Iron in PDB 8rxi: Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
Enzymatic activity of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
All present enzymatic activity of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton:
1.12.7.2;
Protein crystallography data
The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton, PDB code: 8rxi
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)
|
44.90 /
1.48
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.6,
87.967,
89.71,
90,
90,
90
|
|
R / Rfree (%)
|
15.4 /
18.1
|
Other elements in 8rxi:
The structure of Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Iron atom in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
(pdb code 8rxi). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 13 binding sites of Iron where determined in the
Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton, PDB code: 8rxi:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 1 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:13.8
occ:1.00
|
FE1
|
A:SF4503
|
0.0
|
13.8
|
1.0
|
|
SG
|
A:CYS69
|
2.3
|
12.7
|
1.0
|
|
S2
|
A:SF4503
|
2.3
|
13.6
|
1.0
|
|
S4
|
A:SF4503
|
2.3
|
13.5
|
1.0
|
|
S3
|
A:SF4503
|
2.3
|
14.2
|
1.0
|
|
FE3
|
A:SF4503
|
2.7
|
13.6
|
1.0
|
|
FE4
|
A:SF4503
|
2.8
|
13.4
|
1.0
|
|
FE2
|
A:SF4503
|
2.8
|
13.8
|
1.0
|
|
H
|
A:CYS69
|
2.9
|
11.8
|
1.0
|
|
HG
|
A:CYS69
|
3.1
|
12.7
|
0.0
|
|
H
|
A:GLY70
|
3.2
|
12.1
|
1.0
|
|
HD2
|
A:PRO46
|
3.5
|
14.9
|
1.0
|
|
H
|
A:GLN71
|
3.5
|
11.7
|
1.0
|
|
N
|
A:CYS69
|
3.6
|
12.1
|
1.0
|
|
CB
|
A:CYS69
|
3.6
|
11.1
|
1.0
|
|
N
|
A:GLY70
|
3.8
|
11.9
|
1.0
|
|
HB3
|
A:CYS69
|
3.9
|
11.4
|
1.0
|
|
S1
|
A:SF4503
|
4.0
|
13.9
|
1.0
|
|
CA
|
A:CYS69
|
4.0
|
11.4
|
1.0
|
|
HG13
|
A:ILE67
|
4.0
|
12.2
|
1.0
|
|
H
|
A:ASN68
|
4.0
|
11.9
|
1.0
|
|
H
|
A:CYS72
|
4.0
|
13.1
|
1.0
|
|
HG12
|
A:ILE67
|
4.1
|
12.2
|
1.0
|
|
HD3
|
A:PRO46
|
4.1
|
14.9
|
1.0
|
|
H
|
A:ILE67
|
4.2
|
12.1
|
1.0
|
|
HA
|
A:CYS45
|
4.2
|
14.6
|
1.0
|
|
CD
|
A:PRO46
|
4.2
|
15.0
|
1.0
|
|
C
|
A:CYS69
|
4.3
|
12.4
|
1.0
|
|
N
|
A:GLN71
|
4.3
|
11.3
|
1.0
|
|
HB2
|
A:CYS69
|
4.4
|
11.4
|
1.0
|
|
HB2
|
A:GLN71
|
4.4
|
13.2
|
1.0
|
|
N
|
A:ASN68
|
4.4
|
12.0
|
1.0
|
|
CG1
|
A:ILE67
|
4.5
|
12.2
|
1.0
|
|
C
|
A:ASN68
|
4.6
|
11.4
|
1.0
|
|
SG
|
A:CYS72
|
4.6
|
15.0
|
1.0
|
|
HA2
|
A:GLY70
|
4.7
|
11.8
|
1.0
|
|
CA
|
A:GLY70
|
4.7
|
12.1
|
1.0
|
|
SG
|
A:CYS66
|
4.7
|
13.8
|
1.0
|
|
HA
|
A:ASN68
|
4.8
|
11.7
|
1.0
