Iron in PDB 6sdr: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form

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

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

Protein crystallography data

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized Form, PDB code: 6sdr 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) 48.36 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.593, 127.644, 148.213, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.6

Other elements in 6sdr:

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form (pdb code 6sdr). 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 - Oxidized Form, PDB code: 6sdr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 6sdr

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:16.9
occ:1.00
FE1 A:SF41103 0.0 16.9 1.0
S3 A:SF41103 2.2 14.3 1.0
S4 A:SF41103 2.3 18.3 1.0
S2 A:SF41103 2.3 17.7 1.0
SG A:CYS53 2.4 18.7 1.0
FE4 A:SF41103 2.7 16.9 1.0
FE2 A:SF41103 2.7 18.4 1.0
FE3 A:SF41103 2.7 18.9 1.0
CB A:CYS53 3.5 14.4 1.0
N A:CYS53 3.7 16.9 1.0
CB A:VAL55 3.8 24.2 1.0
S1 A:SF41103 3.8 20.9 1.0
CA A:CYS53 3.9 15.1 1.0
O A:HOH1357 4.0 15.1 1.0
O A:CYS53 4.0 16.9 1.0
CG2 A:VAL55 4.1 20.4 1.0
C A:CYS53 4.1 20.0 1.0
N A:VAL55 4.4 20.2 1.0
CD A:PRO234 4.5 17.1 1.0
CA A:VAL55 4.7 16.7 1.0
SG A:CYS50 4.7 17.0 1.0
SG A:CYS88 4.8 15.7 1.0
SG A:CYS57 4.8 18.0 1.0
CG1 A:VAL55 4.8 19.2 1.0
C A:TYR52 4.9 27.6 1.0
N A:ALA54 4.9 18.7 1.0

Iron binding site 2 out of 16 in 6sdr

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:18.4
occ:1.00
FE2 A:SF41103 0.0 18.4 1.0
SG A:CYS57 2.3 18.0 1.0
S4 A:SF41103 2.3 18.3 1.0
S1 A:SF41103 2.3 20.9 1.0
S3 A:SF41103 2.3 14.3 1.0
FE3 A:SF41103 2.7 18.9 1.0
FE1 A:SF41103 2.7 16.9 1.0
FE4 A:SF41103 2.8 16.9 1.0
CB A:CYS57 3.2 18.4 1.0
CD1 A:ILE235 3.8 24.3 1.0
S2 A:SF41103 3.9 17.7 1.0
CB A:VAL55 4.0 24.2 1.0
CG1 A:VAL55 4.0 19.2 1.0
N A:CYS57 4.2 18.3 1.0
CG1 A:ILE235 4.3 15.8 1.0
CA A:CYS57 4.3 21.4 1.0
CB A:ILE235 4.3 14.2 1.0
SG A:CYS50 4.6 17.0 1.0
CB A:CYS50 4.7 18.0 1.0
CG2 A:VAL55 4.7 20.4 1.0
SG A:CYS53 4.8 18.7 1.0
CD2 A:LEU87 4.9 19.5 1.0
N A:GLY56 5.0 14.9 1.0

Iron binding site 3 out of 16 in 6sdr

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:18.9
occ:1.00
FE3 A:SF41103 0.0 18.9 1.0
S1 A:SF41103 2.2 20.9 1.0
SG A:CYS50 2.2 17.0 1.0
S4 A:SF41103 2.3 18.3 1.0
S2 A:SF41103 2.3 17.7 1.0
FE2 A:SF41103 2.7 18.4 1.0
FE4 A:SF41103 2.7 16.9 1.0
FE1 A:SF41103 2.7 16.9 1.0
CB A:CYS50 3.2 18.0 1.0
S3 A:SF41103 3.9 14.3 1.0
CB A:TYR52 4.2 16.9 1.0
CA A:GLY91 4.2 29.8 1.0
N A:GLY91 4.3 25.0 1.0
N A:CYS53 4.3 16.9 1.0
SG A:CYS88 4.6 15.7 1.0
SG A:CYS57 4.6 18.0 1.0
CA A:CYS50 4.6 18.9 1.0
CB A:CYS57 4.7 18.4 1.0
N A:TYR52 4.7 17.5 1.0
CD2 A:TYR52 4.8 23.4 1.0
CA A:TYR52 4.8 17.0 1.0
SG A:CYS53 4.9 18.7 1.0
C A:TYR52 5.0 27.6 1.0
O A:CYS53 5.0 16.9 1.0

