
|
|
HB
|
A:VAL49
|
3.9
|
45.8
|
1.0
|
|
HD13
|
A:LEU37
|
4.1
|
52.0
|
1.0
|
|
CD2
|
A:LEU26
|
4.1
|
42.0
|
1.0
|
|
CD2
|
B:LEU166
|
4.2
|
43.5
|
1.0
|
|
HG13
|
A:ILE33
|
4.2
|
56.3
|
1.0
|
|
HD22
|
B:LEU166
|
4.2
|
53.6
|
1.0
|
|
HG12
|
A:ILE33
|
4.3
|
56.3
|
1.0
|
|
HD11
|
B:LEU166
|
4.3
|
57.7
|
1.0
|
|
CZ
|
B:TYR162
|
4.3
|
42.4
|
1.0
|
|
HG12
|
A:VAL49
|
4.3
|
39.9
|
1.0
|
|
CG1
|
A:VAL49
|
4.4
|
32.1
|
1.0
|
|
HE1
|
B:TYR162
|
4.4
|
57.4
|
1.0
|
|
HD23
|
A:LEU26
|
4.4
|
51.9
|
1.0
|
|
HB3
|
B:HIS124
|
4.5
|
57.3
|
1.0
|
|
HD2
|
B:HIS124
|
4.5
|
45.5
|
1.0
|
|
HG23
|
A:ILE33
|
4.5
|
50.9
|
1.0
|
|
HG21
|
A:VAL49
|
4.6
|
37.3
|
1.0
|
|
CB
|
A:VAL49
|
4.6
|
37.0
|
1.0
|
|
HG21
|
A:ILE33
|
4.6
|
50.9
|
1.0
|
|
HD23
|
B:LEU166
|
4.7
|
53.6
|
1.0
|
|
CG1
|
A:ILE33
|
4.7
|
45.8
|
1.0
|
|
CE1
|
B:TYR162
|
4.7
|
46.7
|
1.0
|
|
HZ
|
B:PHE139
|
4.7
|
68.7
|
1.0
|
|
HE1
|
B:PHE139
|
4.7
|
66.2
|
1.0
|
|
HD13
|
B:LEU166
|
4.8
|
57.7
|
1.0
|
|
CD1
|
B:LEU166
|
4.9
|
46.9
|
1.0
|
|
Krypton binding site 9 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 9 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 9 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Kr508
b:36.3
occ:0.24
|
KR
|
B:KR507
|
2.0
|
40.7
|
0.5
|
|
HB3
|
B:HIS124
|
2.8
|
57.3
|
1.0
|
|
HD21
|
B:LEU166
|
3.2
|
53.6
|
1.0
|
|
HD22
|
A:LEU26
|
3.4
|
51.9
|
1.0
|
|
HD21
|
A:LEU26
|
3.5
|
51.9
|
1.0
|
|
HG12
|
A:VAL49
|
3.5
|
39.9
|
1.0
|
|
HG11
|
A:VAL49
|
3.6
|
39.9
|
1.0
|
|
HD2
|
B:HIS124
|
3.7
|
45.5
|
1.0
|
|
CB
|
B:HIS124
|
3.7
|
46.6
|
1.0
|
|
OH
|
B:TYR162
|
3.7
|
45.4
|
1.0
|
|
CG
|
B:HIS124
|
3.9
|
41.1
|
1.0
|
|
CD2
|
A:LEU26
|
3.9
|
42.0
|
1.0
|
|
CD2
|
B:HIS124
|
3.9
|
36.8
|
1.0
|
|
HB
|
A:VAL49
|
3.9
|
45.8
|
1.0
|
|
HD13
|
A:LEU26
|
4.0
|
36.3
|
1.0
|
|
CG1
|
A:VAL49
|
4.0
|
32.1
|
1.0
|
|
CD2
|
B:LEU166
|
4.0
|
43.5
|
1.0
|
|
HD23
|
B:LEU166
|
4.1
|
53.6
|
1.0
|
|
HB2
|
B:HIS124
|
4.1
|
57.3
|
1.0
|
|
HH
|
B:TYR162
|
4.2
|
55.9
|
1.0
|
|
HD11
|
A:LEU26
|
4.2
|
36.3
|
1.0
|
|
HD22
|
B:LEU166
|
4.2
|
53.6
|
1.0
|
|
CZ
|
B:TYR162
|
4.5
|
42.4
|
1.0
|
|
CD1
|
A:LEU26
|
4.5
|
29.0
|
1.0
|
|
CB
|
A:VAL49
|
4.5
|
37.0
|
1.0
|
|
HD23
|
A:LEU26
|
4.6
|
51.9
|
1.0
|
|
HA
|
B:HIS124
|
4.6
|
56.8
|
1.0
|
|
CA
|
B:HIS124
|
4.8
|
46.1
|
1.0
|
|
HG13
|
A:VAL49
|
4.8
|
39.9
|
1.0
|
|
CG
|
A:LEU26
|
4.8
|
37.6
|
1.0
|
|
NE2
|
B:HIS124
|
4.9
|
40.0
|
1.0
|
|
ND1
|
B:HIS124
|
4.9
|
47.6
|
1.0
|
|
HD12
|
B:LEU120
|
4.9
|
46.8
|
1.0
|
|
HE2
|
B:TYR162
|
4.9
|
57.6
|
1.0
|
|
Krypton binding site 10 out
