Krypton in PDB 6zlf: Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Protein crystallography data
The structure of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton, PDB code: 6zlf
was solved by
S.Engilberge,
T.Wagner,
P.Carpentier,
E.Girard,
S.Shima,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.40 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.025,
162.553,
134.376,
90.00,
93.75,
90.00
|
R / Rfree (%)
|
18.2 /
19.7
|
Other elements in 6zlf:
The structure of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton also contains other interesting chemical elements:
Krypton Binding Sites:
Krypton binding site 1 out
of 48 in 6zlf
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Krypton Binding Sites List in 6zlf
Krypton binding site 1 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 1 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr506
b:64.9
occ:0.75
|
CZ
|
A:PHE173
|
3.9
|
32.0
|
1.0
|
CB
|
A:ALA172
|
4.1
|
29.8
|
1.0
|
CE1
|
A:PHE215
|
4.2
|
49.6
|
1.0
|
CG2
|
A:VAL211
|
4.3
|
41.4
|
1.0
|
CD2
|
A:LEU151
|
4.3
|
61.0
|
1.0
|
CZ
|
A:PHE158
|
4.3
|
39.6
|
1.0
|
CD1
|
A:LEU151
|
4.4
|
62.3
|
1.0
|
CE1
|
A:PHE173
|
4.4
|
31.1
|
1.0
|
CD2
|
A:TYR248
|
4.4
|
28.0
|
1.0
|
CE2
|
A:PHE173
|
4.4
|
31.9
|
1.0
|
CE2
|
A:TYR248
|
4.4
|
30.6
|
1.0
|
CG1
|
A:VAL211
|
4.5
|
38.6
|
1.0
|
CB
|
A:VAL211
|
4.7
|
40.1
|
1.0
|
CA
|
A:VAL211
|
4.7
|
39.7
|
1.0
|
CG
|
A:LEU151
|
4.8
|
65.8
|
1.0
|
CZ
|
A:PHE215
|
4.9
|
43.3
|
1.0
|
CE2
|
A:PHE158
|
4.9
|
42.3
|
1.0
|
CG
|
A:LYS214
|
4.9
|
71.6
|
1.0
|
CD1
|
A:PHE215
|
4.9
|
51.0
|
1.0
|
|
Krypton binding site 2 out
of 48 in 6zlf
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Krypton Binding Sites List in 6zlf
Krypton binding site 2 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 2 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr507
b:63.4
occ:0.75
|
CZ
|
A:PHE173
|
3.9
|
32.0
|
1.0
|
CD1
|
A:ILE227
|
4.0
|
45.0
|
1.0
|
CD2
|
A:LEU167
|
4.0
|
32.2
|
1.0
|
CE2
|
A:PHE173
|
4.1
|
31.9
|
1.0
|
CE1
|
A:PHE215
|
4.4
|
49.6
|
1.0
|
CG2
|
A:VAL218
|
4.4
|
69.3
|
1.0
|
CG1
|
A:VAL218
|
4.5
|
66.7
|
1.0
|
KR
|
A:KR511
|
4.6
|
50.7
|
0.1
|
CD1
|
A:PHE215
|
4.6
|
51.0
|
1.0
|
CD1
|
A:ILE245
|
4.8
|
36.0
|
1.0
|
CE2
|
A:PHE158
|
4.8
|
42.3
|
1.0
|
CB
|
A:VAL218
|
4.8
|
66.5
|
1.0
|
CG1
|
A:ILE245
|
4.9
|
34.1
|
1.0
|
KR
|
A:KR508
|
5.0
|
51.2
|
0.2
|
|
Krypton binding site 3 out
of 48 in 6zlf
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Krypton Binding Sites List in 6zlf
Krypton binding site 3 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 3 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr508
