Iron in PDB 8rcg: W-Formate Dehydrogenase M405S From Desulfovibrio Vulgaris

Protein crystallography data

The structure of W-Formate Dehydrogenase M405S From Desulfovibrio Vulgaris, PDB code: 8rcg was solved by G.Vilela-Alves, R.R.Manuel, I.C.Pereira, M.J.Romao, C.Mota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.59 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.341, 127.226, 148.266, 90, 90, 90
R / Rfree (%) 21.2 / 25.3

Other elements in 8rcg:

The structure of W-Formate Dehydrogenase M405S From Desulfovibrio Vulgaris 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 M405S From Desulfovibrio Vulgaris (pdb code 8rcg). 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 M405S From Desulfovibrio Vulgaris, PDB code: 8rcg:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 8rcg

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Iron binding site 1 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:23.4
occ:1.00
 FE1 A:SF41103 0.0 23.4 1.0
S2 A:SF41103 2.3 24.6 1.0
S4 A:SF41103 2.3 24.4 1.0
S3 A:SF41103 2.3 21.6 1.0
SG A:CYS53 2.3 23.1 1.0
FE3 A:SF41103 2.7 24.0 1.0
FE4 A:SF41103 2.8 23.2 1.0
FE2 A:SF41103 2.8 23.7 1.0
CB A:CYS53 3.4 23.9 1.0
N A:CYS53 3.7 26.2 1.0
CA A:CYS53 3.8 24.4 1.0
O A:CYS53 3.9 22.8 1.0
O A:HOH1326 3.9 28.9 1.0
S1 A:SF41103 3.9 24.2 1.0
C A:CYS53 4.1 23.3 1.0
CB A:VAL55 4.1 21.4 1.0
CG2 A:VAL55 4.3 22.0 1.0
CD A:PRO234 4.5 21.9 1.0
SG A:CYS88 4.6 22.4 1.0
N A:VAL55 4.6 21.8 1.0
SG A:CYS57 4.6 25.1 1.0
SG A:CYS50 4.7 25.5 1.0
C A:TYR52 4.9 26.5 1.0
CA A:VAL55 4.9 22.5 1.0
N A:ALA54 5.0 21.6 1.0

Iron binding site 2 out of 16 in 8rcg

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Iron binding site 2 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:23.7
occ:1.00
 FE2 A:SF41103 0.0 23.7 1.0
SG A:CYS57 2.1 25.1 1.0
S1 A:SF41103 2.3 24.2 1.0
S3 A:SF41103 2.3 21.6 1.0
S4 A:SF41103 2.3 24.4 1.0
FE3 A:SF41103 2.6 24.0 1.0
FE4 A:SF41103 2.7 23.2 1.0
FE1 A:SF41103 2.8 23.4 1.0
CB A:CYS57 3.1 24.2 1.0
S2 A:SF41103 3.9 24.6 1.0
CD1 A:ILE235 4.0 22.0 1.0
N A:CYS57 4.2 22.9 1.0
CG1 A:ILE235 4.3 21.7 1.0
CA A:CYS57 4.3 24.5 1.0
CB A:VAL55 4.3 21.4 1.0
CB A:ILE235 4.4 22.3 1.0
CG1 A:VAL55 4.5 22.2 1.0
CB A:CYS50 4.6 24.2 1.0
SG A:CYS50 4.6 25.5 1.0
CD2 A:LEU87 4.7 22.6 1.0
SG A:CYS88 4.8 22.4 1.0
SG A:CYS53 4.8 23.1 1.0
N A:CYS88 5.0 23.7 1.0

Iron binding site 3 out of 16 in 8rcg

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Iron binding site 3 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1103

b:24.0
occ:1.00
 FE3 A:SF41103 0.0 24.0 1.0
S4 A:SF41103 2.2 24.4 1.0
SG A:CYS50 2.3 25.5 1.0
S1 A:SF41103 2.3 24.2 1.0
S2 A:SF41103 2.3 24.6 1.0
FE2 A:SF41103 2.6 23.7 1.0
FE1 A:SF41103 2.7 23.4 1.0
FE4 A:SF41103 2.7 23.2 1.0
CB A:CYS50 3.1 24.2 1.0
S3 A:SF41103 3.8 21.6 1.0
CB A:TYR52 4.2 26.1 1.0
CA A:GLY91 4.2 27.4 1.0
N A:GLY91 4.3 27.5 1.0
N A:CYS53 4.3 26.2 1.0
SG A:CYS57 4.5 25.1 1.0
SG A:CYS88 4.5 22.4 1.0
CA A:CYS50 4.5 25.9 1.0
CB A:CYS57 4.6 24.2 1.0
N A:TYR52 4.8 26.4 1.0
O A:CYS53 4.8 22.8 1.0
CA A:TYR52 4.9 26.1 1.0
CD2 A:TYR52 4.9 26.5 1.0
SG A:CYS53 4.9 23.1 1.0
C A:TYR52 5.0 26.5 1.0

