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Iron in PDB 6b6x: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster

All present enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster, PDB code: 6b6x was solved by E.C.Wittenborn, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.87 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.650, 154.870, 66.490, 90.00, 102.67, 90.00
R / Rfree (%) 14.4 / 17.1

Other elements in 6b6x:

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 4 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster (pdb code 6b6x). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster, PDB code: 6b6x:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 18 in 6b6x

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Iron binding site 1 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:19.3
occ:1.00
 FE1 A:SF4701 0.0 19.3 1.0
SG A:CYS51 2.3 17.0 1.0
S2 A:SF4701 2.3 17.8 1.0
S3 A:SF4701 2.3 20.8 1.0
S4 A:SF4701 2.3 19.1 1.0
FE2 A:SF4701 2.7 19.5 1.0
FE4 A:SF4701 2.7 18.1 1.0
FE3 A:SF4701 2.7 18.1 1.0
CB A:CYS51 3.1 16.6 1.0
NH2 A:ARG84 3.6 17.9 1.0
S1 A:SF4701 3.8 17.6 1.0
N A:ASN53 4.1 19.2 1.0
CB A:ASN53 4.2 17.8 1.0
C A:CYS51 4.3 18.5 1.0
CA A:CYS51 4.3 16.7 1.0
O A:CYS51 4.5 19.2 1.0
CA A:ASN53 4.6 15.6 1.0
N A:CYS54 4.6 17.3 1.0
N A:ARG52 4.7 17.0 1.0
CZ A:ARG84 4.7 22.9 1.0
SG A:CYS59 4.7 19.5 1.0
SG A:CYS74 4.9 18.7 1.0
C A:ASN53 4.9 16.7 1.0
SG A:CYS54 4.9 17.7 1.0
O A:HOH1051 5.0 19.1 1.0
CG A:ASN53 5.0 28.0 1.0

Iron binding site 2 out of 18 in 6b6x

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Iron binding site 2 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:19.5
occ:1.00
 FE2 A:SF4701 0.0 19.5 1.0
S1 A:SF4701 2.3 17.6 1.0
SG A:CYS59 2.3 19.5 1.0
S4 A:SF4701 2.3 19.1 1.0
S3 A:SF4701 2.3 20.8 1.0
FE1 A:SF4701 2.7 19.3 1.0
FE4 A:SF4701 2.7 18.1 1.0
FE3 A:SF4701 2.8 18.1 1.0
CB A:CYS59 3.3 22.5 1.0
S2 A:SF4701 3.9 17.8 1.0
N A:VAL73 4.0 19.4 1.0
CA A:GLY57 4.1 22.0 1.0
N A:GLY57 4.2 22.1 1.0
N A:CYS59 4.3 18.8 1.0
CA A:GLY72 4.3 22.4 1.0
CA A:CYS59 4.4 19.9 1.0
CB A:CYS51 4.6 16.6 1.0
C A:GLY72 4.6 20.4 1.0
SG A:CYS51 4.6 17.0 1.0
SG A:CYS54 4.7 17.7 1.0
CB A:VAL73 4.7 21.0 1.0
O A:CYS51 4.8 19.2 1.0
SG A:CYS74 4.8 18.7 1.0
N A:CYS74 4.8 18.2 1.0
CG2 A:VAL73 4.8 20.0 1.0
C A:PRO58 4.9 21.5 1.0
CA A:VAL73 4.9 20.6 1.0