b:51.2
occ:0.20
|
CG2
|
A:VAL218
|
4.0
|
69.3
|
1.0
|
CD2
|
A:LEU146
|
4.0
|
65.6
|
1.0
|
CD1
|
A:LEU167
|
4.1
|
33.6
|
1.0
|
CD1
|
A:ILE227
|
4.1
|
45.0
|
1.0
|
CB
|
A:LEU223
|
4.1
|
78.5
|
1.0
|
CG1
|
A:VAL218
|
4.2
|
66.7
|
1.0
|
KR
|
A:KR510
|
4.3
|
59.1
|
0.1
|
CG1
|
A:ILE227
|
4.5
|
42.1
|
1.0
|
CD2
|
A:LEU167
|
4.7
|
32.2
|
1.0
|
CB
|
A:VAL218
|
4.7
|
66.5
|
1.0
|
KR
|
A:KR507
|
5.0
|
63.4
|
0.8
|
CG
|
A:LEU167
|
5.0
|
33.9
|
1.0
|
|
Krypton binding site 4 out
of 48 in 6zlf
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Krypton Binding Sites List in 6zlf
Krypton binding site 4 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 4 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr509
b:44.6
occ:0.20
|
N
|
A:HIS152
|
3.3
|
58.8
|
1.0
|
C
|
A:LEU151
|
3.3
|
65.1
|
1.0
|
CD1
|
A:ILE204
|
3.4
|
28.6
|
1.0
|
N
|
A:ALA172
|
3.5
|
28.7
|
1.0
|
O
|
A:LEU151
|
3.5
|
62.3
|
1.0
|
CB
|
A:HIS152
|
3.5
|
58.6
|
1.0
|
CA
|
A:ALA172
|
3.7
|
28.5
|
1.0
|
CB
|
A:ASP171
|
3.8
|
29.8
|
1.0
|
O
|
A:HOH732
|
3.8
|
39.6
|
1.0
|
CA
|
A:HIS152
|
3.9
|
56.0
|
1.0
|
C
|
A:ASP171
|
3.9
|
31.2
|
1.0
|
CB
|
A:ALA172
|
4.0
|
29.8
|
1.0
|
CA
|
A:LEU151
|
4.1
|
61.6
|
1.0
|
CG
|
A:HIS152
|
4.2
|
57.5
|
1.0
|
CD2
|
A:HIS152
|
4.3
|
55.3
|
1.0
|
CA
|
A:ASP171
|
4.4
|
28.9
|
1.0
|
O
|
A:ASP171
|
4.5
|
30.3
|
1.0
|
O
|
A:HOH657
|
4.5
|
45.3
|
1.0
|
CB
|
A:LEU151
|
4.7
|
62.1
|
1.0
|
CG1
|
A:ILE204
|
4.8
|
26.6
|
1.0
|
|
Krypton binding site 5 out
of 48 in 6zlf
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Krypton Binding Sites List in 6zlf
Krypton binding site 5 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 5 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr510
b:59.1
occ:0.10
|
CB
|
A:LEU146
|
3.8
|
45.9
|
1.0
|
CG2
|
A:THR144
|
3.8
|
47.5
|
1.0
|
CD2
|
A:LEU160
|
3.9
|
41.9
|
1.0
|
CB
|
A:LEU160
|
4.1
|
38.2
|
1.0
|
KR
|
A:KR508
|
4.3
|
51.2
|
0.2
|
O
|
A:THR144
|
4.3
|
40.1
|
1.0
|
CD2
|
A:LEU146
|
4.3
|
65.6
|
1.0
|
CB
|
A:THR144
|
4.3
|
47.7
|
1.0
|
O
|
A:PHE145
|
4.4
|
47.9
|
1.0
|
CG
|
A:LEU146
|
4.5
|
60.9
|
1.0
|
CD2
|
A:LEU133
|
4.5
|
57.2
|
1.0
|
C
|
A:PHE145
|
4.6
|
48.3
|
1.0
|
CA
|
A:LEU146
|
4.7
|
45.7
|
1.0
|
CG
|
A:LEU160
|
4.7
|
41.9
|
1.0
|
N
|
A:LEU146
|
4.7
|
45.8
|
1.0
|
C
|
A:THR144
|
4.7
|
41.3
|
1.0
|
CD1
|
A:LEU146
|
4.8
|
66.0
|
1.0
|
|
Krypton binding site 6 out
of 48 in 6zlf
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Krypton Binding Sites List in 6zlf
Krypton binding site 6 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 6 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr511
b:50.7
occ:0.15
|
CD2
|
A:LEU224
|
3.3
|
55.7
|
1.0
|
CG
|
