Iron 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:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Page 4, Binding sites: 31 -
36;
Binding sites:
The binding sites of Iron 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 Iron atom.
In total 36 binding sites of Iron 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 Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 1 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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:Fe301
b:41.8
occ:1.00
|
FE1
|
A:SF4301
|
0.0
|
41.8
|
1.0
|
SG
|
A:CYS238
|
2.3
|
35.2
|
1.0
|
S2
|
A:SF4301
|
2.3
|
37.0
|
1.0
|
S3
|
A:SF4301
|
2.3
|
40.3
|
1.0
|
S4
|
A:SF4301
|
2.3
|
49.0
|
1.0
|
FE4
|
A:SF4301
|
2.7
|
25.3
|
1.0
|
FE3
|
A:SF4301
|
2.7
|
51.6
|
1.0
|
FE2
|
A:SF4301
|
2.7
|
44.4
|
1.0
|
HB3
|
A:CYS238
|
2.9
|
47.5
|
1.0
|
CB
|
A:CYS238
|
3.1
|
38.4
|
1.0
|
HB2
|
A:CYS238
|
3.4
|
47.5
|
1.0
|
HB2
|
A:ARG233
|
3.7
|
45.5
|
1.0
|
HD3
|
A:PRO241
|
3.8
|
44.2
|
1.0
|
H
|
A:GLY240
|
3.8
|
45.6
|
1.0
|
HA3
|
A:GLY240
|
3.9
|
46.4
|
1.0
|
S1
|
A:SF4301
|
3.9
|
55.4
|
1.0
|
H
|
A:ARG233
|
3.9
|
57.1
|
1.0
|
HG11
|
A:VAL260
|
4.0
|
48.2
|
1.0
|
HG22
|
A:VAL260
|
4.0
|
46.4
|
1.0
|
HG21
|
A:VAL260
|
4.3
|
46.4
|
1.0
|
HG13
|
A:VAL260
|
4.3
|
48.2
|
1.0
|
H
|
A:TYR234
|
4.5
|
54.3
|
1.0
|
CA
|
A:CYS238
|
4.5
|
35.0
|
1.0
|
N
|
A:GLY240
|
4.5
|
36.9
|
1.0
|
HA
|
A:TYR234
|
4.5
|
53.1
|
1.0
|
CG1
|
A:VAL260
|
4.6
|
39.0
|
1.0
|
CG2
|
A:VAL260
|
4.6
|
37.5
|
1.0
|
N
|
A:TYR234
|
4.6
|
44.1
|
1.0
|
SG
|
A:CYS232
|
4.6
|
42.2
|
1.0
|
CB
|
A:ARG233
|
4.6
|
36.8
|
1.0
|
CA
|
A:GLY240
|
4.6
|
37.5
|
1.0
|
N
|
A:ARG233
|
4.7
|
46.4
|
1.0
|
SG
|
A:CYS211
|
4.7
|
37.6
|
1.0
|
HB2
|
A:TYR234
|
4.7
|
50.3
|
1.0
|
CD
|
A:PRO241
|
4.7
|
35.6
|
1.0
|
C
|
A:CYS238
|
4.8
|
36.8
|
1.0
|
ND1
|
A:HIS208
|
4.8
|
40.0
|
1.0
|
C
|
A:ARG233
|
4.9
|
38.1
|
1.0
|
HB3
|
A:ARG233
|
4.9
|
45.5
|
1.0
|
HA
|
A:CYS238
|
4.9
|
43.5
|
1.0
|
CA
|
A:ARG233
|
5.0
|
40.9
|
1.0
|
|
Iron binding site 2 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 2 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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:Fe301
b:44.4
occ:1.00
|
FE2
|
A:SF4301
|
0.0
|
44.4
|
1.0
|
ND1
|
A:HIS208
|
2.2
|
40.0
|
1.0
|
S3
|
A:SF4301
|
2.3
|
40.3
|
1.0
|
S4
|
A:SF4301
|
2.3
|
49.0
|
1.0
|
S1
|
A:SF4301
