Iron in PDB 8rtg: Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
Enzymatic activity of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
All present enzymatic activity of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form:
1.12.7.2;
Protein crystallography data
The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form, PDB code: 8rtg
was solved by
K.Bikbaev,
I.Span,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.06 /
1.46
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.15,
84.786,
88.036,
90,
90,
90
|
|
R / Rfree (%)
|
16.5 /
18.9
|
Other elements in 8rtg:
The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Iron atom in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
(pdb code 8rtg). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the
Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form, PDB code: 8rtg:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 1 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:11.1
occ:1.00
|
FE1
|
A:SF4501
|
0.0
|
11.1
|
1.0
|
|
SG
|
A:CYS378
|
2.3
|
11.1
|
1.0
|
|
S3
|
A:SF4501
|
2.3
|
11.1
|
1.0
|
|
HG
|
A:CYS378
|
2.3
|
11.1
|
0.0
|
|
S2
|
A:SF4501
|
2.3
|
11.6
|
1.0
|
|
S4
|
A:SF4501
|
2.3
|
10.9
|
1.0
|
|
FE3
|
A:SF4501
|
2.7
|
10.7
|
1.0
|
|
FE2
|
A:SF4501
|
2.7
|
11.2
|
1.0
|
|
FE4
|
A:SF4501
|
2.8
|
11.0
|
1.0
|
|
HB2
|
A:CYS378
|
3.0
|
10.6
|
1.0
|
|
CB
|
A:CYS378
|
3.2
|
10.6
|
1.0
|
|
H
|
A:CYS378
|
3.2
|
10.4
|
1.0
|
|
HA2
|
A:GLY385
|
3.6
|
11.0
|
1.0
|
|
N
|
A:CYS378
|
3.7
|
10.4
|
1.0
|
|
HB2
|
A:ALA377
|
3.8
|
11.8
|
1.0
|
|
S1
|
A:SF4501
|
3.9
|
10.9
|
1.0
|
|
HB3
|
A:CYS378
|
3.9
|
10.6
|
1.0
|
|
HA
|
A:CYS382
|
4.0
|
10.6
|
1.0
|
|
CA
|
A:CYS378
|
4.0
|
9.9
|
1.0
|
|
HA3
|
A:GLY385
|
4.2
|
11.0
|
1.0
|
|
O
|
A:HOH652
|
4.2
|
11.0
|
1.0
|
|
H
|
A:GLY386
|
4.3
|
10.7
|
1.0
|
|
H
|
A:ALA377
|
4.3
|
10.7
|
1.0
|
|
CA
|
A:GLY385
|
4.4
|
11.0
|
1.0
|
|
SG
|
A:CYS234
|
4.5
|
10.4
|
1.0
|
|
HB2
|
A:CYS69
|
4.5
|
11.3
|
1.0
|
|
C
|
A:ALA377
|
4.6
|
10.9
|
1.0
|
|
HG
|
A:CYS234
|
4.6
|
10.4
|
0.0
|
|
HA
|
A:CYS378
|
4.6
|
9.9
|
1.0
|
|
HA
|
A:CYS69
|
4.7
|
11.4
|
1.0
|
|
N
|
A:ALA377
|
4.7
|
10.7
|
1.0
|
|
SG
|
A:CYS179
|
4.7
|
10.5
|
1.0
|
|
HB2
|
A:CYS234
|
4.7
|
10.3
|
1.0
|
|
CB
|
A:ALA377
|
4.7
|
11.8
|
1.0
|
|
HG
|
A:CYS179
|
4.8
|
10.5
|
0.0
|
|
HE22
|
A:GLN71
|
4.8
|
11.8
|
1.0
|
|
CA
|
A:ALA377
|
4.9
|
11.4
|
1.0
|
|
O
|