Iron binding site 4 out of 16 in 6sdr

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:16.9
occ:1.00
FE4 A:SF41103 0.0 16.9 1.0
S1 A:SF41103 2.3 20.9 1.0
S2 A:SF41103 2.3 17.7 1.0
S3 A:SF41103 2.3 14.3 1.0
SG A:CYS88 2.3 15.7 1.0
FE1 A:SF41103 2.7 16.9 1.0
FE3 A:SF41103 2.7 18.9 1.0
FE2 A:SF41103 2.8 18.4 1.0
CB A:CYS88 3.3 18.3 1.0
S4 A:SF41103 3.9 18.3 1.0
N A:CYS88 3.9 19.6 1.0
CA A:CYS88 4.1 20.9 1.0
CD1 A:ILE235 4.2 24.3 1.0
CD A:PRO234 4.2 17.1 1.0
NZ A:LYS90 4.4 15.8 1.0
N A:GLY91 4.4 25.0 1.0
CG A:PRO234 4.5 20.6 1.0
O A:HOH1357 4.5 15.1 1.0
C A:CYS88 4.7 22.5 1.0
SG A:CYS53 4.8 18.7 1.0
SG A:CYS50 4.8 17.0 1.0
O A:CYS88 4.8 18.7 1.0
CB A:PRO234 4.9 16.0 1.0
SG A:CYS57 4.9 18.0 1.0
CA A:GLY91 4.9 29.8 1.0
CE A:LYS90 5.0 20.2 1.0

Iron binding site 5 out of 16 in 6sdr

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:19.7
occ:1.00
FE1 B:SF4301 0.0 19.7 1.0
S3 B:SF4301 2.3 24.3 1.0
S4 B:SF4301 2.3 24.4 1.0
S2 B:SF4301 2.3 23.0 1.0
SG B:CYS157 2.3 25.5 1.0
FE2 B:SF4301 2.7 21.5 1.0
FE4 B:SF4301 2.7 22.2 1.0
FE3 B:SF4301 2.8 22.1 1.0
CB B:CYS157 3.3 22.0 1.0
OG1 B:THR159 3.8 16.9 1.0
CA B:CYS157 3.8 18.3 1.0
S1 B:SF4301 3.9 18.6 1.0
CB B:THR161 4.0 22.7 1.0
CG B:MET162 4.3 25.4 1.0
CD B:PRO158 4.3 16.1 1.0
OG1 B:THR161 4.4 26.1 1.0
CG2 B:THR161 4.5 19.8 1.0
C B:CYS157 4.6 22.5 1.0
SG B:CYS15 4.6 19.8 1.0
N B:PRO158 4.7 18.1 1.0
SG B:CYS18 4.8 28.4 1.0
SG B:CYS12 4.9 21.5 1.0
N B:THR159 5.0 20.5 1.0

Iron binding site 6 out of 16 in 6sdr

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:21.5
occ:1.00
FE2 B:SF4301 0.0 21.5 1.0
S4 B:SF4301 2.3 24.4 1.0
SG B:CYS18 2.3 28.4 1.0
S3 B:SF4301 2.3 24.3 1.0
S1 B:SF4301 2.3 18.6 1.0
FE1 B:SF4301 2.7 19.7 1.0
FE3 B:SF4301 2.7 22.1 1.0
FE4 B:SF4301 2.7 22.2 1.0
CB B:CYS18 3.2 20.1 1.0
O B:HOH444 3.8 21.1 1.0
N B:CYS18 3.8 20.9 1.0
S2 B:SF4301 3.9 23.0 1.0
CA B:CYS18 4.2 20.0 1.0
CG B:PRO71 4.4 24.9 1.0
N B:ARG16 4.5 21.5 1.0
SG B:CYS15 4.6 19.8 1.0
N B:GLY17 4.7 18.1 1.0
CA B:ARG16 4.7 25.3 1.0
SG B:CYS12 4.7 21.5 1.0
SG B:CYS157 4.8 25.5 1.0
CB B:PRO71 4.8 24.2 1.0
CG2 B:VAL53 4.9 31.3 1.0
C B:ARG16 5.0 25.5 1.0
C B:GLY17 5.0 25.5 1.0

Iron binding site 7 out of 16 in 6sdr

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:22.1
occ:1.00
FE3 B:SF4301 0.0 22.1 1.0
S1 B:SF4301 2.3 18.6 1.0
S2 B:SF4301 2.3 23.0 1.0
S4 B:SF4301 2.3 24.4 1.0
SG B:CYS15 2.3 19.8 1.0
FE2 B:SF4301 2.7 21.5 1.0
FE4 B:SF4301 2.7 22.2 1.0
FE1 B:SF4301 2.8 19.7 1.0
N B:CYS15 3.4 27.4 1.0
CB B:CYS15 3.4 23.1 1.0
N B:ARG16 3.6 21.5 1.0
CA B:CYS15 3.8 16.7 1.0
S3 B:SF4301 3.9 24.3 1.0
C B:CYS15 4.0 20.1 1.0
N B:GLY17 4.2 18.1 1.0
C B:ALA14 4.4 27.1 1.0
CD B:PRO158 4.4 16.1 1.0
OG1 B:THR13 4.5 23.0 1.0
CA B:ARG16 4.5 25.3 1.0
N B:ALA14 4.5 17.5 1.0
SG B:CYS12 4.7 21.5 1.0
SG B:CYS18 4.7 28.4 1.0
CA B:ALA14 4.8 22.6 1.0
SG B:CYS157 4.8 25.5 1.0
N B:CYS18 4.9 20.9 1.0
C B:ARG16 4.9 25.5 1.0
N B:THR13 5.0 20.5 1.0