|
2.3
|
55.4
|
1.0
|
FE1
|
A:SF4301
|
2.7
|
41.8
|
1.0
|
FE4
|
A:SF4301
|
2.7
|
25.3
|
1.0
|
FE3
|
A:SF4301
|
2.7
|
51.6
|
1.0
|
CE1
|
A:HIS208
|
2.9
|
51.5
|
1.0
|
HE1
|
A:HIS208
|
2.9
|
63.3
|
1.0
|
HA
|
A:HIS208
|
3.2
|
55.7
|
1.0
|
HD3
|
A:PRO241
|
3.2
|
44.2
|
1.0
|
CG
|
A:HIS208
|
3.3
|
40.0
|
1.0
|
HB2
|
A:HIS208
|
3.6
|
55.7
|
1.0
|
HG3
|
A:PRO241
|
3.7
|
44.5
|
1.0
|
CB
|
A:HIS208
|
3.8
|
45.2
|
1.0
|
HA3
|
A:GLY240
|
3.9
|
46.4
|
1.0
|
S2
|
A:SF4301
|
3.9
|
37.0
|
1.0
|
CA
|
A:HIS208
|
3.9
|
45.3
|
1.0
|
NE2
|
A:HIS208
|
4.0
|
50.6
|
1.0
|
CD
|
A:PRO241
|
4.0
|
35.6
|
1.0
|
HB2
|
A:CYS211
|
4.2
|
52.6
|
1.0
|
CD2
|
A:HIS208
|
4.2
|
45.2
|
1.0
|
HB3
|
A:CYS211
|
4.2
|
52.6
|
1.0
|
CG
|
A:PRO241
|
4.3
|
35.9
|
1.0
|
N
|
A:PRO241
|
4.5
|
42.0
|
1.0
|
CB
|
A:CYS211
|
4.5
|
42.6
|
1.0
|
SG
|
A:CYS238
|
4.6
|
35.2
|
1.0
|
HB2
|
A:TYR217
|
4.6
|
64.6
|
1.0
|
CA
|
A:GLY240
|
4.7
|
37.5
|
1.0
|
HE2
|
A:HIS208
|
4.7
|
62.1
|
1.0
|
C
|
A:GLY240
|
4.7
|
41.4
|
1.0
|
HB3
|
A:HIS208
|
4.7
|
55.7
|
1.0
|
SG
|
A:CYS211
|
4.8
|
37.6
|
1.0
|
HD13
|
A:LEU214
|
4.8
|
58.8
|
1.0
|
H
|
A:GLY240
|
4.8
|
45.6
|
1.0
|
SG
|
A:CYS232
|
4.8
|
42.2
|
1.0
|
HD2
|
A:PRO241
|
4.8
|
44.2
|
1.0
|
HB2
|
A:TYR234
|
4.8
|
50.3
|
1.0
|
N
|
A:HIS208
|
4.8
|
46.0
|
1.0
|
HG2
|
A:PRO241
|
4.8
|
44.5
|
1.0
|
HA
|
A:PRO241
|
4.9
|
50.5
|
1.0
|
HB3
|
A:CYS238
|
4.9
|
47.5
|
1.0
|
C
|
A:HIS208
|
4.9
|
47.7
|
1.0
|
H
|
A:HIS208
|
5.0
|
56.6
|
1.0
|
|
Iron binding site 3 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 3 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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:Fe301
b:51.6
occ:1.00
|
FE3
|
A:SF4301
|
0.0
|
51.6
|
1.0
|
S2
|
A:SF4301
|
2.3
|
37.0
|
1.0
|
SG
|
A:CYS232
|
2.3
|
42.2
|
1.0
|
S1
|
A:SF4301
|
2.3
|
55.4
|
1.0
|
S4
|
A:SF4301
|
2.3
|
49.0
|
1.0
|
FE4
|
A:SF4301
|
2.7
|
25.3
|
1.0
|
FE1
|
A:SF4301
|
2.7
|
41.8
|
1.0
|
FE2
|
A:SF4301
|
2.7
|
44.4
|
1.0
|
H
|
A:ARG233
|
3.1
|
57.1
|
1.0
|
HB2
|
A:TYR217
|
3.4
|
64.6
|
1.0
|
HB2
|
A:CYS232
|
3.5
|
55.4
|
1.0
|
CB
|
A:CYS232
|
3.5
|
45.0
|
1.0
|
H
|
A:TYR234
|
3.5
|
54.3
|
1.0
|
HB2
|
A:TYR234
|
3.8
|
50.3
|
1.0
|
N
|
A:ARG233
|
3.8
|
46.4
|
1.0
|
HA
|
A:CYS232
|
3.8
|
55.7
|
1.0
|
S3
|
A:SF4301
|
3.9
|
40.3
|
1.0
|
HE1
|
A:HIS208
|
3.9
|
63.3
|
1.0
|
HB2
|
A:TYR213
|
4.0
|
50.8
|
1.0
|
CA
|
A:CYS232
|
4.1
|