Iron binding site 3 out of 18 in 6b6x

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Iron binding site 3 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.1
occ:1.00
 FE3 A:SF4701 0.0 18.1 1.0
S4 A:SF4701 2.3 19.1 1.0
SG A:CYS74 2.3 18.7 1.0
S1 A:SF4701 2.3 17.6 1.0
S2 A:SF4701 2.3 17.8 1.0
FE1 A:SF4701 2.7 19.3 1.0
FE2 A:SF4701 2.8 19.5 1.0
FE4 A:SF4701 2.8 18.1 1.0
CB A:CYS74 3.3 17.2 1.0
N A:CYS74 3.9 18.2 1.0
S3 A:SF4701 3.9 20.8 1.0
NH2 A:ARG84 4.0 17.9 1.0
CA A:CYS74 4.2 18.1 1.0
CG A:MET203 4.3 16.6 1.0
N A:VAL73 4.6 19.4 1.0
SG A:CYS54 4.6 17.7 1.0
CB A:ALA76 4.7 18.0 1.0
O A:HOH911 4.7 18.9 1.0
SG A:CYS59 4.8 19.5 1.0
SG A:CYS51 4.8 17.0 1.0
CA A:GLY72 4.8 22.4 1.0
C A:GLY72 4.9 20.4 1.0
CZ A:ARG84 5.0 22.9 1.0

Iron binding site 4 out of 18 in 6b6x

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Iron binding site 4 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:18.1
occ:1.00
 FE4 A:SF4701 0.0 18.1 1.0
SG A:CYS54 2.3 17.7 1.0
S3 A:SF4701 2.3 20.8 1.0
S1 A:SF4701 2.3 17.6 1.0
S2 A:SF4701 2.3 17.8 1.0
FE1 A:SF4701 2.7 19.3 1.0
FE2 A:SF4701 2.7 19.5 1.0
FE3 A:SF4701 2.8 18.1 1.0
CB A:CYS54 3.4 16.6 1.0
N A:CYS54 3.6 17.3 1.0
S4 A:SF4701 3.9 19.1 1.0
CA A:CYS54 3.9 17.8 1.0
O A:CYS54 4.0 21.8 1.0
N A:GLY57 4.1 22.1 1.0
C A:CYS54 4.2 20.2 1.0
C A:ASN53 4.4 16.7 1.0
CG A:MET203 4.6 16.6 1.0
CA A:GLY57 4.7 22.0 1.0
CB A:MET56 4.7 19.8 1.0
SG A:CYS74 4.8 18.7 1.0
N A:ASN53 4.8 19.2 1.0
SG A:CYS51 4.8 17.0 1.0
SG A:CYS59 4.8 19.5 1.0
CB A:MET203 4.9 19.9 1.0
N A:MET56 4.9 18.6 1.0
CA A:ASN53 5.0 15.6 1.0

Iron binding site 5 out of 18 in 6b6x

Go back to Iron Binding Sites List in 6b6x
Iron binding site 5 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:30.3
occ:1.00
 FE1 A:XCC702 0.0 30.3 1.0
S4 A:XCC702 2.3 26.0 1.0
S2 A:XCC702 2.3 27.7 1.0
S3 A:XCC702 2.4 28.7 1.0
SG A:CYS340 2.4 27.2 1.0
FE3 A:XCC702 2.6 26.7 1.0
FE4 A:XCC702 2.8 26.1 1.0
FE2 A:XCC702 3.3 39.0 1.0
NI A:XCC702 3.4 27.9 0.5
CB A:CYS340 3.4 23.9 1.0
S1 A:XCC702 3.8 27.2 1.0
O A:HOH884 3.9 37.5 1.0
NZ A:LYS556 4.0 30.7 1.0
NE2 A:HIS266 4.1 32.3 1.0
CE2 A:TYR553 4.2 26.4 1.0
CE1 A:HIS266 4.3 32.1 1.0
OH A:TYR553 4.4 35.7 1.0
CE A:LYS556 4.7 26.9 1.0
SG A:CYS448 4.7 23.5 1.0
CA A:CYS340 4.8 23.9 1.0
CZ A:TYR553 4.8 32.2 1.0
OG A:SER554 4.8 20.0 1.0
SG A:CYS478 5.0 27.9 1.0