|
|
HG3
|
A:PRO46
|
4.8
|
15.6
|
1.0
|
|
O
|
A:HOH679
|
4.8
|
13.9
|
1.0
|
|
SG
|
A:CYS45
|
4.8
|
15.2
|
1.0
|
|
HG
|
A:CYS72
|
4.9
|
15.1
|
0.0
|
|
CA
|
A:ASN68
|
4.9
|
11.5
|
1.0
|
|
N
|
A:ILE67
|
4.9
|
11.9
|
1.0
|
|
CG
|
A:PRO46
|
4.9
|
15.6
|
1.0
|
|
HA
|
A:CYS69
|
4.9
|
11.7
|
1.0
|
|
N
|
A:CYS72
|
4.9
|
12.8
|
1.0
|
|
HG2
|
A:PRO46
|
5.0
|
15.6
|
1.0
|
|
Iron binding site 2 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 2 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:13.8
occ:1.00
|
FE2
|
A:SF4503
|
0.0
|
13.8
|
1.0
|
|
S1
|
A:SF4503
|
2.3
|
13.9
|
1.0
|
|
S4
|
A:SF4503
|
2.3
|
13.5
|
1.0
|
|
SG
|
A:CYS45
|
2.3
|
15.2
|
1.0
|
|
S3
|
A:SF4503
|
2.3
|
14.2
|
1.0
|
|
FE3
|
A:SF4503
|
2.7
|
13.6
|
1.0
|
|
FE4
|
A:SF4503
|
2.7
|
13.4
|
1.0
|
|
FE1
|
A:SF4503
|
2.8
|
13.8
|
1.0
|
|
HG
|
A:CYS45
|
2.8
|
15.2
|
0.0
|
|
HD2
|
A:PRO46
|
3.0
|
14.9
|
1.0
|
|
HB2
|
A:CYS45
|
3.2
|
14.6
|
1.0
|
|
CB
|
A:CYS45
|
3.2
|
14.4
|
1.0
|
|
HA
|
A:CYS45
|
3.2
|
14.6
|
1.0
|
|
HB2
|
A:ALA49
|
3.3
|
14.0
|
1.0
|
|
HG13
|
A:ILE50
|
3.6
|
16.0
|
1.0
|
|
CA
|
A:CYS45
|
3.7
|
14.3
|
1.0
|
|
S2
|
A:SF4503
|
3.9
|
13.6
|
1.0
|
|
CD
|
A:PRO46
|
3.9
|
15.0
|
1.0
|
|
HD12
|
A:ILE50
|
3.9
|
16.1
|
1.0
|
|
HG1
|
A:THR47
|
4.0
|
16.4
|
0.0
|
|
HB3
|
A:CYS45
|
4.1
|
14.6
|
1.0
|
|
CB
|
A:ALA49
|
4.2
|
13.9
|
1.0
|
|
HD3
|
A:PRO46
|
4.2
|
14.9
|
1.0
|
|
HB1
|
A:ALA49
|
4.3
|
14.0
|
1.0
|
|
H
|
A:ALA49
|
4.3
|
15.9
|
1.0
|
|
HA
|
A:CYS66
|
4.4
|
13.4
|
1.0
|
|
CG1
|
A:ILE50
|
4.4
|
16.3
|
1.0
|
|
H
|
A:THR47
|
4.4
|
15.9
|
1.0
|
|
HG
|
A:CYS72
|
4.4
|
15.1
|
0.0
|
|
HB3
|
A:CYS72
|
4.5
|
14.8
|
1.0
|
|
OG1
|
A:THR47
|
4.5
|
16.6
|
1.0
|
|
CD1
|
A:ILE50
|
4.5
|
16.0
|
1.0
|
|
N
|
A:PRO46
|
4.6
|
14.0
|
1.0
|
|
C
|
A:CYS45
|
4.6
|
15.5
|
1.0
|
|
HG12
|
A:ILE50
|
4.6
|
16.0
|
1.0
|
|
HB3
|
A:ALA49
|
4.6
|
14.0
|
1.0
|
|
HD11
|
A:ILE50
|
4.7
|
16.1
|
1.0
|
|
H
|
A:ILE67
|
4.7
|
12.1
|
1.0
|
|
SG
|
A:CYS69
|
4.8
|
12.7
|
1.0
|
|
HG2
|
A:PRO46
|
4.8
|
15.6
|
1.0
|
|
SG
|
A:CYS72
|
4.8
|
15.0
|
1.0
|
|
SG
|
A:CYS66
|
4.9
|
13.8
|
1.0
|
|
N
|
A:CYS45
|
4.9
|
14.7
|
1.0
|
|
H
|
A:CYS72
|
4.9
|
13.1
|
1.0
|
|
CG
|
A:PRO46
|
5.0
|
15.6
|
1.0
|
|
Iron binding site 3 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 3 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:13.6
occ:1.00
|
FE3
|
A:SF4503
|
0.0
|
13.6
|
1.0
|
|
HG
|
A:CYS72
|
2.1
|
15.1
|
0.0
|
|
S4
|
A:SF4503
|
2.2
|
13.5
|
1.0
|
|
SG
|
A:CYS72
|