45.2
|
1.0
|
N
|
A:TYR234
|
4.1
|
44.1
|
1.0
|
HD1
|
A:TYR217
|
4.2
|
52.3
|
1.0
|
HB3
|
A:CYS232
|
4.3
|
55.4
|
1.0
|
CB
|
A:TYR217
|
4.3
|
52.6
|
1.0
|
C
|
A:CYS232
|
4.4
|
46.9
|
1.0
|
CE1
|
A:HIS208
|
4.5
|
51.5
|
1.0
|
HB2
|
A:ARG233
|
4.5
|
45.5
|
1.0
|
ND1
|
A:HIS208
|
4.5
|
40.0
|
1.0
|
HB3
|
A:CYS238
|
4.5
|
47.5
|
1.0
|
CB
|
A:TYR234
|
4.6
|
40.8
|
1.0
|
CD1
|
A:TYR217
|
4.6
|
42.4
|
1.0
|
O
|
A:TYR213
|
4.7
|
50.3
|
1.0
|
HB3
|
A:TYR213
|
4.7
|
50.8
|
1.0
|
CG
|
A:TYR217
|
4.7
|
46.4
|
1.0
|
CA
|
A:ARG233
|
4.8
|
40.9
|
1.0
|
HA
|
A:LEU214
|
4.8
|
59.0
|
1.0
|
HA
|
A:TYR234
|
4.8
|
53.1
|
1.0
|
CA
|
A:TYR234
|
4.8
|
43.0
|
1.0
|
CB
|
A:TYR213
|
4.8
|
41.1
|
1.0
|
SG
|
A:CYS211
|
4.8
|
37.6
|
1.0
|
HB3
|
A:TYR234
|
4.8
|
50.3
|
1.0
|
HB3
|
A:TYR217
|
4.8
|
64.6
|
1.0
|
C
|
A:ARG233
|
4.8
|
38.1
|
1.0
|
SG
|
A:CYS238
|
4.9
|
35.2
|
1.0
|
HA
|
A:TYR217
|
4.9
|
64.3
|
1.0
|
|
Iron binding site 4 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 4 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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:Fe301
b:25.3
occ:1.00
|
FE4
|
A:SF4301
|
0.0
|
25.3
|
1.0
|
SG
|
A:CYS211
|
2.3
|
37.6
|
1.0
|
S2
|
A:SF4301
|
2.3
|
37.0
|
1.0
|
S1
|
A:SF4301
|
2.3
|
55.4
|
1.0
|
S3
|
A:SF4301
|
2.3
|
40.3
|
1.0
|
FE3
|
A:SF4301
|
2.7
|
51.6
|
1.0
|
FE1
|
A:SF4301
|
2.7
|
41.8
|
1.0
|
FE2
|
A:SF4301
|
2.7
|
44.4
|
1.0
|
HB3
|
A:CYS211
|
2.9
|
52.6
|
1.0
|
CB
|
A:CYS211
|
3.0
|
42.6
|
1.0
|
HB2
|
A:CYS211
|
3.0
|
52.6
|
1.0
|
HB2
|
A:TYR213
|
3.3
|
50.8
|
1.0
|
HG11
|
A:VAL260
|
3.4
|
48.2
|
1.0
|
S4
|
A:SF4301
|
3.9
|
49.0
|
1.0
|
HD2
|
A:TYR213
|
3.9
|
54.8
|
1.0
|
HA
|
A:HIS208
|
4.0
|
55.7
|
1.0
|
H
|
A:TYR213
|
4.1
|
55.7
|
1.0
|
CB
|
A:TYR213
|
4.3
|
41.1
|
1.0
|
CG1
|
A:VAL260
|
4.4
|
39.0
|
1.0
|
HG21
|
A:VAL260
|
4.4
|
46.4
|
1.0
|
CA
|
A:CYS211
|
4.4
|
40.1
|
1.0
|
HG13
|
A:VAL260
|
4.5
|
48.2
|
1.0
|
ND1
|
A:HIS208
|
4.6
|
40.0
|
1.0
|
H
|
A:ARG233
|
4.6
|
57.1
|
1.0
|
HG22
|
A:ILE207
|
4.7
|
48.9
|
1.0
|
C
|
A:TYR213
|
4.7
|
45.1
|
1.0
|
HA
|
A:LEU214
|
4.7
|
59.0
|
1.0
|
SG
|
A:CYS238
|
4.7
|
35.2
|
1.0
|
HB3
|
A:TYR213
|
4.7
|
50.8
|
1.0
|
HA
|
A:CYS211
|
4.7
|
49.5
|
1.0
|
CD2
|
A:TYR213
|
4.7
|
44.5
|
1.0
|
N
|
A:LEU214
|
4.8
|
48.2
|
1.0
|
N
|
A:TYR213
|
4.8
|
45.2
|
1.0
|
HG12
|
A:VAL260
|
4.8
|
48.2
|
1.0
|
CA
|
A:TYR213
|
4.8
|
43.4