A:PHE215
|
3.4
|
48.1
|
1.0
|
CD1
|
A:PHE215
|
3.4
|
51.0
|
1.0
|
CB
|
A:PHE215
|
3.5
|
48.3
|
1.0
|
CA
|
A:PHE215
|
3.6
|
49.4
|
1.0
|
CG
|
A:LEU224
|
3.8
|
64.6
|
1.0
|
O
|
A:PHE215
|
3.8
|
49.8
|
1.0
|
CD2
|
A:PHE215
|
4.0
|
46.5
|
1.0
|
CG2
|
A:ILE245
|
4.0
|
35.4
|
1.0
|
CE1
|
A:PHE215
|
4.1
|
49.6
|
1.0
|
C
|
A:PHE215
|
4.2
|
51.1
|
1.0
|
CG1
|
A:VAL218
|
4.2
|
66.7
|
1.0
|
CG1
|
A:ILE219
|
4.3
|
61.8
|
1.0
|
CD1
|
A:ILE219
|
4.4
|
62.8
|
1.0
|
CB
|
A:VAL218
|
4.4
|
66.5
|
1.0
|
CB
|
A:LEU224
|
4.5
|
66.0
|
1.0
|
KR
|
A:KR507
|
4.6
|
63.4
|
0.8
|
CE2
|
A:PHE215
|
4.6
|
45.4
|
1.0
|
CZ
|
A:PHE215
|
4.6
|
43.3
|
1.0
|
N
|
A:PHE215
|
4.8
|
50.2
|
1.0
|
|
Krypton binding site 7 out
of 48 in 6zlf
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Krypton Binding Sites List in 6zlf
Krypton binding site 7 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 7 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Kr512
b:44.9
occ:0.15
|
CG
|
A:GLU147
|
2.5
|
62.9
|
1.0
|
N
|
A:GLU147
|
3.1
|
61.2
|
1.0
|
CA
|
A:GLU147
|
3.3
|
60.2
|
1.0
|
CB
|
A:GLU147
|
3.4
|
54.6
|
1.0
|
C
|
A:LEU146
|
3.5
|
53.2
|
1.0
|
CD
|
A:GLU147
|
3.5
|
71.9
|
1.0
|
N
|
A:SER132
|
3.5
|
55.8
|
1.0
|
C
|
A:LYS131
|
3.5
|
55.2
|
1.0
|
O
|
A:LYS131
|
3.9
|
53.5
|
1.0
|
CA
|
A:SER132
|
3.9
|
50.9
|
1.0
|
O
|
A:LEU146
|
3.9
|
52.3
|
1.0
|
CA
|
A:LYS131
|
4.0
|
55.2
|
1.0
|
N
|
A:LEU146
|
4.0
|
45.8
|
1.0
|
OE1
|
A:GLU147
|
4.0
|
59.9
|
1.0
|
CB
|
A:PHE145
|
4.0
|
44.0
|
1.0
|
CB
|
A:MET157
|
4.1
|
37.8
|
1.0
|
O
|
A:VAL130
|
4.1
|
50.0
|
1.0
|
CA
|
A:LEU146
|
4.1
|
45.7
|
1.0
|
OG
|
A:SER132
|
4.1
|
67.0
|
1.0
|
C
|
A:PHE145
|
4.2
|
48.3
|
1.0
|
SD
|
A:MET157
|
4.2
|
41.1
|
1.0
|
OE2
|
A:GLU147
|
4.3
|
66.4
|
1.0
|
N
|
A:LYS131
|
4.3
|
56.5
|
1.0
|
CG2
|
A:THR108
|
4.3
|
43.8
|
1.0
|
C
|
A:VAL130
|
4.4
|
52.4
|
1.0
|
O
|
A:PHE145
|
4.5
|
47.9
|
1.0
|
CG2
|
A:VAL130
|
4.6
|
49.5
|
1.0
|
CB
|
A:SER132
|
4.7
|
64.5
|
1.0
|
CA
|
A:PHE145
|
4.7
|
43.4
|
1.0
|
C
|
A:GLU147
|
4.7
|
60.0
|
1.0
|
CG
|
A:MET157
|
4.8
|
38.2
|
1.0
|
CB
|
A:VAL130
|
5.0
|
50.0
|
1.0
|
|
Krypton binding site 8 out
of 48 in 6zlf
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Krypton Binding Sites List in 6zlf
Krypton binding site 8 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 8 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Kr501
b:66.2
occ:0.75
|
CZ
|
F:PHE173
|
3.9
|
34.7
|
1.0
|
CB
|
F:ALA172
|
4.2
|
31.2
|
1.0
|
CE1
|
F:PHE215
|
4.2
|
61.5
|
1.0
|
CG2
|
F:VAL211
|
4.2
|
44.2
|
1.0
|
CD2
|
F:LEU151
|
4.3
|
53.2
|
1.0
|
CD1
|
F:LEU151
|
4.4
|
55.5
|
1.0
|
CZ
|
F:PHE158
|
4.4
|
38.0
|
1.0
|
CE1
|
F:PHE173
|
4.4
|
29.9
|
1.0
|