2.3
|
15.0
|
1.0
|
|
S1
|
A:SF4503
|
2.3
|
13.9
|
1.0
|
|
S2
|
A:SF4503
|
2.3
|
13.6
|
1.0
|
|
FE2
|
A:SF4503
|
2.7
|
13.8
|
1.0
|
|
FE4
|
A:SF4503
|
2.7
|
13.4
|
1.0
|
|
FE1
|
A:SF4503
|
2.7
|
13.8
|
1.0
|
|
HB3
|
A:CYS72
|
3.1
|
14.8
|
1.0
|
|
H
|
A:CYS72
|
3.3
|
13.1
|
1.0
|
|
CB
|
A:CYS72
|
3.3
|
15.2
|
1.0
|
|
HD12
|
A:ILE50
|
3.4
|
16.1
|
1.0
|
|
HG13
|
A:VAL28
|
3.7
|
22.5
|
1.0
|
|
S3
|
A:SF4503
|
3.9
|
14.2
|
1.0
|
|
H
|
A:GLY70
|
4.0
|
12.1
|
1.0
|
|
HB2
|
A:CYS72
|
4.0
|
14.9
|
1.0
|
|
N
|
A:CYS72
|
4.0
|
12.8
|
1.0
|
|
HD12
|
A:ILE60
|
4.2
|
15.2
|
1.0
|
|
CA
|
A:CYS72
|
4.3
|
13.8
|
1.0
|
|
CD1
|
A:ILE50
|
4.3
|
16.0
|
1.0
|
|
HA2
|
A:GLY70
|
4.4
|
11.8
|
1.0
|
|
HD13
|
A:ILE60
|
4.4
|
15.2
|
1.0
|
|
H
|
A:GLN71
|
4.4
|
11.7
|
1.0
|
|
HG13
|
A:ILE50
|
4.5
|
16.0
|
1.0
|
|
HG21
|
A:VAL28
|
4.5
|
23.8
|
1.0
|
|
HB2
|
A:CYS45
|
4.5
|
14.6
|
1.0
|
|
H
|
A:LEU73
|
4.6
|
13.0
|
1.0
|
|
CG1
|
A:VAL28
|
4.6
|
23.5
|
1.0
|
|
HG12
|
A:ILE50
|
4.6
|
16.0
|
1.0
|
|
SG
|
A:CYS69
|
4.6
|
12.7
|
1.0
|
|
HB
|
A:VAL28
|
4.6
|
20.8
|
1.0
|
|
N
|
A:GLY70
|
4.6
|
11.9
|
1.0
|
|
CG1
|
A:ILE50
|
4.7
|
16.3
|
1.0
|
|
SG
|
A:CYS66
|
4.7
|
13.8
|
1.0
|
|
CD1
|
A:ILE60
|
4.7
|
15.2
|
1.0
|
|
HG12
|
A:VAL28
|
4.8
|
22.5
|
1.0
|
|
N
|
A:GLN71
|
4.8
|
11.3
|
1.0
|
|
HD11
|
A:ILE50
|
4.8
|
16.1
|
1.0
|
|
SG
|
A:CYS45
|
4.8
|
15.2
|
1.0
|
|
HA
|
A:CYS45
|
4.8
|
14.6
|
1.0
|
|
CA
|
A:GLY70
|
4.9
|
12.1
|
1.0
|
|
HD13
|
A:ILE50
|
4.9
|
16.1
|
1.0
|
|
H
|
A:CYS69
|
4.9
|
11.8
|
1.0
|
|
HA
|
A:CYS72
|
5.0
|
13.7
|
1.0
|
|
HG
|
A:CYS45
|
5.0
|
15.2
|
0.0
|
|
Iron binding site 4 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 4 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe503
b:13.4
occ:1.00
|
FE4
|
A:SF4503
|
0.0
|
13.4
|
1.0
|
|
S2
|
A:SF4503
|
2.3
|
13.6
|
1.0
|
|
S1
|
A:SF4503
|
2.3
|
13.9
|
1.0
|
|
SG
|
A:CYS66
|
2.3
|
13.8
|
1.0
|
|
S3
|
A:SF4503
|
2.3
|
14.2
|
1.0
|
|
FE3
|
A:SF4503
|
2.7
|
13.6
|
1.0
|
|
FE2
|
A:SF4503
|
2.7
|
13.8
|
1.0
|
|
FE1
|
A:SF4503
|
2.8
|
13.8
|
1.0
|
|
HG
|
A:CYS66
|
3.1
|
13.8
|
0.0
|
|
H
|
A:ASN68
|
3.2
|
11.9
|
1.0
|
|
HA
|
A:CYS66
|
3.2
|
13.4
|
1.0
|
|
CB
|
A:CYS66
|
3.4
|
14.8
|
1.0
|
|
H
|
A:ILE67
|
3.5
|
12.1
|
1.0
|
|
HB2
|
A:CYS66
|
3.6
|
14.2
|
1.0
|
|
CA
|
A:CYS66
|
3.8
|
13.1
|
1.0
|
|
S4
|
A:SF4503
|
3.9
|
13.5
|
1.0
|
|
H
|
A:CYS69
|
4.0
|
11.8
|
1.0
|
|
N
|
A:ILE67
|
4.0
|
11.9
|
1.0
|
|
N
|
A:ASN68
|
4.0
|
12.0
|
1.0
|
|
HB2
|
A:ALA49
|
4.0