Iron binding site 6 out of 18 in 6b6x

Go back to Iron Binding Sites List in 6b6x
Iron binding site 6 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:39.0
occ:1.00
 FE2 A:XCC702 0.0 39.0 1.0
O A:HOH884 2.0 37.5 1.0
NE2 A:HIS266 2.2 32.3 1.0
S3 A:XCC702 2.3 28.7 1.0
SG A:CYS302 2.3 26.5 1.0
CD2 A:HIS266 2.9 23.9 1.0
NI A:XCC702 3.0 27.9 0.5
FE1 A:XCC702 3.3 30.3 1.0
CE1 A:HIS266 3.3 32.1 1.0
CB A:CYS302 3.3 24.2 1.0
SG A:CYS519 3.3 21.8 0.6
SG A:CYS519 3.5 37.0 0.4
S4 A:XCC702 3.7 26.0 1.0
NZ A:LYS556 3.8 30.7 1.0
O A:HOH1078 3.8 25.2 0.6
CB A:CYS519 3.9 22.4 0.4
CB A:CYS519 3.9 21.9 0.6
FE4 A:XCC702 4.0 26.1 1.0
CG A:HIS266 4.1 30.7 1.0
S1 A:XCC702 4.2 27.2 1.0
ND1 A:HIS266 4.2 29.4 1.0
O A:HOH1011 4.3 32.0 1.0
CA A:CYS302 4.4 20.6 1.0
N A:CYS302 4.4 20.8 1.0
O A:HOH1040 4.4 29.8 1.0
SG A:CYS340 4.6 27.2 1.0
FE3 A:XCC702 4.6 26.7 1.0
N A:CYS519 4.8 18.9 0.4
N A:CYS519 4.8 18.5 0.6
CE A:LYS556 4.9 26.9 1.0

Iron binding site 7 out of 18 in 6b6x

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Iron binding site 7 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:26.7
occ:1.00
 FE3 A:XCC702 0.0 26.7 1.0
S1 A:XCC702 2.3 27.2 1.0
S2 A:XCC702 2.3 27.7 1.0
S4 A:XCC702 2.3 26.0 1.0
SG A:CYS448 2.4 23.5 1.0
FE1 A:XCC702 2.6 30.3 1.0
FE4 A:XCC702 2.6 26.1 1.0
NI A:XCC702 2.7 27.9 0.5
CB A:CYS448 3.1 19.8 1.0
CA A:CYS448 3.5 25.5 1.0
N A:CYS448 3.8 29.2 1.0
OG A:SER554 4.0 20.0 1.0
S3 A:XCC702 4.0 28.7 1.0
C A:GLY447 4.1 30.7 1.0
CE2 A:TYR553 4.2 26.4 1.0
CA A:GLY447 4.5 33.0 1.0
CD2 A:TYR553 4.5 28.1 1.0
O A:GLY447 4.6 29.4 1.0
SG A:CYS519 4.6 21.8 0.6
FE2 A:XCC702 4.6 39.0 1.0
SG A:CYS340 4.7 27.2 1.0
CB A:SER554 4.7 18.4 1.0
SG A:CYS478 4.7 27.9 1.0
O A:HOH884 4.9 37.5 1.0
C A:CYS448 4.9 26.4 1.0

Iron binding site 8 out of 18 in 6b6x

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Iron binding site 8 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe702

b:26.1
occ:1.00
 FE4 A:XCC702 0.0 26.1 1.0
S2 A:XCC702 2.2 27.7 1.0
S1 A:XCC702 2.3 27.2 1.0
S3 A:XCC702 2.4 28.7 1.0
SG A:CYS478 2.4 27.9 1.0
FE3 A:XCC702 2.6 26.7 1.0
FE1 A:XCC702 2.8 30.3 1.0
CB A:CYS478 3.5 26.9 1.0
NI A:XCC702 3.5 27.9 0.5
O A:HOH1011 3.6 32.0 1.0
FE2 A:XCC702 4.0 39.0 1.0
N A:CYS478 4.0 25.6 1.0
S4 A:XCC702 4.0 26.0 1.0
CA A:CYS478 4.3 28.3 1.0
CA A:CYS448 4.3 25.5 1.0
CB A:CYS448 4.6 19.8 1.0
CB A:HIS319 4.6 29.3 1.0
O A:GLY447 4.7 29.4 1.0
SG A:CYS519 4.7 21.8 0.6
SG A:CYS448 4.8 23.5 1.0
SG A:CYS301 4.8 32.1 1.0
C A:GLY447 4.8 30.7 1.0
CB A:CYS301 4.9 28.3 1.0
C A:GLY477 5.0 27.4 1.0
N A:CYS448 5.0 29.2 1.0
SG A:CYS302 5.0 26.5 1.0