CD2
|
F:TYR248
|
4.4
|
30.6
|
1.0
|
CG1
|
F:VAL211
|
4.4
|
46.1
|
1.0
|
CE2
|
F:TYR248
|
4.4
|
31.2
|
1.0
|
CE2
|
F:PHE173
|
4.4
|
33.3
|
1.0
|
CB
|
F:VAL211
|
4.7
|
46.0
|
1.0
|
CA
|
F:VAL211
|
4.7
|
48.9
|
1.0
|
CZ
|
F:PHE215
|
4.8
|
50.3
|
1.0
|
CG
|
F:LEU151
|
4.8
|
55.6
|
1.0
|
CE2
|
F:PHE158
|
4.9
|
40.8
|
1.0
|
CG
|
F:LYS214
|
4.9
|
82.0
|
1.0
|
CD1
|
F:PHE215
|
4.9
|
64.5
|
1.0
|
|
Krypton binding site 9 out
of 48 in 6zlf
Go back to
Krypton Binding Sites List in 6zlf
Krypton binding site 9 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 9 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Kr502
b:63.2
occ:0.75
|
CZ
|
F:PHE173
|
4.0
|
34.7
|
1.0
|
CG2
|
F:VAL218
|
4.1
|
77.2
|
1.0
|
CE2
|
F:PHE173
|
4.1
|
33.3
|
1.0
|
CD2
|
F:LEU167
|
4.1
|
36.7
|
1.0
|
CD1
|
F:ILE227
|
4.2
|
53.6
|
1.0
|
CE1
|
F:PHE215
|
4.2
|
61.5
|
1.0
|
CD1
|
F:PHE215
|
4.4
|
64.5
|
1.0
|
CG1
|
F:VAL218
|
4.4
|
73.5
|
1.0
|
CB
|
F:VAL218
|
4.6
|
76.8
|
1.0
|
CE2
|
F:PHE158
|
4.7
|
40.8
|
1.0
|
|
Krypton binding site 10 out
of 48 in 6zlf
Go back to
Krypton Binding Sites List in 6zlf
Krypton binding site 10 out
of 48 in the Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton
Mono view
Stereo pair view
|
A full contact list of Krypton with other atoms in the Kr binding
site number 10 of Aerobic Crystal Structure of F420H2-Oxidase From Methanothermococcus Thermolithotrophicus at 1.8A Resolution Under 125 Bars of Krypton within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Kr503
b:67.5
occ:0.20
|
CD2
|
F:LEU146
|
2.1
|
90.2
|
0.5
|
CD1
|
F:LEU146
|
2.2
|
68.4
|
0.5
|
CG
|
F:LEU146
|
2.3
|
68.8
|
0.5
|
CG2
|
F:THR144
|
3.7
|
42.1
|
1.0
|
CB
|
F:LEU146
|
3.8
|
43.5
|
0.5
|
CB
|
F:LEU146
|
3.8
|
43.5
|
0.5
|
CD2
|
F:LEU160
|
4.0
|
55.2
|
1.0
|
CD2
|
F:LEU146
|
4.1
|
90.1
|
0.5
|
O
|
F:THR144
|
4.2
|
38.4
|
1.0
|
CB
|
F:LEU160
|
4.2
|
38.2
|
1.0
|
O
|
F:PHE145
|
4.2
|
40.7
|
1.0
|
CB
|
F:THR144
|
4.2
|
42.0
|
1.0
|
CG
|
F:LEU146
|
4.3
|
68.7
|
0.5
|
CD1
|
F:LEU146
|
4.3
|
68.3
|
0.5
|
CD2
|
F:LEU133
|
4.4
|
51.5
|
1.0
|
C
|
F:PHE145
|
4.5
|
42.0
|
1.0
|
C
|
F:THR144
|
4.6
|
40.9
|
1.0
|
KR
|
F:KR504
|
4.7
|
51.8
|
0.2
|
CA
|
F:LEU146
|
4.7
|
42.3
|
0.5
|
CA
|
F:LEU146
|
4.7
|
42.3
|
0.5
|
CG
|
F:LEU160
|
4.8
|
48.0
|
1.0
|
N
|
F:LEU146
|
4.8
|
39.0
|
1.0
|
|
Reference:
S.Engilberge,
T.Wagner,
P.Carpentier,
E.Girard,
S.Shima.
Krypton-Derivatization Highlights O 2 -Channeling in A Four-Electron Reducing Oxidase. Chem.Commun.(Camb.) V. 56 10863 2020.
ISSN: ESSN 1364-548X
PubMed: 32940290
DOI: 10.1039/D0CC04557H
Page generated: Tue Aug 13 01:30:31 2024
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