|
14.0
|
1.0
|
|
HD13
|
A:ILE60
|
4.0
|
15.2
|
1.0
|
|
HA
|
A:ASN68
|
4.1
|
11.7
|
1.0
|
|
C
|
A:CYS66
|
4.3
|
12.7
|
1.0
|
|
HB3
|
A:CYS66
|
4.3
|
14.2
|
1.0
|
|
HG
|
A:CYS72
|
4.4
|
15.1
|
0.0
|
|
H
|
A:GLY70
|
4.5
|
12.1
|
1.0
|
|
HG21
|
A:ILE60
|
4.5
|
14.8
|
1.0
|
|
HB
|
A:VAL28
|
4.5
|
20.8
|
1.0
|
|
CA
|
A:ASN68
|
4.6
|
11.5
|
1.0
|
|
HB3
|
A:ALA49
|
4.6
|
14.0
|
1.0
|
|
CB
|
A:ALA49
|
4.7
|
13.9
|
1.0
|
|
N
|
A:CYS69
|
4.7
|
12.1
|
1.0
|
|
HB1
|
A:ALA49
|
4.8
|
14.0
|
1.0
|
|
HD12
|
A:ILE60
|
4.8
|
15.2
|
1.0
|
|
CD1
|
A:ILE60
|
4.8
|
15.2
|
1.0
|
|
SG
|
A:CYS45
|
4.8
|
15.2
|
1.0
|
|
SG
|
A:CYS72
|
4.8
|
15.0
|
1.0
|
|
HG12
|
A:ILE67
|
4.9
|
12.2
|
1.0
|
|
HD2
|
A:PRO46
|
4.9
|
14.9
|
1.0
|
|
HG21
|
A:VAL28
|
5.0
|
23.8
|
1.0
|
|
HG22
|
A:ILE60
|
5.0
|
14.8
|
1.0
|
|
C
|
A:ILE67
|
5.0
|
12.1
|
1.0
|
|
HG12
|
A:ILE60
|
5.0
|
15.0
|
1.0
|
|
SG
|
A:CYS69
|
5.0
|
12.7
|
1.0
|
|
Iron binding site 5 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 5 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe504
b:13.8
occ:1.00
|
FE1
|
A:SF4504
|
0.0
|
13.8
|
1.0
|
|
S3
|
A:SF4504
|
2.3
|
13.1
|
1.0
|
|
SG
|
A:CYS382
|
2.3
|
14.4
|
1.0
|
|
S2
|
A:SF4504
|
2.3
|
12.7
|
1.0
|
|
S4
|
A:SF4504
|
2.3
|
12.4
|
1.0
|
|
FE4
|
A:SF4504
|
2.7
|
13.9
|
1.0
|
|
FE2
|
A:SF4504
|
2.7
|
12.1
|
1.0
|
|
FE3
|
A:SF4504
|
2.8
|
13.0
|
1.0
|
|
HA
|
A:CYS382
|
2.8
|
11.5
|
1.0
|
|
H7
|
A:LFH507
|
3.1
|
14.4
|
0.6
|
|
HG
|
A:CYS382
|
3.2
|
14.4
|
0.0
|
|
CB
|
A:CYS382
|
3.3
|
12.4
|
1.0
|
|
CA
|
A:CYS382
|
3.4
|
11.2
|
1.0
|
|
HB3
|
A:CYS382
|
3.6
|
12.4
|
1.0
|
|
C3
|
A:LFH507
|
3.8
|
12.8
|
0.6
|
|
O3
|
A:LFH507
|
3.9
|
12.9
|
0.6
|
|
N
|
A:CYS382
|
3.9
|
11.2
|
1.0
|
|
S1
|
A:SF4504
|
3.9
|
13.1
|
1.0
|
|
FE1
|
A:LFH507
|
4.1
|
13.1
|
0.6
|
|
HG
|
A:CYS234
|
4.1
|
13.7
|
0.0
|
|
HB2
|
A:CYS234
|
4.1
|
12.6
|
1.0
|
|
C2
|
A:LFH507
|
4.1
|
13.8
|
0.6
|
|
H
|
A:CYS382
|
4.2
|
11.3
|
1.0
|
|
HB2
|
A:CYS382
|
4.2
|
12.5
|
1.0
|
|
S2
|
A:LFH507
|
4.3
|
14.2
|
0.6
|
|
HG2
|
A:PRO233
|
4.4
|
10.7
|
1.0
|
|
HS2
|
A:LFH507
|
4.4
|
14.1
|
0.6
|
|
HB2
|
A:CYS378
|
4.6
|
11.5
|
1.0
|
|
HG
|
A:CYS378
|
4.6
|
12.7
|
0.0
|
|
SD
|
A:MET376
|
4.6
|
15.7
|
1.0
|
|
C
|
A:GLY381
|
4.6
|
11.7
|
1.0
|
|
H12
|
A:LFH507
|
4.6
|
13.8
|
0.6
|
|
SG
|
A:CYS234
|
4.7
|
13.7
|
1.0
|
|
H8
|
A:LFH507
|
4.7
|
14.4
|
0.6
|
|
HB3
|
A:MET376
|
4.7
|
12.5
|
1.0
|
|
HB2
|
A:CYS179
|
4.8
|
10.6
|
1.0
|
|
C
|
A:CYS382
|
4.8
|
11.7
|
1.0
|
|