Iron binding site 4 out of 16 in 8rcg

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Iron binding site 4 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S 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 22.4 1.0
S3 A:SF41103 2.3 21.6 1.0
S1 A:SF41103 2.3 24.2 1.0
S2 A:SF41103 2.3 24.6 1.0
FE2 A:SF41103 2.7 23.7 1.0
FE3 A:SF41103 2.7 24.0 1.0
FE1 A:SF41103 2.8 23.4 1.0
CB A:CYS88 3.2 23.6 1.0
N A:CYS88 3.8 23.7 1.0
S4 A:SF41103 3.9 24.4 1.0
CA A:CYS88 4.0 23.8 1.0
CD A:PRO234 4.3 21.9 1.0
CD1 A:ILE235 4.4 22.0 1.0
N A:GLY91 4.4 27.5 1.0
NZ A:LYS90 4.5 27.4 1.0
CG A:PRO234 4.5 22.0 1.0
O A:HOH1326 4.6 28.9 1.0
C A:CYS88 4.6 24.9 1.0
SG A:CYS57 4.7 25.1 1.0
O A:CYS88 4.8 24.7 1.0
SG A:CYS53 4.8 23.1 1.0
SG A:CYS50 4.8 25.5 1.0
CB A:PRO234 4.9 22.2 1.0
CA A:GLY91 5.0 27.4 1.0
C A:LEU87 5.0 24.0 1.0

Iron binding site 5 out of 16 in 8rcg

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Iron binding site 5 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:25.6
occ:1.00
 FE1 B:SF4301 0.0 25.6 1.0
SG B:CYS157 2.2 28.2 1.0
S4 B:SF4301 2.2 27.3 1.0
S3 B:SF4301 2.3 28.0 1.0
S2 B:SF4301 2.3 27.8 1.0
FE2 B:SF4301 2.7 27.5 1.0
FE3 B:SF4301 2.8 27.0 1.0
FE4 B:SF4301 2.8 27.3 1.0
CB B:CYS157 3.1 28.4 1.0
CA B:CYS157 3.8 27.1 1.0
S1 B:SF4301 3.9 28.0 1.0
OG1 B:THR159 3.9 24.3 1.0
CB B:THR161 4.0 27.2 1.0
CG B:MET162 4.3 32.5 1.0
CD B:PRO158 4.3 28.3 1.0
OG1 B:THR161 4.4 28.8 1.0
CG2 B:THR161 4.5 27.1 1.0
C B:CYS157 4.5 27.2 1.0
N B:PRO158 4.7 27.6 1.0
SG B:CYS15 4.7 28.1 1.0
SG B:CYS18 4.7 26.7 1.0
N B:MET162 4.9 31.7 1.0
N B:CYS157 5.0 28.3 1.0

Iron binding site 6 out of 16 in 8rcg

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Iron binding site 6 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:27.5
occ:1.00
 FE2 B:SF4301 0.0 27.5 1.0
SG B:CYS18 2.2 26.7 1.0
S4 B:SF4301 2.2 27.3 1.0
S3 B:SF4301 2.2 28.0 1.0
S1 B:SF4301 2.3 28.0 1.0
FE1 B:SF4301 2.7 25.6 1.0
FE3 B:SF4301 2.8 27.0 1.0
FE4 B:SF4301 2.8 27.3 1.0
CB B:CYS18 3.2 27.3 1.0
O B:HOH421 3.7 26.5 1.0
S2 B:SF4301 3.9 27.8 1.0
N B:CYS18 3.9 27.9 1.0
CA B:CYS18 4.1 27.4 1.0
CG B:PRO71 4.3 28.0 1.0
N B:ARG16 4.7 28.2 1.0
CB B:PRO71 4.7 29.2 1.0
SG B:CYS15 4.7 28.1 1.0
N B:GLY17 4.7 26.4 1.0
SG B:CYS157 4.8 28.2 1.0
CA B:ARG16 4.8 27.2 1.0
CG2 B:VAL53 4.8 32.5 1.0
SG B:CYS12 4.8 27.1 1.0
CB B:CYS157 5.0 28.4 1.0
CG B:MET162 5.0 32.5 1.0

Iron binding site 7 out of 16 in 8rcg

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Iron binding site 7 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:27.0
occ:1.00
 FE3 B:SF4301 0.0 27.0 1.0
S2 B:SF4301 2.2 27.8 1.0
S1 B:SF4301 2.3 28.0 1.0
SG B:CYS15 2.3 28.1 1.0
S4 B:SF4301 2.3 27.3 1.0
FE4 B:SF4301 2.7 27.3 1.0
FE2 B:SF4301 2.8 27.5 1.0
FE1 B:SF4301 2.8 25.6 1.0
CB B:CYS15 3.5 28.1 1.0
N B:CYS15 3.5 26.2 1.0
N B:ARG16 3.7 28.2 1.0
S3 B:SF4301 3.9 28.0 1.0
CA B:CYS15 3.9 26.9 1.0
N B:GLY17 4.1 26.4 1.0
C B:CYS15 4.2 27.5 1.0
OG1 B:THR13 4.3 27.6 1.0
CD B:PRO158 4.4 28.3 1.0
C B:ALA14 4.5 25.4 1.0
CA B:ARG16 4.6 27.2 1.0
N B:ALA14 4.6 24.2 1.0
SG B:CYS18 4.6 26.7 1.0
SG B:CYS157 4.7 28.2 1.0
CA B:ALA14 4.7 26.3 1.0
SG B:CYS12 4.8 27.1 1.0
C B:ARG16 4.9 25.9 1.0
N B:CYS18 4.9 27.9 1.0
CA B:GLY17 4.9 27.6 1.0
CG B:PRO158 4.9 28.0 1.0
N B:THR13 5.0 26.7 1.0