Iron binding site 8 out of 16 in 6sdr

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Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:22.2
occ:1.00
FE4 B:SF4301 0.0 22.2 1.0
S2 B:SF4301 2.3 23.0 1.0
SG B:CYS12 2.3 21.5 1.0
S3 B:SF4301 2.3 24.3 1.0
S1 B:SF4301 2.3 18.6 1.0
FE1 B:SF4301 2.7 19.7 1.0
FE3 B:SF4301 2.7 22.1 1.0
FE2 B:SF4301 2.7 21.5 1.0
CB B:CYS12 3.4 21.7 1.0
CA B:CYS12 3.8 19.1 1.0
S4 B:SF4301 3.9 24.4 1.0
N B:ALA14 4.0 17.5 1.0
N B:THR13 4.1 20.5 1.0
C B:CYS12 4.4 20.1 1.0
CG B:PRO71 4.4 24.9 1.0
OG1 B:THR161 4.4 26.1 1.0
CA B:ALA14 4.5 22.6 1.0
CG2 B:THR161 4.5 19.8 1.0
N B:CYS15 4.5 27.4 1.0
CB B:THR161 4.6 22.7 1.0
SG B:CYS18 4.8 28.4 1.0
OG1 B:THR159 4.8 16.9 1.0
SG B:CYS157 4.9 25.5 1.0
C B:THR13 5.0 19.4 1.0
C B:ALA14 5.0 27.1 1.0

Iron binding site 9 out of 16 in 6sdr

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:41.3
occ:1.00
FE1 B:SF4302 0.0 41.3 1.0
S3 B:SF4302 2.3 39.9 1.0
S2 B:SF4302 2.3 41.8 1.0
S4 B:SF4302 2.3 37.0 1.0
SG B:CYS77 2.4 47.0 1.0
FE4 B:SF4302 2.7 41.0 1.0
FE2 B:SF4302 2.8 40.7 1.0
FE3 B:SF4302 2.8 40.5 1.0
CB B:CYS77 3.6 45.5 1.0
N B:CYS77 3.7 42.0 1.0
S1 B:SF4302 3.9 45.6 1.0
CA B:CYS77 4.2 45.0 1.0
N B:HIS76 4.3 33.9 1.0
CB B:PRO80 4.5 48.9 1.0
CD2 B:TYR123 4.6 44.1 1.0
SG B:CYS74 4.6 36.7 1.0
SG B:CYS121 4.7 40.6 1.0
CA B:HIS76 4.7 34.9 1.0
C B:HIS76 4.7 38.6 1.0
CB B:ARG75 4.7 32.7 1.0
CD B:PRO81 4.7 43.5 1.0
CA B:PRO80 4.7 45.5 1.0
N B:ARG75 4.7 37.6 1.0
SG B:CYS82 4.8 43.1 1.0
CE2 B:TYR123 4.9 42.2 1.0
C B:ARG75 4.9 40.5 1.0

Iron binding site 10 out of 16 in 6sdr

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Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Oxidized 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 - Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:40.7
occ:1.00
FE2 B:SF4302 0.0 40.7 1.0
S1 B:SF4302 2.3 45.6 1.0
S3 B:SF4302 2.3 39.9 1.0
S4 B:SF4302 2.3 37.0 1.0
SG B:CYS82 2.3 43.1 1.0
FE4 B:SF4302 2.7 41.0 1.0
FE3 B:SF4302 2.7 40.5 1.0
FE1 B:SF4302 2.8 41.3 1.0
CB B:CYS82 3.1 42.8 1.0
S2 B:SF4302 3.9 41.8 1.0
CB B:PRO80 4.2 48.9 1.0
N B:CYS82 4.2 52.5 1.0
CA B:CYS82 4.2 53.8 1.0
CG1 B:VAL103 4.5 42.3 1.0
CE B:LYS137 4.7 40.5 1.0
SG B:CYS74 4.7 36.7 1.0
CB B:CYS121 4.8 43.8 1.0
SG B:CYS121 4.8 40.6 1.0
CA B:PRO80 4.8 45.5 1.0
SG B:CYS77 4.9 47.0 1.0
CD B:LYS137 5.0 49.8 1.0
CZ B:PHE105 5.0 47.4 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 17:05:47 2020

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