SG
|
A:CYS179
|
4.8
|
11.2
|
1.0
|
|
HA
|
A:CYS179
|
4.8
|
11.0
|
1.0
|
|
HA3
|
A:GLY385
|
4.8
|
12.1
|
1.0
|
|
HD2
|
A:PRO180
|
4.8
|
11.5
|
1.0
|
|
CB
|
A:CYS234
|
4.9
|
12.6
|
1.0
|
|
H
|
A:CYS378
|
4.9
|
11.2
|
1.0
|
|
HA2
|
A:GLY381
|
4.9
|
11.7
|
1.0
|
|
SG
|
A:CYS378
|
4.9
|
12.8
|
1.0
|
|
Iron binding site 6 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 6 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe504
b:12.1
occ:1.00
|
FE2
|
A:SF4504
|
0.0
|
12.1
|
1.0
|
|
S3
|
A:SF4504
|
2.2
|
13.1
|
1.0
|
|
S1
|
A:SF4504
|
2.3
|
13.1
|
1.0
|
|
SG
|
A:CYS179
|
2.3
|
11.2
|
1.0
|
|
S4
|
A:SF4504
|
2.3
|
12.4
|
1.0
|
|
FE4
|
A:SF4504
|
2.7
|
13.9
|
1.0
|
|
FE3
|
A:SF4504
|
2.7
|
13.0
|
1.0
|
|
FE1
|
A:SF4504
|
2.7
|
13.8
|
1.0
|
|
HG
|
A:CYS179
|
2.8
|
11.2
|
0.0
|
|
H
|
A:ALA377
|
3.2
|
11.1
|
1.0
|
|
HB2
|
A:CYS179
|
3.3
|
10.6
|
1.0
|
|
CB
|
A:CYS179
|
3.4
|
10.3
|
1.0
|
|
HB2
|
A:ALA377
|
3.4
|
10.9
|
1.0
|
|
HA
|
A:CYS179
|
3.5
|
11.0
|
1.0
|
|
HD2
|
A:PRO180
|
3.6
|
11.5
|
1.0
|
|
H
|
A:GLY181
|
3.6
|
11.2
|
1.0
|
|
H7
|
A:LFH507
|
3.8
|
14.4
|
0.6
|
|
CA
|
A:CYS179
|
3.9
|
11.0
|
1.0
|
|
S2
|
A:SF4504
|
3.9
|
12.7
|
1.0
|
|
N
|
A:ALA377
|
4.0
|
11.1
|
1.0
|
|
H
|
A:CYS378
|
4.1
|
11.2
|
1.0
|
|
HG
|
A:CYS234
|
4.1
|
13.7
|
0.0
|
|
CB
|
A:ALA377
|
4.2
|
10.8
|
1.0
|
|
HB3
|
A:CYS179
|
4.2
|
10.7
|
1.0
|
|
HA
|
A:MET376
|
4.2
|
11.7
|
1.0
|
|
HB1
|
A:ALA377
|
4.3
|
10.9
|
1.0
|
|
C
|
A:CYS179
|
4.3
|
11.2
|
1.0
|
|
CD
|
A:PRO180
|
4.4
|
11.7
|
1.0
|
|
H
|
A:TRP182
|
4.4
|
10.9
|
1.0
|
|
HA3
|
A:GLY181
|
4.4
|
11.2
|
1.0
|
|
N
|
A:GLY181
|
4.5
|
10.6
|
1.0
|
|
N
|
A:PRO180
|
4.5
|
10.8
|
1.0
|
|
HB3
|
A:MET376
|
4.6
|
12.5
|
1.0
|
|
CA
|
A:ALA377
|
4.6
|
11.3
|
1.0
|
|
C2
|
A:LFH507
|
4.7
|
13.8
|
0.6
|
|
H8
|
A:LFH507
|
4.7
|
14.4
|
0.6
|
|
SG
|
A:CYS234
|
4.7
|
13.7
|
1.0
|
|
SG
|
A:CYS382
|
4.7
|
14.4
|
1.0
|
|
SG
|
A:CYS378
|
4.7
|
12.8
|
1.0
|
|
HG2
|
A:PRO180
|
4.8
|
11.7
|
1.0
|
|
N
|
A:CYS378
|
4.8
|
11.2
|
1.0
|
|
SD
|
A:MET376
|
4.8
|
15.7
|
1.0
|
|
HB2
|
A:ALA236
|
4.9
|
10.4
|
1.0
|
|
C
|
A:MET376
|
4.9
|
11.0
|
1.0
|
|
CA
|
A:MET376
|
4.9
|
12.2
|
1.0
|
|
HB3
|
A:ALA377
|
5.0
|
10.9
|
1.0
|
|
Iron binding site 7 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 7 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe504
b:13.0
occ:1.00
|
FE3
|
A:SF4504
|
0.0
|
13.0
|
1.0
|
|
S4
|
A:SF4504
|
2.3
|
12.4
|
1.0
|
|
SG
|
A:CYS378
|
2.3
|
12.8
|
1.0
|
|
S1
|