A:CYS69
|
4.9
|
10.6
|
1.0
|
|
SG
|
A:CYS382
|
4.9
|
11.8
|
1.0
|
|
CA
|
A:CYS382
|
4.9
|
10.6
|
1.0
|
|
Iron binding site 2 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 2 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:11.2
occ:1.00
|
FE2
|
A:SF4501
|
0.0
|
11.2
|
1.0
|
|
SG
|
A:CYS179
|
2.3
|
10.5
|
1.0
|
|
S4
|
A:SF4501
|
2.3
|
10.9
|
1.0
|
|
S1
|
A:SF4501
|
2.3
|
10.9
|
1.0
|
|
S3
|
A:SF4501
|
2.3
|
11.1
|
1.0
|
|
FE3
|
A:SF4501
|
2.7
|
10.7
|
1.0
|
|
FE1
|
A:SF4501
|
2.7
|
11.1
|
1.0
|
|
FE4
|
A:SF4501
|
2.7
|
11.0
|
1.0
|
|
HG
|
A:CYS179
|
2.7
|
10.5
|
0.0
|
|
H
|
A:ALA377
|
3.1
|
10.7
|
1.0
|
|
HB2
|
A:CYS179
|
3.2
|
10.5
|
1.0
|
|
CB
|
A:CYS179
|
3.3
|
10.5
|
1.0
|
|
HB2
|
A:ALA377
|
3.5
|
11.8
|
1.0
|
|
HA
|
A:CYS179
|
3.5
|
10.5
|
1.0
|
|
H
|
A:GLY181
|
3.6
|
10.2
|
1.0
|
|
HD2
|
A:PRO180
|
3.7
|
10.8
|
1.0
|
|
CA
|
A:CYS179
|
3.9
|
10.5
|
1.0
|
|
S2
|
A:SF4501
|
3.9
|
11.6
|
1.0
|
|
N
|
A:ALA377
|
3.9
|
10.7
|
1.0
|
|
H
|
A:CYS378
|
4.0
|
10.4
|
1.0
|
|
HB3
|
A:CYS179
|
4.1
|
10.5
|
1.0
|
|
HA
|
A:MET376
|
4.2
|
11.5
|
1.0
|
|
HG
|
A:CYS234
|
4.2
|
10.4
|
0.0
|
|
CB
|
A:ALA377
|
4.3
|
11.8
|
1.0
|
|
C
|
A:CYS179
|
4.3
|
11.1
|
1.0
|
|
HB1
|
A:ALA377
|
4.4
|
11.8
|
1.0
|
|
H
|
A:TRP182
|
4.4
|
9.9
|
1.0
|
|
HA3
|
A:GLY181
|
4.4
|
10.3
|
1.0
|
|
N
|
A:GLY181
|
4.4
|
10.2
|
1.0
|
|
CD
|
A:PRO180
|
4.5
|
10.8
|
1.0
|
|
N
|
A:PRO180
|
4.5
|
10.7
|
1.0
|
|
CA
|
A:ALA377
|
4.6
|
11.4
|
1.0
|
|
SG
|
A:CYS382
|
4.7
|
11.8
|
1.0
|
|
SD
|
A:MET376
|
4.7
|
12.1
|
1.0
|
|
N
|
A:CYS378
|
4.7
|
10.4
|
1.0
|
|
SG
|
A:CYS378
|
4.7
|
11.1
|
1.0
|
|
HB3
|
A:MET376
|
4.7
|
11.2
|
1.0
|
|
SG
|
A:CYS234
|
4.7
|
10.4
|
1.0
|
|
O
|
A:HOH824
|
4.8
|
24.3
|
1.0
|
|
HG2
|
A:PRO180
|
4.8
|
10.9
|
1.0
|
|
C
|
A:MET376
|
4.9
|
11.0
|
1.0
|
|
CA
|
A:MET376
|
4.9
|
11.5
|
1.0
|
|
HB2
|
A:ALA236
|
4.9
|
9.9
|
1.0
|
|
CA
|
A:GLY181
|
5.0
|
10.3
|
1.0
|
|
Iron binding site 3 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 3 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:10.7
occ:1.00
|
FE3
|
A:SF4501
|
0.0
|
10.7
|
1.0
|
|
HG
|
A:CYS234
|
1.9
|
10.4
|
0.0
|
|
SG
|
A:CYS234
|
2.2
|
10.4
|
1.0
|
|
S1
|
A:SF4501
|
2.3
|
10.9
|
1.0
|
|
S4
|
A:SF4501
|
2.3
|
10.9
|
1.0
|
|
S2
|
A:SF4501
|
2.3
|
11.6
|
1.0
|
|
FE2
|
A:SF4501
|
2.7
|
11.2
|
1.0
|
|
FE1
|
A:SF4501
|
2.7
|
11.1
|
1.0
|
|
FE4
|
A:SF4501
|
2.7
|
11.0
|
1.0
|
|
HB2
