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Iron in PDB 8cm7: W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris

Protein crystallography data

The structure of W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris, PDB code: 8cm7 was solved by G.Vilela-Alves, C.Mota, A.R.Oliveira, R.R.Manuel, I.C.Pereira, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.06 / 2.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.874, 123.833, 149.891, 90, 90, 90
R / Rfree (%) 19.7 / 25.2

Other elements in 8cm7:

The structure of W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
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 M405A From Desulfovibrio Vulgaris (pdb code 8cm7). 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 M405A From Desulfovibrio Vulgaris, PDB code: 8cm7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8cm7

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:26.9
occ:1.00
 FE1 A:SF41103 0.0 26.9 1.0
SG A:CYS53 2.2 26.3 1.0
S3 A:SF41103 2.2 24.5 1.0
S4 A:SF41103 2.3 26.7 1.0
S2 A:SF41103 2.3 22.1 1.0
FE4 A:SF41103 2.7 23.2 1.0
FE2 A:SF41103 2.7 25.1 1.0
FE3 A:SF41103 2.8 25.3 1.0
CB A:CYS53 3.3 25.4 1.0
N A:CYS53 3.8 26.1 1.0
CA A:CYS53 3.9 25.4 1.0
S1 A:SF41103 3.9 25.7 1.0
O A:CYS53 4.0 29.3 1.0
C A:CYS53 4.1 26.5 1.0
CB A:VAL55 4.2 17.2 1.0
CG2 A:VAL55 4.4 16.6 1.0
N A:VAL55 4.6 19.2 1.0
CD A:PRO234 4.6 21.3 1.0
SG A:CYS57 4.7 20.7 1.0
SG A:CYS88 4.7 25.4 1.0
SG A:CYS50 4.8 26.6 1.0
N A:ALA54 4.9 25.6 1.0

Iron binding site 2 out of 16 in 8cm7

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:25.1
occ:1.00
 FE2 A:SF41103 0.0 25.1 1.0
S1 A:SF41103 2.2 25.7 1.0
SG A:CYS57 2.2 20.7 1.0
S4 A:SF41103 2.3 26.7 1.0
S3 A:SF41103 2.3 24.5 1.0
FE3 A:SF41103 2.6 25.3 1.0
FE1 A:SF41103 2.7 26.9 1.0
FE4 A:SF41103 2.8 23.2 1.0
CB A:CYS57 3.1 21.4 1.0
S2 A:SF41103 3.8 22.1 1.0
CD1 A:ILE235 4.1 24.0 1.0
N A:CYS57 4.3 21.1 1.0
CA A:CYS57 4.3 22.3 1.0
CB A:ILE235 4.4 24.5 1.0
CB A:VAL55 4.4 17.2 1.0
CG1 A:ILE235 4.5 23.2 1.0
SG A:CYS50 4.6 26.6 1.0
CG1 A:VAL55 4.6 16.4 1.0
CB A:CYS50 4.6 24.7 1.0
SG A:CYS53 4.7 26.3 1.0
SG A:CYS88 4.9 25.4 1.0
CD2 A:LEU87 5.0 27.9 1.0

Iron binding site 3 out of 16 in 8cm7

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:25.3
occ:1.00
 FE3 A:SF41103 0.0 25.3 1.0
S2 A:SF41103 2.3 22.1 1.0
SG A:CYS50 2.3 26.6 1.0
S1 A:SF41103 2.3 25.7 1.0
S4 A:SF41103 2.3 26.7 1.0
FE2 A:SF41103 2.6 25.1 1.0
FE4 A:SF41103 2.7 23.2 1.0
FE1 A:SF41103 2.8 26.9 1.0
CB A:CYS50 3.2 24.7 1.0
S3 A:SF41103 3.8 24.5 1.0
N A:GLY91 4.2 24.5 1.0
CA A:GLY91 4.2 24.5 1.0
CB A:TYR52 4.3 30.8 1.0
N A:CYS53 4.4 26.1 1.0
CB A:CYS57 4.5 21.4 1.0
SG A:CYS57 4.5 20.7 1.0
SG A:CYS88 4.6 25.4 1.0
CA A:CYS50 4.6 25.2 1.0
SG A:CYS53 4.8 26.3 1.0
N A:TYR52 4.9 28.1 1.0
O A:CYS53 4.9 29.3 1.0
CA A:TYR52 5.0 29.7 1.0