A:SF4504
|
2.3
|
13.1
|
1.0
|
|
S2
|
A:SF4504
|
2.3
|
12.7
|
1.0
|
|
HG
|
A:CYS378
|
2.4
|
12.7
|
0.0
|
|
FE4
|
A:SF4504
|
2.6
|
13.9
|
1.0
|
|
FE2
|
A:SF4504
|
2.7
|
12.1
|
1.0
|
|
FE1
|
A:SF4504
|
2.8
|
13.8
|
1.0
|
|
HB2
|
A:CYS378
|
3.0
|
11.5
|
1.0
|
|
CB
|
A:CYS378
|
3.2
|
11.5
|
1.0
|
|
H
|
A:CYS378
|
3.3
|
11.2
|
1.0
|
|
HA2
|
A:GLY385
|
3.7
|
12.1
|
1.0
|
|
HB2
|
A:ALA377
|
3.8
|
10.9
|
1.0
|
|
N
|
A:CYS378
|
3.8
|
11.2
|
1.0
|
|
S3
|
A:SF4504
|
3.9
|
13.1
|
1.0
|
|
HA
|
A:CYS382
|
3.9
|
11.5
|
1.0
|
|
HB3
|
A:CYS378
|
4.0
|
11.5
|
1.0
|
|
CA
|
A:CYS378
|
4.1
|
10.8
|
1.0
|
|
HA3
|
A:GLY385
|
4.1
|
12.1
|
1.0
|
|
O
|
A:HOH641
|
4.2
|
13.4
|
1.0
|
|
H
|
A:GLY386
|
4.2
|
11.6
|
1.0
|
|
H
|
A:ALA377
|
4.3
|
11.1
|
1.0
|
|
CA
|
A:GLY385
|
4.4
|
12.5
|
1.0
|
|
SG
|
A:CYS234
|
4.4
|
13.7
|
1.0
|
|
HG
|
A:CYS234
|
4.5
|
13.7
|
0.0
|
|
HB2
|
A:CYS69
|
4.6
|
11.4
|
1.0
|
|
HA
|
A:CYS378
|
4.6
|
10.9
|
1.0
|
|
C
|
A:ALA377
|
4.6
|
11.7
|
1.0
|
|
HB2
|
A:CYS234
|
4.6
|
12.6
|
1.0
|
|
CB
|
A:ALA377
|
4.6
|
10.8
|
1.0
|
|
SG
|
A:CYS179
|
4.7
|
11.2
|
1.0
|
|
N
|
A:ALA377
|
4.7
|
11.1
|
1.0
|
|
HA
|
A:CYS69
|
4.7
|
11.7
|
1.0
|
|
HG
|
A:CYS179
|
4.8
|
11.2
|
0.0
|
|
CA
|
A:CYS382
|
4.8
|
11.2
|
1.0
|
|
HE22
|
A:GLN71
|
4.8
|
13.2
|
1.0
|
|
CA
|
A:ALA377
|
4.9
|
11.3
|
1.0
|
|
SG
|
A:CYS382
|
4.9
|
14.4
|
1.0
|
|
O
|
A:CYS69
|
5.0
|
12.8
|
1.0
|
|
Iron binding site 8 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 8 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe504
b:13.9
occ:1.00
|
FE4
|
A:SF4504
|
0.0
|
13.9
|
1.0
|
|
HG
|
A:CYS234
|
1.9
|
13.7
|
0.0
|
|
SG
|
A:CYS234
|
2.2
|
13.7
|
1.0
|
|
S3
|
A:SF4504
|
2.3
|
13.1
|
1.0
|
|
S2
|
A:SF4504
|
2.3
|
12.7
|
1.0
|
|
S1
|
A:SF4504
|
2.3
|
13.1
|
1.0
|
|
FE3
|
A:SF4504
|
2.6
|
13.0
|
1.0
|
|
FE2
|
A:SF4504
|
2.7
|
12.1
|
1.0
|
|
FE1
|
A:SF4504
|
2.7
|
13.8
|
1.0
|
|
HB2
|
A:CYS234
|
2.9
|
12.6
|
1.0
|
|
CB
|
A:CYS234
|
3.2
|
12.6
|
1.0
|
|
HB2
|
A:ALA236
|
3.7
|
10.4
|
1.0
|
|
HD2
|
A:PRO180
|
3.7
|
11.5
|
1.0
|
|
HB3
|
A:CYS234
|
3.8
|
12.6
|
1.0
|
|
S4
|
A:SF4504
|
3.8
|
12.4
|
1.0
|
|
O3
|
A:LFH507
|
4.0
|
12.9
|
0.6
|
|
O
|
A:HOH641
|
4.0
|
13.4
|
1.0
|
|
HG2
|
A:LYS237
|
4.0
|
12.1
|
1.0
|
|
HA
|
A:CYS234
|
4.1
|
12.0
|
1.0
|
|
HG2
|
A:PRO180
|
4.2
|
11.7
|
1.0
|
|
HE2
|
A:LYS237
|
4.2
|
12.6
|
1.0
|
|
CA
|
A:CYS234
|
4.3
|
11.7
|
1.0
|
|
HG
|
A:CYS378
|
4.4
|
12.7
|
0.0
|
|
H
|
A:GLY181
|
4.4
|
11.2
|
1.0
|
|
H
|
A:ALA236
|