|
A:CYS234
|
2.9
|
10.3
|
1.0
|
|
CB
|
A:CYS234
|
3.2
|
10.3
|
1.0
|
|
HB2
|
A:ALA236
|
3.7
|
9.9
|
1.0
|
|
HD2
|
A:PRO180
|
3.7
|
10.8
|
1.0
|
|
HB3
|
A:CYS234
|
3.8
|
10.3
|
1.0
|
|
S3
|
A:SF4501
|
3.8
|
11.1
|
1.0
|
|
O
|
A:HOH652
|
3.9
|
11.0
|
1.0
|
|
HG2
|
A:LYS237
|
4.0
|
10.0
|
1.0
|
|
HA
|
A:CYS234
|
4.1
|
9.8
|
1.0
|
|
HG2
|
A:PRO180
|
4.1
|
10.9
|
1.0
|
|
HE2
|
A:LYS237
|
4.2
|
9.6
|
1.0
|
|
CA
|
A:CYS234
|
4.3
|
9.8
|
1.0
|
|
HG
|
A:CYS378
|
4.4
|
11.1
|
0.0
|
|
H
|
A:GLY181
|
4.4
|
10.2
|
1.0
|
|
H
|
A:ALA236
|
4.5
|
9.6
|
1.0
|
|
CD
|
A:PRO180
|
4.6
|
10.8
|
1.0
|
|
SG
|
A:CYS378
|
4.6
|
11.1
|
1.0
|
|
CB
|
A:ALA236
|
4.7
|
9.9
|
1.0
|
|
SG
|
A:CYS382
|
4.7
|
11.8
|
1.0
|
|
H
|
A:LYS237
|
4.7
|
9.9
|
1.0
|
|
SG
|
A:CYS179
|
4.7
|
10.5
|
1.0
|
|
HA
|
A:CYS179
|
4.8
|
10.5
|
1.0
|
|
HG2
|
A:PRO233
|
4.8
|
9.8
|
1.0
|
|
CG
|
A:PRO180
|
4.8
|
10.9
|
1.0
|
|
HA
|
A:CYS382
|
4.9
|
10.6
|
1.0
|
|
CG
|
A:LYS237
|
4.9
|
10.0
|
1.0
|
|
HB1
|
A:ALA236
|
4.9
|
9.9
|
1.0
|
|
HA3
|
A:GLY385
|
4.9
|
11.0
|
1.0
|
|
HG3
|
A:LYS237
|
4.9
|
10.0
|
1.0
|
|
Iron binding site 4 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 4 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:11.0
occ:1.00
|
FE4
|
A:SF4501
|
0.0
|
11.0
|
1.0
|
|
S2
|
A:SF4501
|
2.2
|
11.6
|
1.0
|
|
SG
|
A:CYS382
|
2.2
|
11.8
|
1.0
|
|
S1
|
A:SF4501
|
2.3
|
10.9
|
1.0
|
|
S3
|
A:SF4501
|
2.3
|
11.1
|
1.0
|
|
FE3
|
A:SF4501
|
2.7
|
10.7
|
1.0
|
|
FE2
|
A:SF4501
|
2.7
|
11.2
|
1.0
|
|
FE1
|
A:SF4501
|
2.8
|
11.1
|
1.0
|
|
HA
|
A:CYS382
|
2.9
|
10.6
|
1.0
|
|
HG
|
A:CYS382
|
3.1
|
11.8
|
0.0
|
|
CB
|
A:CYS382
|
3.3
|
11.2
|
1.0
|
|
CA
|
A:CYS382
|
3.5
|
10.6
|
1.0
|
|
HB3
|
A:CYS382
|
3.5
|
11.2
|
1.0
|
|
S4
|
A:SF4501
|
3.9
|
10.9
|
1.0
|
|
N
|
A:CYS382
|
4.0
|
10.7
|
1.0
|
|
HB2
|
A:CYS382
|
4.1
|
11.2
|
1.0
|
|
HB2
|
A:CYS234
|
4.2
|
10.3
|
1.0
|
|
HG
|
A:CYS234
|
4.2
|
10.4
|
0.0
|
|
H
|
A:CYS382
|
4.3
|
10.7
|
1.0
|
|
O
|
A:HOH824
|
4.3
|
24.3
|
1.0
|
|
HG2
|
A:PRO233
|
4.4
|
9.8
|
1.0
|
|
O
|
A:HOH854
|
4.4
|
19.4
|
1.0
|
|
SD
|
A:MET376
|
4.4
|
12.1
|
1.0
|
|
HB2
|
A:CYS378
|
4.5
|
10.6
|
1.0
|
|
HG
|
A:CYS378
|
4.6
|
11.1
|
0.0
|
|
HB2
|
A:CYS179
|
4.6
|
10.5
|
1.0
|
|
C
|
A:GLY381
|
4.6
|
11.1
|
1.0
|
|
SG
|
A:CYS234
|
4.7
|
10.4
|
1.0
|
|
H
|
A:CYS378
|
4.7
|
10.4
|
1.0
|
|
SG
|
A:CYS179
|
4.8
|
10.5
|
1.0
|
|
HA
|
A:CYS179
|
4.8
|
10.5
|
1.0
|
|