Iron binding site 4 out of 16 in 8cm7

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:23.2
occ:1.00
 FE4 A:SF41103 0.0 23.2 1.0
SG A:CYS88 2.2 25.4 1.0
S1 A:SF41103 2.3 25.7 1.0
S2 A:SF41103 2.3 22.1 1.0
S3 A:SF41103 2.3 24.5 1.0
FE3 A:SF41103 2.7 25.3 1.0
FE1 A:SF41103 2.7 26.9 1.0
FE2 A:SF41103 2.8 25.1 1.0
CB A:CYS88 3.2 25.2 1.0
S4 A:SF41103 3.9 26.7 1.0
N A:CYS88 4.0 25.9 1.0
CA A:CYS88 4.1 27.0 1.0
N A:GLY91 4.4 24.5 1.0
CD A:PRO234 4.4 21.3 1.0
NZ A:LYS90 4.4 25.7 1.0
CG A:PRO234 4.5 20.2 1.0
CD1 A:ILE235 4.6 24.0 1.0
C A:CYS88 4.6 26.7 1.0
SG A:CYS53 4.7 26.3 1.0
O A:CYS88 4.7 27.5 1.0
CB A:LYS90 4.8 23.9 1.0
CB A:PRO234 4.8 20.6 1.0
SG A:CYS50 4.8 26.6 1.0
SG A:CYS57 4.9 20.7 1.0
CE A:LYS90 4.9 23.9 1.0
CA A:GLY91 5.0 24.5 1.0

Iron binding site 5 out of 16 in 8cm7

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:29.0
occ:1.00
 FE1 B:SF4301 0.0 29.0 1.0
SG B:CYS157 2.2 23.3 1.0
S4 B:SF4301 2.2 26.9 1.0
S3 B:SF4301 2.3 27.8 1.0
S2 B:SF4301 2.3 26.7 1.0
FE2 B:SF4301 2.7 25.5 1.0
FE3 B:SF4301 2.7 25.5 1.0
FE4 B:SF4301 2.8 27.5 1.0
CB B:CYS157 3.0 24.7 1.0
CA B:CYS157 3.6 24.5 1.0
S1 B:SF4301 3.9 26.4 1.0
OG1 B:THR159 4.0 26.4 1.0
CD B:PRO158 4.1 26.8 1.0
CG B:MET162 4.2 30.5 1.0
CB B:THR161 4.3 26.4 1.0
C B:CYS157 4.4 24.1 1.0
N B:PRO158 4.5 25.6 1.0
SG B:CYS15 4.6 25.1 1.0
OG1 B:THR161 4.7 20.5 1.0
SG B:CYS18 4.7 27.2 1.0
CG2 B:THR161 4.7 25.7 1.0
N B:CYS157 4.8 27.7 1.0
N B:MET162 5.0 29.8 1.0
SG B:CYS12 5.0 28.3 1.0

Iron binding site 6 out of 16 in 8cm7

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:25.5
occ:1.00
 FE2 B:SF4301 0.0 25.5 1.0
SG B:CYS18 2.2 27.2 1.0
S4 B:SF4301 2.3 26.9 1.0
S3 B:SF4301 2.3 27.8 1.0
S1 B:SF4301 2.3 26.4 1.0
FE1 B:SF4301 2.7 29.0 1.0
FE3 B:SF4301 2.7 25.5 1.0
FE4 B:SF4301 2.7 27.5 1.0
CB B:CYS18 3.3 28.9 1.0
S2 B:SF4301 3.9 26.7 1.0
N B:CYS18 3.9 25.0 1.0
CA B:CYS18 4.2 26.5 1.0
N B:GLY17 4.6 27.9 1.0
N B:ARG16 4.6 24.6 1.0
CG B:PRO71 4.7 35.3 1.0
SG B:CYS15 4.7 25.1 1.0
CA B:ARG16 4.7 25.2 1.0
SG B:CYS12 4.7 28.3 1.0
SG B:CYS157 4.7 23.3 1.0
CB B:PRO71 4.8 31.4 1.0
CE B:MET162 4.9 34.4 1.0
C B:ARG16 4.9 25.7 1.0
CG2 B:VAL53 4.9 32.3 1.0
C B:GLY17 5.0 24.4 1.0

Iron binding site 7 out of 16 in 8cm7

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:25.5
occ:1.00
 FE3 B:SF4301 0.0 25.5 1.0
S2 B:SF4301 2.3 26.7 1.0
S1 B:SF4301 2.3 26.4 1.0
S4 B:SF4301 2.3 26.9 1.0
SG B:CYS15 2.4 25.1 1.0
FE2 B:SF4301 2.7 25.5 1.0
FE1 B:SF4301 2.7 29.0 1.0
FE4 B:SF4301 2.7 27.5 1.0
CB B:CYS15 3.5 23.9 1.0
N B:CYS15 3.6 26.1 1.0
N B:ARG16 3.6 24.6 1.0
S3 B:SF4301 3.8 27.8 1.0
CA B:CYS15 3.9 25.4 1.0
N B:GLY17 4.1 27.9 1.0
C B:CYS15 4.2 26.0 1.0
OG1 B:THR13 4.3 25.7 1.0
CD B:PRO158 4.4 26.8 1.0
CA B:ARG16 4.5 25.2 1.0
C B:ALA14 4.5 27.1 1.0
SG B:CYS18 4.6 27.2 1.0
N B:ALA14 4.6 22.8 1.0
SG B:CYS157 4.6 23.3 1.0
SG B:CYS12 4.6 28.3 1.0
C B:ARG16 4.8 25.7 1.0
CA B:ALA14 4.8 23.4 1.0
N B:THR13 4.8 21.9 1.0
CA B:GLY17 4.9 25.0 1.0
N B:CYS18 5.0 25.0 1.0