|
1.0
|
SG
|
A:CYS232
|
4.9
|
42.2
|
1.0
|
H
|
A:LEU214
|
4.9
|
59.3
|
1.0
|
CA
|
A:HIS208
|
4.9
|
45.3
|
1.0
|
HA3
|
A:GLY240
|
5.0
|
46.4
|
1.0
|
HG22
|
A:VAL260
|
5.0
|
46.4
|
1.0
|
|
Iron binding site 5 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 5 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_05.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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:Fe302
b:34.6
occ:1.00
|
FE1
|
A:SF4302
|
0.0
|
34.6
|
1.0
|
S4
|
A:SF4302
|
2.3
|
26.3
|
1.0
|
S3
|
A:SF4302
|
2.3
|
32.6
|
1.0
|
S2
|
A:SF4302
|
2.3
|
41.4
|
1.0
|
SG
|
A:CYS268
|
2.3
|
23.1
|
1.0
|
FE2
|
A:SF4302
|
2.7
|
24.3
|
1.0
|
FE3
|
A:SF4302
|
2.7
|
29.2
|
1.0
|
FE4
|
A:SF4302
|
2.8
|
32.8
|
1.0
|
H
|
A:CYS268
|
2.9
|
49.5
|
1.0
|
HH22
|
B:ARG182
|
3.3
|
40.5
|
1.0
|
HH12
|
B:ARG182
|
3.3
|
38.3
|
1.0
|
HB3
|
A:CYS268
|
3.3
|
33.4
|
1.0
|
CB
|
A:CYS268
|
3.4
|
26.7
|
1.0
|
NH2
|
B:ARG182
|
3.6
|
32.6
|
1.0
|
NH1
|
B:ARG182
|
3.6
|
30.7
|
1.0
|
N
|
A:CYS268
|
3.6
|
40.0
|
1.0
|
CZ
|
B:ARG182
|
3.8
|
29.7
|
1.0
|
S1
|
A:SF4302
|
3.9
|
30.7
|
1.0
|
HG13
|
A:VAL269
|
3.9
|
44.8
|
1.0
|
HH21
|
B:ARG182
|
4.1
|
40.5
|
1.0
|
HH11
|
B:ARG182
|
4.1
|
38.3
|
1.0
|
CA
|
A:CYS268
|
4.1
|
28.5
|
1.0
|
H
|
A:VAL269
|
4.2
|
41.3
|
1.0
|
HB2
|
A:CYS268
|
4.2
|
33.4
|
1.0
|
HG13
|
A:ILE266
|
4.4
|
35.6
|
1.0
|
H
|
A:GLY267
|
4.5
|
49.9
|
1.0
|
H
|
A:ILE266
|
4.5
|
41.2
|
1.0
|
HH2
|
A:TRP165
|
4.6
|
45.3
|
1.0
|
HG12
|
A:ILE266
|
4.6
|
35.6
|
1.0
|
HZ2
|
A:TRP252
|
4.6
|
40.4
|
1.0
|
N
|
A:VAL269
|
4.6
|
33.2
|
1.0
|
SG
|
A:CYS259
|
4.7
|
30.4
|
1.0
|
NE
|
B:ARG182
|
4.7
|
30.6
|
1.0
|
C
|
A:GLY267
|
4.7
|
32.8
|
1.0
|
C
|
A:CYS268
|
4.7
|
29.9
|
1.0
|
HA2
|
A:GLY267
|
4.8
|
38.9
|
1.0
|
H
|
A:CYS159
|
4.8
|
37.6
|
1.0
|
N
|
A:GLY267
|
4.8
|
40.4
|
1.0
|
SG
|
A:CYS265
|
4.8
|
27.9
|
1.0
|
CG1
|
A:VAL269
|
4.9
|
36.2
|
1.0
|
SG
|
A:CYS247
|
4.9
|
36.0
|
1.0
|
HA
|
A:CYS268
|
4.9
|
35.6
|
1.0
|
CG1
|
A:ILE266
|
5.0
|
28.5
|
1.0
|
HG22
|
A:VAL269
|
5.0
|
54.5
|
1.0
|
HG21
|
A:THR243
|
5.0
|
50.2
|
1.0
|
|
Iron binding site 6 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 6 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_06.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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:Fe302
b:24.3
occ:1.00
|
FE2
|
A:SF4302
|
0.0
|
24.3