HB3
|
A:MET376
|
4.8
|
11.2
|
1.0
|
|
C
|
A:CYS382
|
4.8
|
10.4
|
1.0
|
|
HA3
|
A:GLY385
|
4.8
|
11.0
|
1.0
|
|
SG
|
A:CYS378
|
4.9
|
11.1
|
1.0
|
|
HA2
|
A:GLY381
|
4.9
|
11.9
|
1.0
|
|
HD2
|
A:PRO180
|
4.9
|
10.8
|
1.0
|
|
CB
|
A:CYS234
|
5.0
|
10.3
|
1.0
|
|
O
|
A:HOH750
|
5.0
|
11.7
|
1.0
|
|
HG
|
A:CYS179
|
5.0
|
10.5
|
0.0
|
|
Iron binding site 5 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 5 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:11.4
occ:1.00
|
FE1
|
A:SF4502
|
0.0
|
11.4
|
1.0
|
|
S4
|
A:SF4502
|
2.3
|
10.6
|
1.0
|
|
S2
|
A:SF4502
|
2.3
|
11.4
|
1.0
|
|
S3
|
A:SF4502
|
2.3
|
11.0
|
1.0
|
|
SG
|
A:CYS69
|
2.3
|
10.8
|
1.0
|
|
FE2
|
A:SF4502
|
2.7
|
10.4
|
1.0
|
|
FE3
|
A:SF4502
|
2.8
|
10.6
|
1.0
|
|
FE4
|
A:SF4502
|
2.8
|
11.3
|
1.0
|
|
H
|
A:CYS69
|
2.8
|
11.5
|
1.0
|
|
HG
|
A:CYS69
|
3.1
|
10.8
|
0.0
|
|
H
|
A:GLY70
|
3.1
|
10.2
|
1.0
|
|
N
|
A:CYS69
|
3.6
|
11.5
|
1.0
|
|
H
|
A:GLN71
|
3.6
|
11.3
|
1.0
|
|
HD2
|
A:PRO46
|
3.6
|
12.2
|
1.0
|
|
CB
|
A:CYS69
|
3.6
|
11.3
|
1.0
|
|
N
|
A:GLY70
|
3.8
|
10.2
|
1.0
|
|
HB3
|
A:CYS69
|
3.9
|
11.3
|
1.0
|
|
S1
|
A:SF4502
|
3.9
|
10.7
|
1.0
|
|
HD3
|
A:PRO46
|
4.0
|
12.2
|
1.0
|
|
CA
|
A:CYS69
|
4.0
|
11.4
|
1.0
|
|
HG13
|
A:ILE67
|
4.0
|
11.3
|
1.0
|
|
H
|
A:ASN68
|
4.1
|
10.8
|
1.0
|
|
H
|
A:CYS72
|
4.1
|
11.3
|
1.0
|
|
HG12
|
A:ILE67
|
4.1
|
11.3
|
1.0
|
|
H
|
A:ILE67
|
4.1
|
11.6
|
1.0
|
|
HA
|
A:CYS45
|
4.2
|
12.5
|
1.0
|
|
CD
|
A:PRO46
|
4.2
|
12.2
|
1.0
|
|
C
|
A:CYS69
|
4.3
|
10.9
|
1.0
|
|
N
|
A:GLN71
|
4.4
|
11.3
|
1.0
|
|
HB2
|
A:GLN71
|
4.4
|
11.1
|
1.0
|
|
HB2
|
A:CYS69
|
4.4
|
11.3
|
1.0
|
|
N
|
A:ASN68
|
4.4
|
10.8
|
1.0
|
|
CG1
|
A:ILE67
|
4.5
|
11.3
|
1.0
|
|
SG
|
A:CYS72
|
4.6
|
10.9
|
1.0
|
|
C
|
A:ASN68
|
4.6
|
12.6
|
1.0
|
|
SG
|
A:CYS66
|
4.7
|
11.5
|
1.0
|
|
O
|
A:HOH690
|
4.7
|
16.0
|
1.0
|
|
HG
|
A:CYS72
|
4.7
|
10.9
|
0.0
|
|
HA
|
A:ASN68
|
4.8
|
11.7
|
1.0
|
|
HG3
|
A:PRO46
|
4.8
|
12.7
|
1.0
|
|
CA
|
A:GLY70
|
4.8
|
10.0
|
1.0
|
|
HA2
|
A:GLY70
|
4.8
|
10.0
|
1.0
|
|
SG
|
A:CYS45
|
4.9
|
12.2
|
1.0
|
|
N
|
A:ILE67
|
4.9
|
11.6
|
1.0
|
|
CA
|
A:ASN68
|
4.9
|
11.7
|
1.0
|
|
HA
|
A:CYS69
|
4.9
|
11.4
|
1.0
|
|
CG
|
A:PRO46
|
4.9
|
12.7
|
1.0
|
|
HB3
|
A:CYS72
|
5.0
|
10.8
|
1.0
|
|
N
|
A:CYS72
|
5.0
|
11.3
|
1.0
|
|
HG2
|
A:PRO46
|
5.0
|
12.7
|
1.0
|
|
Iron binding site 6 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 6 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:10.4