of 20 in 6z8o
Go back to
Krypton Binding Sites List in 6z8o
Krypton binding site 10 out
of 20 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
 Mono view
 Stereo pair view
|
|
A full contact list of Krypton with other atoms in the Kr binding
site number 10 of Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Kr509
b:46.0
occ:0.50
|
HB
|
B:VAL131
|
2.9
|
70.8
|
1.0
|
|
HG11
|
B:VAL131
|
3.0
|
73.4
|
1.0
|
|
HG12
|
B:VAL131
|
3.1
|
73.4
|
1.0
|
|
HG2
|
B:GLN128
|
3.1
|
59.5
|
1.0
|
|
CG1
|
B:VAL131
|
3.4
|
60.0
|
1.0
|
|
HD2
|
B:TYR162
|
3.5
|
59.4
|
1.0
|
|
HG22
|
B:VAL159
|
3.6
|
75.1
|
1.0
|
|
CB
|
B:VAL131
|
3.6
|
57.8
|
1.0
|
|
HB2
|
B:TYR162
|
3.7
|
59.0
|
1.0
|
|
HA
|
B:VAL159
|
3.8
|
70.8
|
1.0
|
|
CD2
|
B:TYR162
|
3.8
|
48.3
|
1.0
|
|
HG3
|
B:GLN128
|
3.9
|
59.5
|
1.0
|
|
HA
|
B:GLN128
|
3.9
|
59.3
|
1.0
|
|
CG
|
B:GLN128
|
3.9
|
48.4
|
1.0
|
|
HA2
|
B:GLY133
|
4.0
|
82.0
|
1.0
|
|
HB3
|
B:ALA127
|
4.1
|
59.4
|
1.0
|
|
HG23
|
B:VAL159
|
4.1
|
75.1
|
1.0
|
|
HB3
|
B:TYR162
|
4.2
|
59.0
|
1.0
|
|
HG21
|
B:VAL131
|
4.2
|
67.9
|
1.0
|
|
CG
|
B:TYR162
|
4.2
|
49.0
|
1.0
|
|
CB
|
B:TYR162
|
4.3
|
48.0
|
1.0
|
|
O
|
B:VAL131
|
4.3
|
58.2
|
1.0
|
|
HG13
|
B:VAL131
|
4.3
|
73.4
|
1.0
|
|
CG2
|
B:VAL159
|
4.3
|
61.4
|
1.0
|
|
HB1
|
B:ALA127
|
4.3
|
59.4
|
1.0
|
|
H
|
B:GLY133
|
4.4
|
81.4
|
1.0
|
|
N
|
B:GLY133
|
4.5
|
66.7
|
1.0
|
|
HA3
|
B:GLY133
|
4.5
|
82.0
|
1.0
|
|
CE2
|
B:TYR162
|
4.5
|
46.8
|
1.0
|
|
CA
|
B:GLY133
|
4.5
|
67.2
|
1.0
|
|
CG2
|
B:VAL131
|
4.5
|
55.4
|
1.0
|
|
C
|
B:VAL131
|
4.6
|
58.8
|
1.0
|
|
N
|
B:GLN128
|
4.6
|
51.0
|
1.0
|
|
CA
|
B:GLN128
|
4.6
|
48.2
|
1.0
|
|
O
|
B:GLY158
|
4.6
|
55.5
|
1.0
|
|
CA
|
B:VAL159
|
4.6
|
57.8
|
1.0
|
|
CB
|
B:ALA127
|
4.7
|
48.3
|
1.0
|
|
HE2
|
B:TYR162
|
4.7
|
57.6
|
1.0
|
|
CA
|
B:VAL131
|
4.7
|
59.3
|
1.0
|
|
H
|
B:GLN128
|
4.7
|
62.6
|
1.0
|
|
O
|
B:TYR123
|
4.8
|
45.1
|
1.0
|
|
C
|
B:ALA127
|
4.8
|
53.5
|
1.0
|
|
CD
|
B:GLN128
|
4.9
|
48.3
|
1.0
|
|
CB
|
B:GLN128
|
4.9
|
49.5
|
1.0
|
|
C
|
B:GLY158
|
4.9
|
57.0
|
1.0
|
|
N
|
B:VAL159
|
5.0
|
61.1
|
1.0
|
|
O
|
B:ALA127
|
5.0
|
56.3
|
1.0
|
|
HG23
|
B:VAL131
|
5.0
|
67.9
|
1.0
|
|
Reference:
S.Zacarias,
A.Temporao,
P.Carpentier,
P.Van Der Linden,
I.A.C.Pereira,
P.M.Matias.
Exploring the Gas Access Routes in A [Nifese] Hydrogenase Using Crystals Pressurized with Krypton and Oxygen. J.Biol.Inorg.Chem. V. 25 863 2020.
ISSN: ESSN 1432-1327
PubMed: 32865640
DOI: 10.1007/S00775-020-01814-Y
Page generated: Tue Aug 13 01:29:52 2024
|