Iron binding site 8 out of 16 in 8cm7

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Iron binding site 8 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:27.5
occ:1.00
 FE4 B:SF4301 0.0 27.5 1.0
S1 B:SF4301 2.2 26.4 1.0
S3 B:SF4301 2.3 27.8 1.0
SG B:CYS12 2.3 28.3 1.0
S2 B:SF4301 2.3 26.7 1.0
FE2 B:SF4301 2.7 25.5 1.0
FE3 B:SF4301 2.7 25.5 1.0
FE1 B:SF4301 2.8 29.0 1.0
CB B:CYS12 3.4 23.9 1.0
CA B:CYS12 3.7 24.6 1.0
S4 B:SF4301 3.9 26.9 1.0
N B:THR13 4.1 21.9 1.0
N B:ALA14 4.2 22.8 1.0
C B:CYS12 4.4 22.5 1.0
CG2 B:THR161 4.5 25.7 1.0
CG B:PRO71 4.5 35.3 1.0
OG1 B:THR161 4.5 20.5 1.0
CA B:ALA14 4.6 23.4 1.0
CB B:THR161 4.6 26.4 1.0
SG B:CYS157 4.6 23.3 1.0
SG B:CYS18 4.7 27.2 1.0
N B:CYS15 4.8 26.1 1.0
OG1 B:THR159 4.8 26.4 1.0

Iron binding site 9 out of 16 in 8cm7

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:37.2
occ:1.00
 FE1 B:SF4302 0.0 37.2 1.0
SG B:CYS77 2.2 36.3 1.0
S2 B:SF4302 2.2 43.8 1.0
S3 B:SF4302 2.2 45.0 1.0
S4 B:SF4302 2.3 44.0 1.0
FE4 B:SF4302 2.6 36.7 1.0
FE2 B:SF4302 2.6 38.4 1.0
FE3 B:SF4302 2.8 36.5 1.0
CB B:CYS77 3.6 39.9 1.0
S1 B:SF4302 3.9 38.1 1.0
N B:CYS77 3.9 40.0 1.0
CD2 B:TYR123 4.4 39.6 1.0
CA B:CYS77 4.4 41.6 1.0
N B:HIS76 4.6 32.3 1.0
CD B:PRO81 4.6 42.8 1.0
N B:ARG75 4.7 28.6 1.0
SG B:CYS74 4.7 33.7 1.0
CE2 B:TYR123 4.8 42.6 1.0
SG B:CYS82 4.8 36.2 1.0
SG B:CYS121 4.9 41.4 1.0
CB B:ARG75 4.9 31.9 1.0
C B:HIS76 5.0 36.4 1.0

Iron binding site 10 out of 16 in 8cm7

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Iron binding site 10 out of 16 in the W-Formate Dehydrogenase M405A From Desulfovibrio Vulgaris


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 M405A From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:38.4
occ:1.00
 FE2 B:SF4302 0.0 38.4 1.0
S4 B:SF4302 2.2 44.0 1.0
S3 B:SF4302 2.3 45.0 1.0
S1 B:SF4302 2.3 38.1 1.0
SG B:CYS82 2.3 36.2 1.0
FE1 B:SF4302 2.6 37.2 1.0
FE3 B:SF4302 2.7 36.5 1.0
FE4 B:SF4302 2.7 36.7 1.0
CB B:CYS82 3.4 41.4 1.0
S2 B:SF4302 3.8 43.8 1.0
N B:CYS82 4.2 43.6 1.0
CA B:CYS82 4.4 42.3 1.0
CG1 B:VAL103 4.4 35.0 1.0
SG B:CYS77 4.5 36.3 1.0
SG B:CYS74 4.7 33.7 1.0
CB B:PRO80 4.8 51.7 1.0
CA B:PRO80 4.9 48.4 1.0
SG B:CYS121 4.9 41.4 1.0
CE B:LYS137 5.0 34.5 1.0
CE1 B:PHE105 5.0 44.5 1.0

Reference:

A.R.Oliveira, C.Mota, R.R.Manuel, G.Vilela-Alves, N.Pedrosa, V.Fourmond, K.Klymanska, C.Leger, B.Guigliarelli, M.J.Romao, I.C.Pereira. W-Formate Dehydrogenase C872A From Desulfovibrio Vulgaris - with Formamide Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
Page generated: Fri Aug 9 21:50:25 2024

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