|
1.0
|
SG
|
A:CYS265
|
2.3
|
27.9
|
1.0
|
S3
|
A:SF4302
|
2.3
|
32.6
|
1.0
|
S4
|
A:SF4302
|
2.3
|
26.3
|
1.0
|
S1
|
A:SF4302
|
2.3
|
30.7
|
1.0
|
FE1
|
A:SF4302
|
2.7
|
34.6
|
1.0
|
FE4
|
A:SF4302
|
2.7
|
32.8
|
1.0
|
FE3
|
A:SF4302
|
2.7
|
29.2
|
1.0
|
H
|
A:GLY267
|
3.1
|
49.9
|
1.0
|
HG21
|
A:THR243
|
3.4
|
50.2
|
1.0
|
H
|
A:CYS268
|
3.6
|
49.5
|
1.0
|
H
|
A:ILE266
|
3.6
|
41.2
|
1.0
|
HA2
|
A:GLY267
|
3.7
|
38.9
|
1.0
|
HA
|
A:CYS265
|
3.7
|
37.6
|
1.0
|
CB
|
A:CYS265
|
3.7
|
34.9
|
1.0
|
N
|
A:GLY267
|
3.8
|
40.4
|
1.0
|
S2
|
A:SF4302
|
3.9
|
41.4
|
1.0
|
HB2
|
A:CYS265
|
4.0
|
43.3
|
1.0
|
CA
|
A:CYS265
|
4.2
|
30.2
|
1.0
|
CA
|
A:GLY267
|
4.2
|
31.2
|
1.0
|
N
|
A:ILE266
|
4.2
|
33.2
|
1.0
|
HB2
|
A:CYS259
|
4.2
|
41.5
|
1.0
|
N
|
A:CYS268
|
4.3
|
40.0
|
1.0
|
HG13
|
A:ILE207
|
4.3
|
52.5
|
1.0
|
CG2
|
A:THR243
|
4.4
|
40.6
|
1.0
|
HB3
|
A:CYS265
|
4.5
|
43.3
|
1.0
|
HD12
|
A:ILE207
|
4.6
|
51.5
|
1.0
|
C
|
A:CYS265
|
4.6
|
31.4
|
1.0
|
HD11
|
A:ILE207
|
4.7
|
51.5
|
1.0
|
HG22
|
A:THR243
|
4.7
|
50.2
|
1.0
|
C
|
A:GLY267
|
4.7
|
32.8
|
1.0
|
SG
|
A:CYS268
|
4.7
|
23.1
|
1.0
|
HG23
|
A:THR243
|
4.8
|
50.2
|
1.0
|
SG
|
A:CYS247
|
4.8
|
36.0
|
1.0
|
CB
|
A:CYS259
|
4.8
|
33.4
|
1.0
|
C
|
A:ILE266
|
4.9
|
31.5
|
1.0
|
HB3
|
A:CYS259
|
4.9
|
41.5
|
1.0
|
HG22
|
A:VAL269
|
4.9
|
54.5
|
1.0
|
H
|
A:VAL269
|
4.9
|
41.3
|
1.0
|
SG
|
A:CYS259
|
4.9
|
30.4
|
1.0
|
HG13
|
A:ILE266
|
4.9
|
35.6
|
1.0
|
HG12
|
A:ILE266
|
5.0
|
35.6
|
1.0
|
CD1
|
A:ILE207
|
5.0
|
41.8
|
1.0
|
HB3
|
A:ALA245
|
5.0
|
51.9
|
1.0
|
|
Iron binding site 7 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 7 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_07.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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
|
A:Fe302
b:29.2
occ:1.00
|
FE3
|
A:SF4302
|
0.0
|
29.2
|
1.0
|
SG
|
A:CYS259
|
2.3
|
30.4
|
1.0
|
S2
|
A:SF4302
|
2.3
|
41.4
|
1.0
|
S1
|
A:SF4302
|
2.3
|
30.7
|
1.0
|
S4
|
A:SF4302
|
2.3
|
26.3
|
1.0
|
HB2
|
A:CYS259
|
2.6
|
41.5
|
1.0
|
FE4
|
A:SF4302
|
2.7
|
32.8
|
1.0
|
FE1
|
A:SF4302
|
2.7
|
34.6
|
1.0
|
FE2
|
A:SF4302
|
2.7
|
24.3
|
1.0
|
CB
|
A:CYS259
|
2.9
|
33.4
|
1.0
|
HB3
|
A:CYS259
|
3.2
|
41.5
|
1.0
|
S3
|
A:SF4302
|
3.9
|
32.6
|
1.0
|
H
|
A:CYS259
|
4.0
|
43.9
|
1.0
|
HA
|
A:CYS265
|
4.0
|
37.6
|
1.0
|
HD3
|
B:ARG182
|
4.2
|
41.9
|
1.0
|
HE1