Iron binding site 8 out of 16 in 8rcg

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Iron binding site 8 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:27.3
occ:1.00
 FE4 B:SF4301 0.0 27.3 1.0
S1 B:SF4301 2.3 28.0 1.0
S2 B:SF4301 2.3 27.8 1.0
S3 B:SF4301 2.3 28.0 1.0
SG B:CYS12 2.4 27.1 1.0
FE3 B:SF4301 2.7 27.0 1.0
FE2 B:SF4301 2.8 27.5 1.0
FE1 B:SF4301 2.8 25.6 1.0
CB B:CYS12 3.5 25.3 1.0
CA B:CYS12 3.8 25.4 1.0
S4 B:SF4301 3.9 27.3 1.0
N B:ALA14 4.0 24.2 1.0
N B:THR13 4.1 26.7 1.0
CG B:PRO71 4.2 28.0 1.0
C B:CYS12 4.3 26.7 1.0
OG1 B:THR161 4.4 28.8 1.0
CA B:ALA14 4.4 26.3 1.0
CG2 B:THR161 4.5 27.1 1.0
CB B:THR161 4.5 27.2 1.0
N B:CYS15 4.7 26.2 1.0
SG B:CYS18 4.7 26.7 1.0
SG B:CYS157 4.8 28.2 1.0
OG1 B:THR159 4.8 24.3 1.0
SG B:CYS15 5.0 28.1 1.0
C B:THR13 5.0 24.3 1.0

Iron binding site 9 out of 16 in 8rcg

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Iron binding site 9 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:44.0
occ:1.00
 FE1 B:SF4302 0.0 44.0 1.0
SG B:CYS77 2.1 44.6 1.0
S3 B:SF4302 2.2 47.9 1.0
S2 B:SF4302 2.3 47.0 1.0
S4 B:SF4302 2.3 42.9 1.0
FE4 B:SF4302 2.7 47.2 1.0
FE2 B:SF4302 2.7 48.6 1.0
FE3 B:SF4302 2.8 44.8 1.0
CB B:CYS77 3.4 45.6 1.0
N B:CYS77 3.8 44.3 1.0
S1 B:SF4302 3.9 45.7 1.0
CA B:CYS77 4.2 46.4 1.0
SG B:CYS121 4.5 40.5 1.0
N B:HIS76 4.5 41.7 1.0
CD2 B:TYR123 4.5 41.3 1.0
CB B:PRO80 4.6 51.0 1.0
CD B:PRO81 4.6 49.2 1.0
CA B:PRO80 4.7 50.5 1.0
SG B:CYS74 4.7 39.2 1.0
CB B:ARG75 4.8 41.8 1.0
N B:ARG75 4.8 39.4 1.0
CE2 B:TYR123 4.9 40.1 1.0
SG B:CYS82 4.9 50.3 1.0
C B:HIS76 4.9 42.7 1.0
CA B:HIS76 5.0 43.9 1.0

Iron binding site 10 out of 16 in 8rcg

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Iron binding site 10 out of 16 in the W-Formate Dehydrogenase M405S 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 M405S From Desulfovibrio Vulgaris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:48.6
occ:1.00
 FE2 B:SF4302 0.0 48.6 1.0
S4 B:SF4302 2.3 42.9 1.0
S3 B:SF4302 2.3 47.9 1.0
S1 B:SF4302 2.3 45.7 1.0
SG B:CYS82 2.4 50.3 1.0
FE1 B:SF4302 2.7 44.0 1.0
FE3 B:SF4302 2.7 44.8 1.0
FE4 B:SF4302 2.8 47.2 1.0
CB B:CYS82 3.1 50.7 1.0
S2 B:SF4302 3.9 47.0 1.0
N B:CYS82 4.2 51.2 1.0
CB B:PRO80 4.2 51.0 1.0
CA B:CYS82 4.3 51.3 1.0
CG1 B:VAL103 4.4 41.6 1.0
SG B:CYS121 4.6 40.5 1.0
SG B:CYS74 4.7 39.2 1.0
SG B:CYS77 4.7 44.6 1.0
CE B:LYS137 4.8 44.6 1.0
CA B:PRO80 4.9 50.5 1.0
CB B:CYS121 4.9 43.8 1.0

Reference:

G.Vilela-Alves, R.R.Manuel, N.Pedrosa, I.A.Cardoso Pereira, M.J.Romao, C.Mota. Structural and Biochemical Characterization of the M405S Variant of Formate Dehydrogenase Acta Cryst. F 2024.
DOI: 10.1107/S2053230X24003911
Page generated: Sat Aug 10 16:38:53 2024

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