Iron in PDB 6sdv: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form

Enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form

All present enzymatic activity of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form:
1.2.1.2;

Protein crystallography data

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form, PDB code: 6sdv was solved by A.R.Oliveira, C.Mota, C.Mourato, R.M.Domingos, M.F.A.Santos, D.Gesto, B.Guigliarelli, T.Santos-Silva, M.J.Romao, I.C.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.76 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.885, 128.560, 149.629, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.7

Other elements in 6sdv:

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form also contains other interesting chemical elements:

Tungsten (W) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form (pdb code 6sdv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form, PDB code: 6sdv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 6sdv

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:14.8
occ:1.00
FE1 A:SF41103 0.0 14.8 1.0
S4 A:SF41103 2.3 14.6 1.0
S2 A:SF41103 2.3 14.8 1.0
S3 A:SF41103 2.3 13.1 1.0
SG A:CYS53 2.3 15.0 1.0
FE4 A:SF41103 2.7 15.2 1.0
FE2 A:SF41103 2.7 14.5 1.0
FE3 A:SF41103 2.8 14.0 1.0
CB A:CYS53 3.4 13.4 1.0
N A:CYS53 3.8 13.0 1.0
CA A:CYS53 3.9 14.7 1.0
S1 A:SF41103 3.9 13.3 1.0
O A:HOH1292 3.9 13.5 1.0
CB A:VAL55 4.0 10.5 1.0
O A:CYS53 4.1 17.0 1.0
C A:CYS53 4.1 15.4 1.0
CG2 A:VAL55 4.2 10.5 1.0
CD A:PRO234 4.5 12.9 1.0
N A:VAL55 4.5 10.7 1.0
SG A:CYS88 4.7 13.2 1.0
SG A:CYS50 4.7 14.7 1.0
SG A:CYS57 4.8 14.8 1.0
CA A:VAL55 4.9 10.7 1.0
N A:ALA54 4.9 14.8 1.0
C A:TYR52 5.0 13.2 1.0

Iron binding site 2 out of 16 in 6sdv

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:14.5
occ:1.00
FE2 A:SF41103 0.0 14.5 1.0
S3 A:SF41103 2.3 13.1 1.0
SG A:CYS57 2.3 14.8 1.0
S4 A:SF41103 2.3 14.6 1.0
S1 A:SF41103 2.3 13.3 1.0
FE3 A:SF41103 2.7 14.0 1.0
FE4 A:SF41103 2.7 15.2 1.0
FE1 A:SF41103 2.7 14.8 1.0
CB A:CYS57 3.2 11.7 1.0
S2 A:SF41103 3.9 14.8 1.0
N A:CYS57 4.2 12.0 1.0
CB A:VAL55 4.2 10.5 1.0
CG1 A:ILE235 4.3 13.4 1.0
CA A:CYS57 4.3 13.8 1.0
CD1 A:ILE235 4.3 16.2 1.0
CB A:ILE235 4.3 10.5 1.0
CG1 A:VAL55 4.4 10.5 1.0
SG A:CYS50 4.6 14.7 1.0
CB A:CYS50 4.7 14.7 1.0
SG A:CYS53 4.8 15.0 1.0
CD2 A:LEU87 4.8 15.3 1.0
SG A:CYS88 4.9 13.2 1.0
CG2 A:VAL55 4.9 10.5 1.0
N A:CYS88 5.0 15.6 1.0

Iron binding site 3 out of 16 in 6sdv

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:14.0
occ:1.00
FE3 A:SF41103 0.0 14.0 1.0
SG A:CYS50 2.2 14.7 1.0
S2 A:SF41103 2.3 14.8 1.0
S1 A:SF41103 2.3 13.3 1.0
S4 A:SF41103 2.3 14.6 1.0
FE2 A:SF41103 2.7 14.5 1.0
FE4 A:SF41103 2.7 15.2 1.0
FE1 A:SF41103 2.8 14.8 1.0
CB A:CYS50 3.2 14.7 1.0
S3 A:SF41103 3.9 13.1 1.0
N A:GLY91 4.2 15.7 1.0
CA A:GLY91 4.2 14.4 1.0
CB A:TYR52 4.2 15.5 1.0
N A:CYS53 4.3 13.0 1.0
CA A:CYS50 4.6 15.4 1.0
SG A:CYS88 4.6 13.2 1.0
SG A:CYS57 4.6 14.8 1.0
CB A:CYS57 4.6 11.7 1.0
N A:TYR52 4.7 12.5 1.0
CA A:TYR52 4.9 15.2 1.0
CD2 A:TYR52 4.9 17.1 1.0
O A:CYS53 4.9 17.0 1.0
SG A:CYS53 4.9 15.0 1.0