|
A:TRP252
|
4.2
|
41.6
|
1.0
|
CZ
|
B:ARG182
|
4.3
|
29.7
|
1.0
|
CA
|
A:CYS259
|
4.3
|
33.0
|
1.0
|
HE21
|
B:GLN187
|
4.4
|
35.2
|
1.0
|
SG
|
A:CYS265
|
4.4
|
27.9
|
1.0
|
NH1
|
B:ARG182
|
4.4
|
30.7
|
1.0
|
NE
|
B:ARG182
|
4.4
|
30.6
|
1.0
|
H
|
A:ILE266
|
4.4
|
41.2
|
1.0
|
N
|
A:CYS259
|
4.5
|
35.4
|
1.0
|
HH11
|
B:ARG182
|
4.5
|
38.3
|
1.0
|
NH2
|
B:ARG182
|
4.5
|
32.6
|
1.0
|
SG
|
A:CYS247
|
4.6
|
36.0
|
1.0
|
HH12
|
B:ARG182
|
4.6
|
38.3
|
1.0
|
NE1
|
A:TRP252
|
4.6
|
33.5
|
1.0
|
HE
|
B:ARG182
|
4.7
|
38.1
|
1.0
|
HG3
|
B:GLN187
|
4.7
|
31.4
|
1.0
|
HE3
|
A:TRP258
|
4.7
|
44.6
|
1.0
|
HH22
|
B:ARG182
|
4.8
|
40.5
|
1.0
|
HH21
|
B:ARG182
|
4.8
|
40.5
|
1.0
|
HA
|
A:CYS259
|
4.8
|
41.0
|
1.0
|
CD
|
B:ARG182
|
4.8
|
33.7
|
1.0
|
HB3
|
A:CYS247
|
4.8
|
52.6
|
1.0
|
CA
|
A:CYS265
|
4.9
|
30.2
|
1.0
|
HB2
|
A:CYS265
|
4.9
|
43.3
|
1.0
|
SG
|
A:CYS268
|
4.9
|
23.1
|
1.0
|
HG12
|
A:ILE266
|
4.9
|
35.6
|
1.0
|
HB2
|
A:CYS247
|
4.9
|
52.6
|
1.0
|
CB
|
A:CYS265
|
5.0
|
34.9
|
1.0
|
|
Iron binding site 8 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 8 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_08.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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
|
A:Fe302
b:32.8
occ:1.00
|
FE4
|
A:SF4302
|
0.0
|
32.8
|
1.0
|
S1
|
A:SF4302
|
2.3
|
30.7
|
1.0
|
S2
|
A:SF4302
|
2.3
|
41.4
|
1.0
|
S3
|
A:SF4302
|
2.3
|
32.6
|
1.0
|
SG
|
A:CYS247
|
2.3
|
36.0
|
1.0
|
FE2
|
A:SF4302
|
2.7
|
24.3
|
1.0
|
FE3
|
A:SF4302
|
2.7
|
29.2
|
1.0
|
FE1
|
A:SF4302
|
2.8
|
34.6
|
1.0
|
HH2
|
A:TRP165
|
3.4
|
45.3
|
1.0
|
HB2
|
A:CYS247
|
3.4
|
52.6
|
1.0
|
CB
|
A:CYS247
|
3.5
|
42.7
|
1.0
|
HE1
|
A:TRP252
|
3.5
|
41.6
|
1.0
|
HB3
|
A:CYS247
|
3.7
|
52.6
|
1.0
|
S4
|
A:SF4302
|
3.9
|
26.3
|
1.0
|
HB3
|
A:ALA245
|
4.1
|
51.9
|
1.0
|
HZ2
|
A:TRP252
|
4.2
|
40.4
|
1.0
|
HD11
|
A:ILE207
|
4.2
|
51.5
|
1.0
|
NE1
|
A:TRP252
|
4.2
|
33.5
|
1.0
|
CH2
|
A:TRP165
|
4.3
|
36.5
|
1.0
|
HB1
|
A:ALA245
|
4.3
|
51.9
|
1.0
|
HG13
|
A:VAL269
|
4.4
|
44.8
|
1.0
|
HD12
|
A:ILE207
|
4.4
|
51.5
|
1.0
|
HZ2
|
A:TRP165
|
4.5
|
43.6
|
1.0
|
CB
|
A:ALA245
|
4.6
|
42.0
|
1.0
|
SG
|
A:CYS268
|
4.6
|
23.1
|
1.0
|
H
|
A:CYS247
|
4.7
|
48.1
|
1.0
|
HB2
|
A:CYS259
|
4.7
|
41.5
|
1.0
|
SG
|
A:CYS259
|
4.7
|
30.4
|
1.0
|
SG
|
A:CYS265
|
4.7
|
27.9
|
1.0
|
HG21
|
A:THR243
|
4.8
|
50.2
|
1.0
|