occ:1.00
|
FE2
|
A:SF4502
|
0.0
|
10.4
|
1.0
|
|
HG
|
A:CYS72
|
2.0
|
10.9
|
0.0
|
|
S3
|
A:SF4502
|
2.2
|
11.0
|
1.0
|
|
SG
|
A:CYS72
|
2.2
|
10.9
|
1.0
|
|
S4
|
A:SF4502
|
2.3
|
10.6
|
1.0
|
|
S1
|
A:SF4502
|
2.3
|
10.7
|
1.0
|
|
FE1
|
A:SF4502
|
2.7
|
11.4
|
1.0
|
|
FE4
|
A:SF4502
|
2.8
|
11.3
|
1.0
|
|
FE3
|
A:SF4502
|
2.8
|
10.6
|
1.0
|
|
HB3
|
A:CYS72
|
3.0
|
10.8
|
1.0
|
|
CB
|
A:CYS72
|
3.2
|
10.8
|
1.0
|
|
H
|
A:CYS72
|
3.3
|
11.3
|
1.0
|
|
HD12
|
A:ILE50
|
3.4
|
12.8
|
1.0
|
|
S2
|
A:SF4502
|
3.9
|
11.4
|
1.0
|
|
HG13
|
A:VAL28
|
3.9
|
15.5
|
1.0
|
|
HB2
|
A:CYS72
|
3.9
|
10.8
|
1.0
|
|
HD12
|
A:ILE60
|
4.0
|
11.6
|
1.0
|
|
H
|
A:GLY70
|
4.0
|
10.2
|
1.0
|
|
N
|
A:CYS72
|
4.0
|
11.3
|
1.0
|
|
HD13
|
A:ILE60
|
4.2
|
11.6
|
1.0
|
|
CA
|
A:CYS72
|
4.3
|
10.9
|
1.0
|
|
CD1
|
A:ILE50
|
4.4
|
12.8
|
1.0
|
|
H
|
A:GLN71
|
4.5
|
11.3
|
1.0
|
|
HG13
|
A:ILE50
|
4.5
|
12.3
|
1.0
|
|
HA2
|
A:GLY70
|
4.5
|
10.0
|
1.0
|
|
CD1
|
A:ILE60
|
4.5
|
11.6
|
1.0
|
|
H
|
A:LEU73
|
4.5
|
11.0
|
1.0
|
|
HG21
|
A:VAL28
|
4.5
|
16.1
|
1.0
|
|
HG12
|
A:ILE50
|
4.6
|
12.3
|
1.0
|
|
SG
|
A:CYS69
|
4.6
|
10.8
|
1.0
|
|
HB2
|
A:CYS45
|
4.6
|
12.2
|
1.0
|
|
HB
|
A:VAL28
|
4.6
|
14.7
|
1.0
|
|
N
|
A:GLY70
|
4.7
|
10.2
|
1.0
|
|
CG1
|
A:VAL28
|
4.7
|
15.5
|
1.0
|
|
SG
|
A:CYS66
|
4.7
|
11.5
|
1.0
|
|
CG1
|
A:ILE50
|
4.7
|
12.3
|
1.0
|
|
SG
|
A:CYS45
|
4.8
|
12.2
|
1.0
|
|
N
|
A:GLN71
|
4.8
|
11.3
|
1.0
|
|
HD11
|
A:ILE50
|
4.8
|
12.8
|
1.0
|
|
HA
|
A:CYS45
|
4.9
|
12.5
|
1.0
|
|
HG12
|
A:VAL28
|
4.9
|
15.5
|
1.0
|
|
HG12
|
A:ILE60
|
4.9
|
11.9
|
1.0
|
|
H
|
A:CYS69
|
4.9
|
11.5
|
1.0
|
|
HD13
|
A:ILE50
|
4.9
|
12.8
|
1.0
|
|
HA
|
A:CYS72
|
4.9
|
10.9
|
1.0
|
|
CA
|
A:GLY70
|
4.9
|
10.0
|
1.0
|
|
Iron binding site 7 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 7 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:10.6
occ:1.00
|
FE3
|
A:SF4502
|
0.0
|
10.6
|
1.0
|
|
S2
|
A:SF4502
|
2.3
|
11.4
|
1.0
|
|
SG
|
A:CYS66
|
2.3
|
11.5
|
1.0
|
|
S1
|
A:SF4502
|
2.3
|
10.7
|
1.0
|
|
S4
|
A:SF4502
|
2.3
|
10.6
|
1.0
|
|
FE4
|
A:SF4502
|
2.7
|
11.3
|
1.0
|
|
FE2
|
A:SF4502
|
2.8
|
10.4
|
1.0
|
|
FE1
|
A:SF4502
|
2.8
|
11.4
|
1.0
|
|
HG
|
A:CYS66
|
3.1
|
11.5
|
0.0
|
|
HA
|
A:CYS66
|
3.2
|
11.1
|
1.0
|
|
H
|
A:ASN68
|
3.2
|
10.8
|
1.0
|
|
H
|
A:ILE67
|
3.4
|
11.6
|
1.0
|
|
CB
|
A:CYS66