Iron binding site 4 out of 16 in 6sdv

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:15.2
occ:1.00
FE4 A:SF41103 0.0 15.2 1.0
S1 A:SF41103 2.3 13.3 1.0
S2 A:SF41103 2.3 14.8 1.0
SG A:CYS88 2.3 13.2 1.0
S3 A:SF41103 2.3 13.1 1.0
FE3 A:SF41103 2.7 14.0 1.0
FE1 A:SF41103 2.7 14.8 1.0
FE2 A:SF41103 2.7 14.5 1.0
CB A:CYS88 3.3 14.1 1.0
N A:CYS88 3.9 15.6 1.0
S4 A:SF41103 3.9 14.6 1.0
CA A:CYS88 4.1 13.8 1.0
N A:GLY91 4.3 15.7 1.0
CD A:PRO234 4.3 12.9 1.0
O A:HOH1292 4.4 13.5 1.0
NZ A:LYS90 4.5 15.1 1.0
CG A:PRO234 4.6 14.0 1.0
CD1 A:ILE235 4.6 16.2 1.0
C A:CYS88 4.7 11.0 1.0
SG A:CYS53 4.8 15.0 1.0
SG A:CYS50 4.8 14.7 1.0
CA A:GLY91 4.9 14.4 1.0
O A:CYS88 4.9 13.0 1.0
SG A:CYS57 4.9 14.8 1.0
CB A:PRO234 4.9 14.1 1.0

Iron binding site 5 out of 16 in 6sdv

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:17.2
occ:1.00
FE1 B:SF4301 0.0 17.2 1.0
S4 B:SF4301 2.3 13.6 1.0
S3 B:SF4301 2.3 16.0 1.0
SG B:CYS157 2.3 15.6 1.0
S2 B:SF4301 2.4 15.8 1.0
FE2 B:SF4301 2.7 16.1 1.0
FE4 B:SF4301 2.7 16.6 1.0
FE3 B:SF4301 2.8 16.2 1.0
CB B:CYS157 3.4 11.6 1.0
CA B:CYS157 3.8 11.4 1.0
OG1 B:THR159 3.9 13.9 1.0
S1 B:SF4301 3.9 18.0 1.0
CD B:PRO158 4.1 16.5 1.0
CB B:THR161 4.1 19.2 1.0
CG B:MET162 4.3 15.1 1.0
OG1 B:THR161 4.4 17.6 1.0
N B:PRO158 4.5 16.5 1.0
C B:CYS157 4.5 15.6 1.0
SG B:CYS15 4.6 16.4 1.0
CG2 B:THR161 4.7 16.7 1.0
SG B:CYS18 4.9 17.0 1.0
SG B:CYS12 4.9 18.0 1.0
N B:THR159 5.0 16.1 1.0
N B:MET162 5.0 14.5 1.0

Iron binding site 6 out of 16 in 6sdv

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:16.1
occ:1.00
FE2 B:SF4301 0.0 16.1 1.0
S4 B:SF4301 2.3 13.6 1.0
S1 B:SF4301 2.3 18.0 1.0
S3 B:SF4301 2.3 16.0 1.0
SG B:CYS18 2.3 17.0 1.0
FE1 B:SF4301 2.7 17.2 1.0
FE3 B:SF4301 2.7 16.2 1.0
FE4 B:SF4301 2.8 16.6 1.0
CB B:CYS18 3.3 13.2 1.0
N B:CYS18 3.9 14.1 1.0
O B:HOH417 3.9 18.6 1.0
S2 B:SF4301 3.9 15.8 1.0
CA B:CYS18 4.2 13.6 1.0
CG B:PRO71 4.4 16.7 1.0
SG B:CYS15 4.6 16.4 1.0
N B:GLY17 4.7 13.0 1.0
N B:ARG16 4.7 14.5 1.0
CA B:ARG16 4.8 14.1 1.0
SG B:CYS12 4.8 18.0 1.0
CB B:PRO71 4.8 13.3 1.0
SG B:CYS157 4.8 15.6 1.0
CG2 B:VAL53 4.9 13.9 1.0
C B:ARG16 5.0 13.2 1.0

Iron binding site 7 out of 16 in 6sdv

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:16.2
occ:1.00
FE3 B:SF4301 0.0 16.2 1.0
SG B:CYS15 2.2 16.4 1.0
S1 B:SF4301 2.3 18.0 1.0
S2 B:SF4301 2.3 15.8 1.0
S4 B:SF4301 2.3 13.6 1.0
FE2 B:SF4301 2.7 16.1 1.0
FE1 B:SF4301 2.8 17.2 1.0
FE4 B:SF4301 2.8 16.6 1.0
N B:CYS15 3.5 14.8 1.0
CB B:CYS15 3.5 15.8 1.0
N B:ARG16 3.6 14.5 1.0
CA B:CYS15 3.9 16.2 1.0
S3 B:SF4301 3.9 16.0 1.0
N B:GLY17 4.1 13.0 1.0
CD B:PRO158 4.1 16.5 1.0
C B:CYS15 4.1 16.1 1.0
OG1 B:THR13 4.4 14.4 1.0
C B:ALA14 4.4 14.6 1.0
N B:ALA14 4.5 20.0 1.0
CA B:ARG16 4.5 14.1 1.0
SG B:CYS18 4.6 17.0 1.0
CA B:ALA14 4.7 16.5 1.0
CG B:PRO158 4.7 19.2 1.0
SG B:CYS12 4.8 18.0 1.0
C B:ARG16 4.8 13.2 1.0
N B:CYS18 4.8 14.1 1.0
SG B:CYS157 4.8 15.6 1.0
CA B:GLY17 4.9 15.8 1.0