4.5
|
10.4
|
1.0
|
|
C3
|
A:LFH507
|
4.5
|
12.8
|
0.6
|
|
CD
|
A:PRO180
|
4.6
|
11.7
|
1.0
|
|
SG
|
A:CYS378
|
4.6
|
12.8
|
1.0
|
|
CB
|
A:ALA236
|
4.6
|
10.7
|
1.0
|
|
H
|
A:LYS237
|
4.6
|
11.3
|
1.0
|
|
SG
|
A:CYS382
|
4.7
|
14.4
|
1.0
|
|
SG
|
A:CYS179
|
4.7
|
11.2
|
1.0
|
|
HA
|
A:CYS382
|
4.8
|
11.5
|
1.0
|
|
HG2
|
A:PRO233
|
4.8
|
10.7
|
1.0
|
|
CG
|
A:PRO180
|
4.8
|
11.8
|
1.0
|
|
HA
|
A:CYS179
|
4.8
|
11.0
|
1.0
|
|
H7
|
A:LFH507
|
4.8
|
14.4
|
0.6
|
|
HG3
|
A:LYS237
|
4.9
|
12.1
|
1.0
|
|
HS2
|
A:LFH507
|
4.9
|
14.1
|
0.6
|
|
CG
|
A:LYS237
|
4.9
|
12.2
|
1.0
|
|
HA3
|
A:GLY385
|
4.9
|
12.1
|
1.0
|
|
H
|
A:GLY386
|
4.9
|
11.6
|
1.0
|
|
HB1
|
A:ALA236
|
4.9
|
10.4
|
1.0
|
|
Iron binding site 9 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 9 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe505
b:19.9
occ:1.00
|
FE1
|
A:SF4505
|
0.0
|
19.9
|
1.0
|
|
SG
|
A:CYS76
|
2.2
|
20.8
|
1.0
|
|
S4
|
A:SF4505
|
2.3
|
20.1
|
1.0
|
|
S2
|
A:SF4505
|
2.3
|
22.1
|
1.0
|
|
S3
|
A:SF4505
|
2.3
|
19.0
|
1.0
|
|
HG
|
A:CYS76
|
2.5
|
20.7
|
0.0
|
|
FE2
|
A:SF4505
|
2.6
|
18.9
|
1.0
|
|
FE4
|
A:SF4505
|
2.7
|
19.3
|
1.0
|
|
HB2
|
A:ALA80
|
3.3
|
17.1
|
1.0
|
|
HB2
|
A:CYS76
|
3.4
|
18.6
|
1.0
|
|
HD2
|
A:PRO77
|
3.4
|
19.2
|
1.0
|
|
CB
|
A:CYS76
|
3.4
|
18.8
|
1.0
|
|
HB2
|
A:GLU78
|
3.6
|
26.6
|
1.0
|
|
HB2
|
A:CYS38
|
3.6
|
26.6
|
1.0
|
|
HA
|
A:CYS76
|
3.7
|
16.9
|
1.0
|
|
H
|
A:GLU78
|
3.9
|
20.8
|
1.0
|
|
S1
|
A:SF4505
|
3.9
|
19.8
|
1.0
|
|
HG13
|
A:ILE81
|
4.0
|
17.2
|
1.0
|
|
CA
|
A:CYS76
|
4.1
|
16.6
|
1.0
|
|
CB
|
A:ALA80
|
4.2
|
17.4
|
1.0
|
|
H
|
A:ALA80
|
4.2
|
16.4
|
1.0
|
|
HD12
|
A:ILE81
|
4.2
|
17.8
|
1.0
|
|
HB3
|
A:CYS76
|
4.2
|
18.6
|
1.0
|
|
HB1
|
A:ALA80
|
4.2
|
17.1
|
1.0
|
|
HB3
|
A:CYS41
|
4.3
|
18.7
|
1.0
|
|
CD
|
A:PRO77
|
4.3
|
18.9
|
1.0
|
|
H
|
A:CYS38
|
4.3
|
22.4
|
1.0
|
|
HA
|
A:CYS35
|
4.4
|
22.7
|
1.0
|
|
HG
|
A:CYS41
|
4.5
|
20.2
|
0.0
|
|
CB
|
A:CYS38
|
4.5
|
25.7
|
1.0
|
|
H
|
A:CYS41
|
4.5
|
18.8
|
1.0
|
|
CB
|
A:GLU78
|
4.6
|
26.8
|
1.0
|
|
H
|
A:ASP39
|
4.6
|
21.9
|
1.0
|
|
HG
|
A:CYS38
|
4.6
|
33.2
|
0.0
|
|
C
|
A:CYS76
|
4.7
|
16.7
|
1.0
|
|
HB3
|
A:ALA80
|
4.7
|
17.1
|
1.0
|
|
N
|
A:PRO77
|
4.7
|
18.9
|
1.0
|
|
N
|
A:GLU78
|
4.7
|
20.1
|
1.0
|
|
SG
|
A:CYS41
|
4.7
|
20.1
|
1.0
|
|
CG1
|
A:ILE81
|
4.8
|
17.4
|
1.0
|
|
HD3
|
A:PRO77
|
4.8
|
19.2
|
1.0
|
|
H
|
A:ILE36
|
4.8
|
25.9
|
1.0
|
|
HG2
|
A:GLU78
|
4.8
|
30.1
|
1.0
|
|
SG
|
A:CYS35
|
4.8
|