|
3.4
|
11.4
|
1.0
|
|
HB2
|
A:CYS66
|
3.6
|
11.4
|
1.0
|
|
CA
|
A:CYS66
|
3.7
|
11.1
|
1.0
|
|
S3
|
A:SF4502
|
3.9
|
11.0
|
1.0
|
|
HD13
|
A:ILE60
|
3.9
|
11.6
|
1.0
|
|
N
|
A:ILE67
|
3.9
|
11.6
|
1.0
|
|
H
|
A:CYS69
|
4.0
|
11.5
|
1.0
|
|
N
|
A:ASN68
|
4.0
|
10.8
|
1.0
|
|
HB2
|
A:ALA49
|
4.1
|
11.7
|
1.0
|
|
HA
|
A:ASN68
|
4.1
|
11.7
|
1.0
|
|
C
|
A:CYS66
|
4.2
|
11.5
|
1.0
|
|
HB3
|
A:CYS66
|
4.3
|
11.4
|
1.0
|
|
HG
|
A:CYS72
|
4.3
|
10.9
|
0.0
|
|
HG21
|
A:ILE60
|
4.5
|
12.5
|
1.0
|
|
H
|
A:GLY70
|
4.5
|
10.2
|
1.0
|
|
HB
|
A:VAL28
|
4.5
|
14.7
|
1.0
|
|
CA
|
A:ASN68
|
4.6
|
11.7
|
1.0
|
|
HB3
|
A:ALA49
|
4.7
|
11.7
|
1.0
|
|
HD12
|
A:ILE60
|
4.7
|
11.6
|
1.0
|
|
CD1
|
A:ILE60
|
4.7
|
11.6
|
1.0
|
|
N
|
A:CYS69
|
4.7
|
11.5
|
1.0
|
|
CB
|
A:ALA49
|
4.8
|
11.7
|
1.0
|
|
HG22
|
A:ILE60
|
4.8
|
12.5
|
1.0
|
|
HG12
|
A:ILE67
|
4.8
|
11.3
|
1.0
|
|
SG
|
A:CYS72
|
4.8
|
10.9
|
1.0
|
|
SG
|
A:CYS45
|
4.8
|
12.2
|
1.0
|
|
HG21
|
A:VAL28
|
4.9
|
16.1
|
1.0
|
|
HD2
|
A:PRO46
|
4.9
|
12.2
|
1.0
|
|
HB1
|
A:ALA49
|
4.9
|
11.7
|
1.0
|
|
HG12
|
A:ILE60
|
4.9
|
11.9
|
1.0
|
|
C
|
A:ILE67
|
4.9
|
11.3
|
1.0
|
|
Iron binding site 8 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 8 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:11.3
occ:1.00
|
FE4
|
A:SF4502
|
0.0
|
11.3
|
1.0
|
|
S1
|
A:SF4502
|
2.2
|
10.7
|
1.0
|
|
S2
|
A:SF4502
|
2.3
|
11.4
|
1.0
|
|
SG
|
A:CYS45
|
2.3
|
12.2
|
1.0
|
|
S3
|
A:SF4502
|
2.3
|
11.0
|
1.0
|
|
FE3
|
A:SF4502
|
2.7
|
10.6
|
1.0
|
|
FE2
|
A:SF4502
|
2.8
|
10.4
|
1.0
|
|
FE1
|
A:SF4502
|
2.8
|
11.4
|
1.0
|
|
HG
|
A:CYS45
|
2.8
|
12.2
|
0.0
|
|
HD2
|
A:PRO46
|
3.0
|
12.2
|
1.0
|
|
HB2
|
A:CYS45
|
3.2
|
12.2
|
1.0
|
|
HA
|
A:CYS45
|
3.3
|
12.5
|
1.0
|
|
CB
|
A:CYS45
|
3.3
|
12.2
|
1.0
|
|
HB2
|
A:ALA49
|
3.3
|
11.7
|
1.0
|
|
HG13
|
A:ILE50
|
3.6
|
12.3
|
1.0
|
|
CA
|
A:CYS45
|
3.8
|
12.5
|
1.0
|
|
HD12
|
A:ILE50
|
3.8
|
12.8
|
1.0
|
|
S4
|
A:SF4502
|
3.9
|
10.6
|
1.0
|
|
CD
|
A:PRO46
|
3.9
|
12.2
|
1.0
|
|
HG1
|
A:THR47
|
4.0
|
14.1
|
0.0
|
|
HD3
|
A:PRO46
|
4.1
|
12.2
|
1.0
|
|
HB3
|
A:CYS45
|
4.1
|
12.2
|
1.0
|
|
CB
|
A:ALA49
|
4.2
|
11.7
|
1.0
|
|
CG1
|
A:ILE50
|
4.3
|
12.3
|
1.0
|
|
H
|
A:ALA49
|
4.4
|
11.5
|
1.0
|
|
HG
|
A:CYS72
|
4.4
|
10.9
|
0.0
|
|
HA
|
A:CYS66
|
4.4
|
11.1
|
1.0
|
|
CD1
|
A:ILE50
|
4.4
|
12.8
|
1.0
|
|
HB3
|
A:CYS72
|
4.4
|
10.8
|
1.0
|
|
HB1
|
A:ALA49
|
4.4
|
11.7
|