Iron binding site 9 out of 18 in 6b6x

Go back to Iron Binding Sites List in 6b6x
Iron binding site 9 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:21.8
occ:1.00
 FE1 B:FES701 0.0 21.8 1.0
S1 B:FES701 2.2 23.1 1.0
S2 B:FES701 2.2 24.6 1.0
SG B:CYS45 2.3 22.7 1.0
SG B:CYS42 2.3 24.4 1.0
FE2 B:FES701 2.9 22.6 1.0
CB B:CYS42 3.2 25.8 1.0
CB B:CYS45 3.4 20.4 1.0
N B:CYS45 3.7 19.8 1.0
CA B:CYS45 4.1 19.3 1.0
O A:HOH1086 4.2 21.9 1.0
SG A:CYS45 4.5 21.2 1.0
OG1 A:THR50 4.5 19.5 1.0
C1 B:GOL704 4.5 40.8 1.0
C3 B:GOL704 4.5 34.5 1.0
SG A:CYS42 4.6 25.1 1.0
CB B:PHE44 4.6 19.9 1.0
CA B:CYS42 4.6 25.1 1.0
O3 B:GOL704 4.6 35.8 1.0
C B:PHE44 4.7 23.6 1.0
CG2 B:THR50 4.7 28.2 1.0
O A:HOH818 4.7 54.9 1.0
OG1 B:THR50 4.8 23.0 1.0
CB B:THR50 4.9 25.3 1.0
C B:CYS42 5.0 24.4 1.0

Iron binding site 10 out of 18 in 6b6x

Go back to Iron Binding Sites List in 6b6x
Iron binding site 10 out of 18 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:22.6
occ:1.00
 FE2 B:FES701 0.0 22.6 1.0
S2 B:FES701 2.2 24.6 1.0
S1 B:FES701 2.2 23.1 1.0
SG A:CYS45 2.3 21.2 1.0
SG A:CYS42 2.3 25.1 1.0
FE1 B:FES701 2.9 21.8 1.0
CB A:CYS42 3.2 20.7 1.0
CB A:CYS45 3.5 20.3 1.0
N A:CYS45 3.7 18.8 1.0
CA A:CYS45 4.1 21.5 1.0
O B:HOH1121 4.2 20.5 1.0
C1 B:GOL704 4.4 40.8 1.0
C3 B:GOL704 4.4 34.5 1.0
SG B:CYS45 4.4 22.7 1.0
OG1 B:THR50 4.5 23.0 1.0
CB A:PHE44 4.5 21.5 1.0
SG B:CYS42 4.6 24.4 1.0
CA A:CYS42 4.6 26.1 1.0
CG2 A:THR50 4.6 17.7 1.0
C2 B:GOL704 4.7 42.0 1.0
O A:HOH818 4.7 54.9 1.0
C A:PHE44 4.7 20.0 1.0
OG1 A:THR50 4.7 19.5 1.0
CB A:THR50 4.9 19.3 1.0
C A:CYS42 5.0 22.2 1.0

Reference:

E.C.Wittenborn, M.Merrouch, C.Ueda, L.Fradale, C.Leger, V.Fourmond, M.E.Pandelia, S.Dementin, C.L.Drennan. Redox-Dependent Rearrangements of the Nifes Cluster of Carbon Monoxide Dehydrogenase. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30277213
DOI: 10.7554/ELIFE.39451
Page generated: Tue Aug 6 14:05:15 2024

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