19.2
|
1.0
|
|
CD1
|
A:ILE81
|
4.9
|
17.9
|
1.0
|
|
HG12
|
A:ILE81
|
4.9
|
17.2
|
1.0
|
|
HG2
|
A:PRO77
|
4.9
|
20.4
|
1.0
|
|
SG
|
A:CYS38
|
4.9
|
33.2
|
1.0
|
|
H
|
A:THR40
|
5.0
|
19.6
|
1.0
|
|
N
|
A:ALA80
|
5.0
|
16.2
|
1.0
|
|
Iron binding site 10 out
of 13 in 8rxi
Go back to
Iron Binding Sites List in 8rxi
Iron binding site 10 out
of 13 in the Desulfovibrio Desulfuricans [Fefe] Hydrogenase in Hinact State Derivatized with Krypton
 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 Hinact State Derivatized with Krypton within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe505
b:18.9
occ:1.00
|
FE2
|
A:SF4505
|
0.0
|
18.9
|
1.0
|
|
S3
|
A:SF4505
|
2.2
|
19.0
|
1.0
|
|
HG
|
A:CYS41
|
2.2
|
20.2
|
0.0
|
|
S1
|
A:SF4505
|
2.2
|
19.8
|
1.0
|
|
S4
|
A:SF4505
|
2.3
|
20.1
|
1.0
|
|
SG
|
A:CYS41
|
2.3
|
20.1
|
1.0
|
|
FE1
|
A:SF4505
|
2.6
|
19.9
|
1.0
|
|
FE4
|
A:SF4505
|
2.7
|
19.3
|
1.0
|
|
HB3
|
A:CYS41
|
3.0
|
18.7
|
1.0
|
|
H
|
A:CYS41
|
3.1
|
18.8
|
1.0
|
|
CB
|
A:CYS41
|
3.2
|
18.3
|
1.0
|
|
H
|
A:ASP39
|
3.3
|
21.9
|
1.0
|
|
HD12
|
A:ILE81
|
3.7
|
17.8
|
1.0
|
|
S2
|
A:SF4505
|
3.9
|
22.1
|
1.0
|
|
N
|
A:CYS41
|
3.9
|
18.8
|
1.0
|
|
HB2
|
A:CYS41
|
4.0
|
18.6
|
1.0
|
|
HA
|
A:ASP39
|
4.0
|
20.3
|
1.0
|
|
HB2
|
A:HIS58
|
4.1
|
15.8
|
1.0
|
|
H
|
A:THR40
|
4.1
|
19.6
|
1.0
|
|
N
|
A:ASP39
|
4.1
|
21.8
|
1.0
|
|
HB2
|
A:CYS38
|
4.1
|
26.6
|
1.0
|
|
CA
|
A:CYS41
|
4.2
|
18.7
|
1.0
|
|
HD2
|
A:HIS58
|
4.3
|
17.1
|
1.0
|
|
H
|
A:SER42
|
4.4
|
21.2
|
1.0
|
|
HD13
|
A:ILE30
|
4.4
|
17.8
|
1.0
|
|
H
|
A:CYS38
|
4.4
|
22.4
|
1.0
|
|
CD2
|
A:HIS58
|
4.4
|
16.8
|
1.0
|
|
N
|
A:THR40
|
4.4
|
19.1
|
1.0
|
|
CA
|
A:ASP39
|
4.5
|
19.9
|
1.0
|
|
HB2
|
A:CYS76
|
4.5
|
18.6
|
1.0
|
|
SG
|
A:CYS76
|
4.6
|
20.8
|
1.0
|
|
CG
|
A:HIS58
|
4.6
|
15.3
|
1.0
|
|
CD1
|
A:ILE81
|
4.6
|
17.9
|
1.0
|
|
SG
|
A:CYS35
|
4.6
|
19.2
|
1.0
|
|
HG
|
A:CYS76
|
4.6
|
20.7
|
0.0
|
|
CB
|
A:HIS58
|
4.7
|
16.0
|
1.0
|
|
C
|
A:ASP39
|
4.7
|
19.5
|
1.0
|
|
HB3
|
A:HIS58
|
4.8
|
15.8
|
1.0
|
|
HG21
|
A:ILE50
|
4.8
|
15.1
|
1.0
|
|
HG
|
A:CYS35
|
4.8
|
19.2
|
0.0
|
|
HG13
|
A:ILE81
|
4.8
|
17.2
|
1.0
|
|
HA
|
A:CYS41
|
4.8
|
18.9
|
1.0
|
|
N
|
A:CYS38
|
4.9
|
22.3
|
1.0
|
|
HB
|
A:THR40
|
4.9
|
23.5
|
1.0
|
|
HD11
|
A:ILE81
|
4.9
|
17.7
|
1.0
|
|
HA2
|
A:GLY37
|
4.9
|
20.6
|
1.0
|
|
HD13
|
A:ILE50
|
5.0
|
16.1
|
1.0
|
|
HA
|
A:CYS76
|
5.0
|
16.9
|
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 09:44:19 2025
|