1.0
|
|
HD11
|
A:ILE50
|
4.4
|
12.8
|
1.0
|
|
H
|
A:THR47
|
4.5
|
13.3
|
1.0
|
|
OG1
|
A:THR47
|
4.6
|
14.1
|
1.0
|
|
HG12
|
A:ILE50
|
4.6
|
12.3
|
1.0
|
|
C
|
A:CYS45
|
4.6
|
13.1
|
1.0
|
|
N
|
A:PRO46
|
4.6
|
12.2
|
1.0
|
|
H
|
A:ILE67
|
4.6
|
11.6
|
1.0
|
|
HB3
|
A:ALA49
|
4.7
|
11.7
|
1.0
|
|
HG2
|
A:PRO46
|
4.8
|
12.7
|
1.0
|
|
SG
|
A:CYS72
|
4.8
|
10.9
|
1.0
|
|
SG
|
A:CYS69
|
4.8
|
10.8
|
1.0
|
|
SG
|
A:CYS66
|
4.9
|
11.5
|
1.0
|
|
N
|
A:CYS45
|
4.9
|
11.7
|
1.0
|
|
CG
|
A:PRO46
|
5.0
|
12.7
|
1.0
|
|
Iron binding site 9 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 9 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:12.4
occ:1.00
|
FE1
|
A:SF4503
|
0.0
|
12.4
|
1.0
|
|
SG
|
A:CYS35
|
2.2
|
13.4
|
1.0
|
|
S2
|
A:SF4503
|
2.2
|
13.2
|
1.0
|
|
S4
|
A:SF4503
|
2.3
|
12.0
|
1.0
|
|
S3
|
A:SF4503
|
2.3
|
13.0
|
1.0
|
|
FE2
|
A:SF4503
|
2.7
|
12.2
|
1.0
|
|
FE3
|
A:SF4503
|
2.7
|
12.3
|
1.0
|
|
FE4
|
A:SF4503
|
2.7
|
13.7
|
1.0
|
|
HG
|
A:CYS35
|
2.8
|
13.4
|
0.0
|
|
H
|
A:GLY37
|
3.0
|
16.1
|
1.0
|
|
HA
|
A:CYS35
|
3.2
|
15.4
|
1.0
|
|
CB
|
A:CYS35
|
3.3
|
15.2
|
1.0
|
|
HB2
|
A:CYS35
|
3.3
|
15.2
|
1.0
|
|
H
|
A:ILE36
|
3.4
|
16.7
|
1.0
|
|
HB2
|
A:HIS58
|
3.6
|
12.7
|
1.0
|
|
CA
|
A:CYS35
|
3.7
|
15.4
|
1.0
|
|
S1
|
A:SF4503
|
3.9
|
12.6
|
1.0
|
|
N
|
A:GLY37
|
3.9
|
16.1
|
1.0
|
|
HB2
|
A:ALA80
|
3.9
|
14.4
|
1.0
|
|
H
|
A:CYS38
|
4.0
|
15.2
|
1.0
|
|
N
|
A:ILE36
|
4.0
|
16.7
|
1.0
|
|
HA2
|
A:GLY37
|
4.1
|
14.1
|
1.0
|
|
H
|
A:HIS58
|
4.1
|
12.7
|
1.0
|
|
HB3
|
A:CYS35
|
4.1
|
15.2
|
1.0
|
|
C
|
A:CYS35
|
4.2
|
15.9
|
1.0
|
|
HG
|
A:CYS41
|
4.3
|
12.1
|
0.0
|
|
HG21
|
A:ILE30
|
4.4
|
12.9
|
1.0
|
|
H
|
A:ASP39
|
4.5
|
15.3
|
1.0
|
|
CA
|
A:GLY37
|
4.5
|
14.1
|
1.0
|
|
CB
|
A:HIS58
|
4.5
|
12.7
|
1.0
|
|
HG22
|
A:ILE30
|
4.6
|
12.9
|
1.0
|
|
CB
|
A:ALA80
|
4.7
|
14.4
|
1.0
|
|
HG
|
A:CYS76
|
4.7
|
12.2
|
0.0
|
|
CG
|
A:HIS58
|
4.7
|
12.0
|
1.0
|
|
N
|
A:CYS38
|
4.7
|
15.2
|
1.0
|
|
HB3
|
A:ALA80
|
4.7
|
14.4
|
1.0
|
|
HG12
|
A:ILE36
|
4.7
|
22.9
|
1.0
|
|
SG
|
A:CYS41
|
4.7
|
12.1
|
1.0
|
|
HB1
|
A:ALA80
|
4.8
|
14.4
|
1.0
|
|
SG
|
A:CYS76
|
4.8
|
12.2
|
1.0
|
|
HD13
|
A:ILE30
|
4.9
|
12.8
|
1.0
|
|
ND1
|
A:HIS58
|
4.9
|
11.8
|
1.0
|
|
C
|
A:ILE36
|
4.9
|
18.0
|
1.0
|
|
N
|
A:HIS58
|
4.9
|
12.7
|
1.0
|
|
HB2
|
A:GLU78
|
4.9
|
15.1
|
1.0
|
|
HD1
|
A:HIS58
|
4.9
|
11.8
|
0.0
|
|
CG2
|
A:ILE30
|
5.0
|
12.9
|