HG11
|
A:VAL269
|
4.8
|
44.8
|
1.0
|
CD1
|
A:ILE207
|
4.8
|
41.8
|
1.0
|
HH12
|
B:ARG182
|
4.8
|
38.3
|
1.0
|
CZ2
|
A:TRP252
|
4.8
|
32.5
|
1.0
|
HE3
|
A:TRP258
|
4.9
|
44.6
|
1.0
|
CZ2
|
A:TRP165
|
4.9
|
35.2
|
1.0
|
CA
|
A:CYS247
|
4.9
|
41.5
|
1.0
|
HB2
|
A:ALA245
|
4.9
|
51.9
|
1.0
|
CE2
|
A:TRP252
|
4.9
|
31.9
|
1.0
|
NH1
|
B:ARG182
|
4.9
|
30.7
|
1.0
|
HH11
|
B:ARG182
|
5.0
|
38.3
|
1.0
|
|
Iron binding site 9 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 9 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_09.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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
|
A:Fe303
b:27.4
occ:0.54
|
FE1
|
A:SF4303
|
0.0
|
27.4
|
0.5
|
FE1
|
A:6ML304
|
0.1
|
28.2
|
0.5
|
O12
|
A:6ML304
|
1.8
|
34.4
|
0.5
|
S3
|
A:6ML304
|
2.3
|
25.1
|
0.5
|
S2
|
A:SF4303
|
2.3
|
29.1
|
0.5
|
S4
|
A:SF4303
|
2.3
|
25.2
|
0.5
|
S3
|
A:SF4303
|
2.3
|
38.6
|
0.5
|
SG
|
A:CYS18
|
2.3
|
27.5
|
1.0
|
S2
|
A:6ML304
|
2.4
|
28.9
|
0.5
|
H
|
A:CYS18
|
2.6
|
28.8
|
1.0
|
FE3
|
A:6ML304
|
2.7
|
27.8
|
0.5
|
FE3
|
A:SF4303
|
2.7
|
28.4
|
0.5
|
FE4
|
A:SF4303
|
2.7
|
34.3
|
0.5
|
FE2
|
A:SF4303
|
2.8
|
34.1
|
0.5
|
FE4
|
A:6ML304
|
2.9
|
33.8
|
0.5
|
HB3
|
A:CYS18
|
3.0
|
29.6
|
1.0
|
H
|
A:GLY20
|
3.1
|
56.2
|
1.0
|
FE2
|
A:6ML304
|
3.2
|
37.1
|
0.5
|
CB
|
A:CYS18
|
3.2
|
23.5
|
1.0
|
O24
|
A:6ML304
|
3.3
|
32.4
|
0.5
|
N
|
A:CYS18
|
3.4
|
22.8
|
1.0
|
HA3
|
A:GLY20
|
3.4
|
56.1
|
1.0
|
HE1
|
B:HIS185
|
3.5
|
27.8
|
1.0
|
CA
|
A:CYS18
|
3.7
|
30.0
|
1.0
|
S1
|
A:6ML304
|
3.8
|
39.7
|
0.5
|
N
|
A:GLY20
|
3.8
|
45.7
|
1.0
|
S1
|
A:SF4303
|
3.9
|
29.9
|
0.5
|
S4
|
A:6ML304
|
3.9
|
29.9
|
0.5
|
HB2
|
A:CYS18
|
4.0
|
29.6
|
1.0
|
CA
|
A:GLY20
|
4.1
|
45.6
|
1.0
|
C
|
A:CYS18
|
4.2
|
33.9
|
1.0
|
H
|
A:CYS21
|
4.2
|
72.4
|
0.7
|
HA2
|
A:GLY17
|
4.2
|
34.6
|
1.0
|
HG3
|
B:ARG73
|
4.2
|
30.0
|
1.0
|
H
|
A:CYS21
|
4.3
|
72.0
|
0.3
|
CE1
|
B:HIS185
|
4.4
|
22.0
|
1.0
|
C
|
A:GLY17
|
4.5
|
31.1
|
1.0
|
SG
|
A:CYS21
|
4.5
|
43.9
|
0.3
|
N
|
A:THR19
|
4.6
|
28.2
|
1.0
|
HA
|
A:CYS18
|
4.6
|
37.4
|
1.0
|
HA
|
B:ARG73
|
4.6
|
28.4
|
1.0
|
H
|
A:THR19
|
4.6
|
35.3
|
1.0
|
O
|
B:ARG73
|
4.6
|
20.1
|
1.0
|
O
|
A:CYS18
|
4.7
|
26.7
|
1.0
|
CA
|
A:GLY17
|
4.8
|
27.7
|
1.0
|
N
|
A:CYS21
|
4.8
|
59.2
|
0.7
|
HG2
|
B:ARG73
|
4.8
|
30.0
|
1.0
|
SG
|
A:CYS121
|
4.8
|
22.0
|
1.0
|
HA2
|
A:GLY20