Iron binding site 8 out of 16 in 6sdv

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Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:16.6
occ:1.00
FE4 B:SF4301 0.0 16.6 1.0
S2 B:SF4301 2.3 15.8 1.0
SG B:CYS12 2.3 18.0 1.0
S3 B:SF4301 2.3 16.0 1.0
S1 B:SF4301 2.3 18.0 1.0
FE1 B:SF4301 2.7 17.2 1.0
FE3 B:SF4301 2.8 16.2 1.0
FE2 B:SF4301 2.8 16.1 1.0
CB B:CYS12 3.5 18.3 1.0
CA B:CYS12 3.8 14.2 1.0
S4 B:SF4301 3.9 13.6 1.0
N B:ALA14 3.9 20.0 1.0
N B:THR13 4.1 17.6 1.0
OG1 B:THR161 4.3 17.6 1.0
CG B:PRO71 4.4 16.7 1.0
C B:CYS12 4.4 15.0 1.0
CA B:ALA14 4.4 16.5 1.0
CB B:THR161 4.5 19.2 1.0
CG2 B:THR161 4.5 16.7 1.0
N B:CYS15 4.7 14.8 1.0
OG1 B:THR159 4.8 13.9 1.0
SG B:CYS157 4.8 15.6 1.0
SG B:CYS18 4.9 17.0 1.0
C B:THR13 4.9 19.0 1.0
SG B:CYS15 5.0 16.4 1.0

Iron binding site 9 out of 16 in 6sdv

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:23.4
occ:1.00
FE1 B:SF4302 0.0 23.4 1.0
S4 B:SF4302 2.3 23.7 1.0
S3 B:SF4302 2.3 24.4 1.0
S2 B:SF4302 2.3 23.2 1.0
SG B:CYS77 2.3 26.5 1.0
FE4 B:SF4302 2.7 23.9 1.0
FE2 B:SF4302 2.7 23.0 1.0
FE3 B:SF4302 2.8 21.3 1.0
CB B:CYS77 3.4 26.5 1.0
N B:CYS77 3.8 18.9 1.0
S1 B:SF4302 3.9 21.8 1.0
CA B:CYS77 4.2 23.8 1.0
N B:HIS76 4.5 23.0 1.0
CD2 B:TYR123 4.5 25.2 1.0
SG B:CYS74 4.6 20.0 1.0
SG B:CYS121 4.6 23.8 1.0
CB B:PRO80 4.6 29.0 1.0
CD B:PRO81 4.6 25.3 1.0
CA B:PRO80 4.7 25.9 1.0
N B:ARG75 4.8 21.5 1.0
SG B:CYS82 4.8 23.4 1.0
CB B:ARG75 4.8 21.0 1.0
CE2 B:TYR123 4.8 24.5 1.0
C B:HIS76 4.9 20.3 1.0
CA B:HIS76 4.9 20.5 1.0

Iron binding site 10 out of 16 in 6sdv

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Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Formate Reduced Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:23.0
occ:1.00
FE2 B:SF4302 0.0 23.0 1.0
S4 B:SF4302 2.2 23.7 1.0
S3 B:SF4302 2.3 24.4 1.0
SG B:CYS82 2.3 23.4 1.0
S1 B:SF4302 2.3 21.8 1.0
FE1 B:SF4302 2.7 23.4 1.0
FE4 B:SF4302 2.7 23.9 1.0
FE3 B:SF4302 2.7 21.3 1.0
CB B:CYS82 3.1 26.0 1.0
S2 B:SF4302 3.9 23.2 1.0
N B:CYS82 4.1 23.8 1.0
CB B:PRO80 4.2 29.0 1.0
CA B:CYS82 4.2 28.9 1.0
CG1 B:VAL103 4.6 20.5 1.0
SG B:CYS74 4.6 20.0 1.0
CE B:LYS137 4.8 21.3 1.0
SG B:CYS77 4.8 26.5 1.0
CA B:PRO80 4.8 25.9 1.0
SG B:CYS121 4.8 23.8 1.0
CD B:LYS137 5.0 21.1 1.0

Reference:

A.R.Oliveira, C.Mota, C.Mourato, R.M.Domingos, M.F.A.Santos, D.Gesto, B.Guigliarelli, T.Santos-Silva, M.J.Romao, I.C.Pereira. Towards the Mechanistic Understanding of Enzymatic CO2 Reduction Acs Catalysis 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C00086
Page generated: Sun Dec 13 17:05:48 2020

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