1.0
|
|
SG
|
A:CYS38
|
5.0
|
14.8
|
1.0
|
|
HA
|
A:PRO57
|
5.0
|
13.9
|
1.0
|
|
Iron binding site 10 out
of 12 in 8rtg
Go back to
Iron Binding Sites List in 8rtg
Iron binding site 10 out
of 12 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Apo Form within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:12.2
occ:1.00
|
FE2
|
A:SF4503
|
0.0
|
12.2
|
1.0
|
|
HG
|
A:CYS41
|
2.2
|
12.1
|
0.0
|
|
S1
|
A:SF4503
|
2.3
|
12.6
|
1.0
|
|
SG
|
A:CYS41
|
2.3
|
12.1
|
1.0
|
|
S4
|
A:SF4503
|
2.3
|
12.0
|
1.0
|
|
S3
|
A:SF4503
|
2.3
|
13.0
|
1.0
|
|
FE1
|
A:SF4503
|
2.7
|
12.4
|
1.0
|
|
FE3
|
A:SF4503
|
2.7
|
12.3
|
1.0
|
|
FE4
|
A:SF4503
|
2.7
|
13.7
|
1.0
|
|
HB3
|
A:CYS41
|
2.9
|
12.2
|
1.0
|
|
H
|
A:CYS41
|
3.1
|
11.7
|
1.0
|
|
CB
|
A:CYS41
|
3.2
|
12.2
|
1.0
|
|
HD12
|
A:ILE81
|
3.5
|
12.5
|
1.0
|
|
N
|
A:CYS41
|
3.8
|
11.7
|
1.0
|
|
HB2
|
A:HIS58
|
3.8
|
12.7
|
1.0
|
|
S2
|
A:SF4503
|
3.8
|
13.2
|
1.0
|
|
HB2
|
A:CYS41
|
3.9
|
12.2
|
1.0
|
|
H
|
A:ASP39
|
4.0
|
15.3
|
1.0
|
|
CA
|
A:CYS41
|
4.1
|
12.0
|
1.0
|
|
HD2
|
A:HIS58
|
4.2
|
11.6
|
1.0
|
|
HD13
|
A:ILE30
|
4.2
|
12.8
|
1.0
|
|
H
|
A:THR40
|
4.3
|
12.6
|
1.0
|
|
HB2
|
A:CYS76
|
4.4
|
11.4
|
1.0
|
|
HA
|
A:ASP39
|
4.4
|
14.2
|
1.0
|
|
CD2
|
A:HIS58
|
4.4
|
11.6
|
1.0
|
|
CD1
|
A:ILE81
|
4.4
|
12.5
|
1.0
|
|
SG
|
A:CYS35
|
4.5
|
13.4
|
1.0
|
|
CG
|
A:HIS58
|
4.5
|
12.0
|
1.0
|
|
H
|
A:SER42
|
4.5
|
13.2
|
1.0
|
|
CB
|
A:HIS58
|
4.5
|
12.7
|
1.0
|
|
HG
|
A:CYS35
|
4.6
|
13.4
|
0.0
|
|
HB3
|
A:HIS58
|
4.6
|
12.7
|
1.0
|
|
SG
|
A:CYS38
|
4.6
|
14.8
|
1.0
|
|
N
|
A:THR40
|
4.6
|
12.6
|
1.0
|
|
N
|
A:ASP39
|
4.7
|
15.3
|
1.0
|
|
SG
|
A:CYS76
|
4.7
|
12.2
|
1.0
|
|
HD11
|
A:ILE81
|
4.8
|
12.5
|
1.0
|
|
HG13
|
A:ILE81
|
4.8
|
11.1
|
1.0
|
|
HA
|
A:CYS41
|
4.8
|
12.0
|
1.0
|
|
HG
|
A:CYS76
|
4.8
|
12.2
|
0.0
|
|
HG21
|
A:ILE50
|
4.8
|
12.2
|
1.0
|
|
HB
|
A:THR40
|
4.9
|
13.3
|
1.0
|
|
HA
|
A:CYS76
|
4.9
|
11.2
|
1.0
|
|
CA
|
A:ASP39
|
4.9
|
14.2
|
1.0
|
|
HD13
|
A:ILE50
|
4.9
|
12.8
|
1.0
|
|
HD2
|
A:PRO77
|
4.9
|
13.4
|
1.0
|
|
HD13
|
A:ILE81
|
5.0
|
12.5
|
1.0
|
|
C
|
A:ASP39
|
5.0
|
12.9
|
1.0
|
|
H
|
A:CYS38
|
5.0
|
15.2
|
1.0
|
|
HG12
|
A:ILE81
|
5.0
|
11.1
|
1.0
|
|
Reference:
K.Bikbaev,
M.A.Martini,
D.Oberthuer,
J.A.Birrell,
I.Span.
Structure of [Fefe] Hydrogenase in the Holo and Apo Forms at Room Temperature To Be Published.
Page generated: Thu Aug 7 22:31:35 2025
|