|
4.8
|
56.1
|
1.0
|
HB3
|
B:ARG73
|
4.8
|
28.3
|
1.0
|
N
|
A:CYS21
|
4.8
|
58.8
|
0.3
|
HA3
|
A:GLY17
|
4.9
|
34.6
|
1.0
|
CG
|
B:ARG73
|
4.9
|
23.8
|
1.0
|
SG
|
A:CYS159
|
4.9
|
22.1
|
1.0
|
C
|
A:GLY20
|
4.9
|
48.4
|
1.0
|
OE2
|
A:GLU77
|
4.9
|
49.4
|
1.0
|
|
Iron binding site 10 out
of 36 in 6z8o
Go back to
Iron Binding Sites List in 6z8o
Iron binding site 10 out
of 36 in the Structure of [Nifese] Hydrogenase G491A Variant From Desulfovibrio Vulgaris Hildenborough Pressurized with Krypton Gas - Structure G491A-Kr
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_10.jpg) Mono view
![](/pictures/FE/pdb/z8/6z8o-FE-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe 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
|
A:Fe303
b:34.1
occ:0.54
|
FE2
|
A:SF4303
|
0.0
|
34.1
|
0.5
|
FE4
|
A:6ML304
|
0.1
|
33.8
|
0.5
|
O24
|
A:6ML304
|
1.9
|
32.4
|
0.5
|
S3
|
A:6ML304
|
2.2
|
25.1
|
0.5
|
S4
|
A:SF4303
|
2.3
|
25.2
|
0.5
|
S1
|
A:SF4303
|
2.3
|
29.9
|
0.5
|
S3
|
A:SF4303
|
2.3
|
38.6
|
0.5
|
SG
|
A:CYS121
|
2.3
|
22.0
|
1.0
|
S4
|
A:6ML304
|
2.4
|
29.9
|
0.5
|
FE3
|
A:SF4303
|
2.7
|
28.4
|
0.5
|
FE3
|
A:6ML304
|
2.7
|
27.8
|
0.5
|
HB2
|
A:CYS121
|
2.7
|
33.4
|
1.0
|
FE4
|
A:SF4303
|
2.7
|
34.3
|
0.5
|
FE1
|
A:SF4303
|
2.8
|
27.4
|
0.5
|
FE1
|
A:6ML304
|
2.9
|
28.2
|
0.5
|
CB
|
A:CYS121
|
3.1
|
26.6
|
1.0
|
FE2
|
A:6ML304
|
3.2
|
37.1
|
0.5
|
O12
|
A:6ML304
|
3.3
|
34.4
|
0.5
|
H
|
A:CYS121
|
3.3
|
36.3
|
1.0
|
HB3
|
A:CYS121
|
3.7
|
33.4
|
1.0
|
HA2
|
A:GLY17
|
3.7
|
34.6
|
1.0
|
H
|
A:CYS18
|
3.8
|
28.8
|
1.0
|
S2
|
A:SF4303
|
3.9
|
29.1
|
0.5
|
S2
|
A:6ML304
|
3.9
|
28.9
|
0.5
|
HA2
|
A:GLY78
|
4.0
|
37.3
|
1.0
|
S1
|
A:6ML304
|
4.0
|
39.7
|
0.5
|
N
|
A:CYS121
|
4.1
|
29.0
|
1.0
|
CA
|
A:CYS121
|
4.2
|
31.0
|
1.0
|
HA3
|
A:GLY119
|
4.3
|
47.2
|
1.0
|
SG
|
A:CYS21
|
4.5
|
43.9
|
0.3
|
H
|
A:GLY78
|
4.5
|
37.2
|
1.0
|
N
|
A:CYS18
|
4.6
|
22.8
|
1.0
|
CA
|
A:GLY17
|
4.6
|
27.7
|
1.0
|
SG
|
A:CYS159
|
4.7
|
22.1
|
1.0
|
HA
|
A:CYS121
|
4.7
|
38.6
|
1.0
|
H
|
A:THR120
|
4.7
|
42.7
|
1.0
|
HB3
|
A:CYS18
|
4.8
|
29.6
|
1.0
|
H
|
A:ALA122
|
4.8
|
46.6
|
1.0
|
HG3
|
A:GLU77
|
4.8
|
46.7
|
1.0
|
HA3
|
A:GLY17
|
4.8
|
34.6
|
1.0
|
O
|
A:GLN16
|
4.8
|
26.3
|
1.0
|
CA
|
A:GLY78
|
4.8
|
29.9
|
1.0
|
N
|
A:GLY78
|
5.0
|
29.8
|
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: Wed Aug 7 16:59:22 2024
|