Iron in PDB 8bqi: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min, PDB code: 8bqi 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)	95.73 / 2.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.992, 123.751, 150.358, 90, 90, 90
R / Rfree (%)	21.3 / 24.8

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min also contains other interesting chemical elements:

Tungsten

(W)

1 atom

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 - Soaking with Formate 3 Min (pdb code 8bqi). 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 - Soaking with Formate 3 Min, PDB code: 8bqi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:32.8 occ:1.00 FE1 A:SF41103 0.0 32.8 1.0 S4 A:SF41103 2.2 34.2 1.0 SG A:CYS53 2.3 28.8 1.0 S3 A:SF41103 2.3 31.3 1.0 S2 A:SF41103 2.3 31.2 1.0 FE2 A:SF41103 2.7 34.2 1.0 FE3 A:SF41103 2.7 33.7 1.0 FE4 A:SF41103 2.8 32.4 1.0 CB A:CYS53 3.3 29.4 1.0 N A:CYS53 3.7 31.6 1.0 CA A:CYS53 3.8 31.4 1.0 S1 A:SF41103 3.9 33.4 1.0 O A:CYS53 4.0 34.1 1.0 C A:CYS53 4.0 30.9 1.0 CB A:VAL55 4.0 30.1 1.0 CG2 A:VAL55 4.3 32.1 1.0 SG A:CYS57 4.6 29.9 1.0 N A:VAL55 4.6 28.8 1.0 CD A:PRO234 4.7 29.1 1.0 SG A:CYS50 4.8 27.4 1.0 SG A:CYS88 4.8 27.8 1.0 N A:ALA54 4.8 30.2 1.0 CA A:VAL55 4.9 28.6 1.0 CG1 A:VAL55 4.9 31.4 1.0 C A:TYR52 5.0 33.1 1.0

Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:34.2 occ:1.00 FE2 A:SF41103 0.0 34.2 1.0 SG A:CYS57 2.1 29.9 1.0 S1 A:SF41103 2.3 33.4 1.0 S4 A:SF41103 2.3 34.2 1.0 S3 A:SF41103 2.3 31.3 1.0 FE3 A:SF41103 2.7 33.7 1.0 FE4 A:SF41103 2.7 32.4 1.0 FE1 A:SF41103 2.7 32.8 1.0 CB A:CYS57 3.1 31.1 1.0 S2 A:SF41103 3.9 31.2 1.0 CD1 A:ILE235 4.1 31.2 1.0 N A:CYS57 4.2 30.7 1.0 CA A:CYS57 4.2 31.4 1.0 CG1 A:VAL55 4.3 31.4 1.0 CG1 A:ILE235 4.3 32.3 1.0 CB A:VAL55 4.3 30.1 1.0 CB A:ILE235 4.4 32.7 1.0 SG A:CYS50 4.6 27.4 1.0 CB A:CYS50 4.6 28.8 1.0 SG A:CYS53 4.8 28.8 1.0 CD2 A:LEU87 4.8 25.9 1.0 SG A:CYS88 4.9 27.8 1.0

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


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:33.7 occ:1.00 FE3 A:SF41103 0.0 33.7 1.0 SG A:CYS50 2.3 27.4 1.0 S4 A:SF41103 2.3 34.2 1.0 S2 A:SF41103 2.3 31.2 1.0 S1 A:SF41103 2.3 33.4 1.0 FE2 A:SF41103 2.7 34.2 1.0 FE4 A:SF41103 2.7 32.4 1.0 FE1 A:SF41103 2.7 32.8 1.0 CB A:CYS50 3.1 28.8 1.0 S3 A:SF41103 3.9 31.3 1.0 N A:GLY91 4.2 31.2 1.0 CA A:GLY91 4.2 28.7 1.0 CB A:TYR52 4.2 31.8 1.0 N A:CYS53 4.3 31.6 1.0 SG A:CYS57 4.5 29.9 1.0 CA A:CYS50 4.6 30.2 1.0 CB A:CYS57 4.6 31.1 1.0 SG A:CYS88 4.6 27.8 1.0 N A:TYR52 4.8 33.5 1.0 CA A:TYR52 4.9 33.0 1.0 SG A:CYS53 4.9 28.8 1.0 O A:CYS53 4.9 34.1 1.0 CD2 A:TYR52 4.9 32.5 1.0 C A:TYR52 5.0 33.1 1.0

Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:32.4 occ:1.00 FE4 A:SF41103 0.0 32.4 1.0 S1 A:SF41103 2.2 33.4 1.0 S3 A:SF41103 2.3 31.3 1.0 S2 A:SF41103 2.3 31.2 1.0 SG A:CYS88 2.3 27.8 1.0 FE2 A:SF41103 2.7 34.2 1.0 FE3 A:SF41103 2.7 33.7 1.0 FE1 A:SF41103 2.8 32.8 1.0 CB A:CYS88 3.3 28.6 1.0 S4 A:SF41103 3.9 34.2 1.0 N A:CYS88 3.9 31.9 1.0 CA A:CYS88 4.1 30.9 1.0 CD A:PRO234 4.4 29.1 1.0 N A:GLY91 4.4 31.2 1.0 NZ A:LYS90 4.5 31.8 1.0 CD1 A:ILE235 4.5 31.2 1.0 CG A:PRO234 4.6 28.9 1.0 SG A:CYS57 4.7 29.9 1.0 C A:CYS88 4.7 31.9 1.0 SG A:CYS53 4.8 28.8 1.0 O A:CYS88 4.8 32.1 1.0 SG A:CYS50 4.8 27.4 1.0 CB A:LYS90 4.9 31.0 1.0 CE A:LYS90 4.9 30.8 1.0 CB A:PRO234 4.9 29.3 1.0 CA A:GLY91 4.9 28.7 1.0

Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:35.7 occ:1.00 FE1 B:SF4301 0.0 35.7 1.0 SG B:CYS157 2.2 36.0 1.0 S3 B:SF4301 2.3 34.8 1.0 S4 B:SF4301 2.3 32.7 1.0 S2 B:SF4301 2.3 34.3 1.0 FE3 B:SF4301 2.7 35.2 1.0 FE2 B:SF4301 2.7 33.8 1.0 FE4 B:SF4301 2.7 36.2 1.0 CB B:CYS157 3.1 37.5 1.0 CA B:CYS157 3.7 36.9 1.0 S1 B:SF4301 3.9 33.0 1.0 OG1 B:THR159 3.9 34.4 1.0 CD B:PRO158 4.1 36.1 1.0 CB B:THR161 4.2 34.6 1.0 CG B:MET162 4.2 34.8 1.0 C B:CYS157 4.5 37.8 1.0 N B:PRO158 4.6 37.2 1.0 OG1 B:THR161 4.6 34.6 1.0 CG2 B:THR161 4.6 34.3 1.0 SG B:CYS15 4.7 38.1 1.0 SG B:CYS18 4.9 34.1 1.0 N B:CYS157 4.9 37.8 1.0 N B:MET162 5.0 38.0 1.0

Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:33.8 occ:1.00 FE2 B:SF4301 0.0 33.8 1.0 S4 B:SF4301 2.3 32.7 1.0 S3 B:SF4301 2.3 34.8 1.0 S1 B:SF4301 2.3 33.0 1.0 SG B:CYS18 2.3 34.1 1.0 FE1 B:SF4301 2.7 35.7 1.0 FE3 B:SF4301 2.8 35.2 1.0 FE4 B:SF4301 2.8 36.2 1.0 CB B:CYS18 3.2 34.8 1.0 S2 B:SF4301 3.9 34.3 1.0 N B:CYS18 4.0 34.4 1.0 CA B:CYS18 4.2 34.8 1.0 CG B:PRO71 4.3 36.1 1.0 N B:ARG16 4.6 34.7 1.0 CB B:PRO71 4.6 36.9 1.0 N B:GLY17 4.7 36.5 1.0 SG B:CYS15 4.7 38.1 1.0 CA B:ARG16 4.7 34.5 1.0 SG B:CYS157 4.8 36.0 1.0 SG B:CYS12 4.8 37.7 1.0 CG2 B:VAL53 4.9 37.5 1.0 C B:ARG16 5.0 35.8 1.0

Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:35.2 occ:1.00 FE3 B:SF4301 0.0 35.2 1.0 S2 B:SF4301 2.3 34.3 1.0 S1 B:SF4301 2.3 33.0 1.0 S4 B:SF4301 2.3 32.7 1.0 SG B:CYS15 2.3 38.1 1.0 FE1 B:SF4301 2.7 35.7 1.0 FE2 B:SF4301 2.8 33.8 1.0 FE4 B:SF4301 2.8 36.2 1.0 N B:CYS15 3.6 32.1 1.0 CB B:CYS15 3.6 35.8 1.0 N B:ARG16 3.7 34.7 1.0 S3 B:SF4301 3.9 34.8 1.0 CA B:CYS15 4.0 34.0 1.0 N B:GLY17 4.2 36.5 1.0 CD B:PRO158 4.2 36.1 1.0 C B:CYS15 4.2 34.8 1.0 C B:ALA14 4.5 30.6 1.0 N B:ALA14 4.6 30.5 1.0 OG1 B:THR13 4.6 33.4 1.0 CA B:ARG16 4.6 34.5 1.0 SG B:CYS157 4.6 36.0 1.0 SG B:CYS18 4.7 34.1 1.0 CA B:ALA14 4.7 31.1 1.0 SG B:CYS12 4.8 37.7 1.0 C B:ARG16 4.9 35.8 1.0 N B:CYS18 4.9 34.4 1.0 CA B:GLY17 5.0 35.4 1.0

Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:36.2 occ:1.00 FE4 B:SF4301 0.0 36.2 1.0 S3 B:SF4301 2.3 34.8 1.0 S2 B:SF4301 2.3 34.3 1.0 S1 B:SF4301 2.3 33.0 1.0 SG B:CYS12 2.4 37.7 1.0 FE1 B:SF4301 2.7 35.7 1.0 FE2 B:SF4301 2.8 33.8 1.0 FE3 B:SF4301 2.8 35.2 1.0 CB B:CYS12 3.5 36.4 1.0 CA B:CYS12 3.8 36.1 1.0 S4 B:SF4301 3.9 32.7 1.0 N B:ALA14 4.1 30.5 1.0 N B:THR13 4.2 32.5 1.0 CG B:PRO71 4.3 36.1 1.0 OG1 B:THR161 4.4 34.6 1.0 C B:CYS12 4.4 34.5 1.0 CG2 B:THR161 4.5 34.3 1.0 CA B:ALA14 4.5 31.1 1.0 CB B:THR161 4.5 34.6 1.0 SG B:CYS157 4.7 36.0 1.0 OG1 B:THR159 4.7 34.4 1.0 N B:CYS15 4.8 32.1 1.0 SG B:CYS18 4.9 34.1 1.0

Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:53.0 occ:1.00 FE1 B:SF4302 0.0 53.0 1.0 SG B:CYS77 2.1 46.5 1.0 S3 B:SF4302 2.2 50.3 1.0 S2 B:SF4302 2.3 50.4 1.0 S4 B:SF4302 2.3 51.3 1.0 FE4 B:SF4302 2.7 48.9 1.0 FE2 B:SF4302 2.8 48.7 1.0 FE3 B:SF4302 2.8 49.0 1.0 CB B:CYS77 3.5 46.3 1.0 S1 B:SF4302 3.9 46.6 1.0 N B:CYS77 3.9 47.3 1.0 CA B:CYS77 4.4 48.5 1.0 CD B:PRO81 4.5 53.8 1.0 SG B:CYS74 4.6 44.5 1.0 CD2 B:TYR123 4.6 43.6 1.0 N B:HIS76 4.6 46.8 1.0 SG B:CYS121 4.6 56.6 1.0 N B:ARG75 4.7 42.9 1.0 SG B:CYS82 4.8 54.9 1.0 CE2 B:TYR123 4.9 45.4 1.0 CB B:ARG75 4.9 45.3 1.0 C B:HIS76 5.0 44.5 1.0

Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 3 Min


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 - Soaking with Formate 3 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:48.7 occ:1.00 FE2 B:SF4302 0.0 48.7 1.0 S4 B:SF4302 2.3 51.3 1.0 SG B:CYS82 2.3 54.9 1.0 S1 B:SF4302 2.3 46.6 1.0 S3 B:SF4302 2.3 50.3 1.0 FE3 B:SF4302 2.7 49.0 1.0 FE4 B:SF4302 2.7 48.9 1.0 FE1 B:SF4302 2.8 53.0 1.0 CB B:CYS82 3.1 50.7 1.0 S2 B:SF4302 3.9 50.4 1.0 N B:CYS82 4.2 50.7 1.0 CA B:CYS82 4.3 52.0 1.0 CG1 B:VAL103 4.3 44.4 1.0 SG B:CYS77 4.7 46.5 1.0 SG B:CYS74 4.7 44.5 1.0 SG B:CYS121 4.7 56.6 1.0 CB B:PRO80 4.7 57.2 1.0 CE B:LYS137 4.8 45.3 1.0 CZ B:PHE105 4.9 46.6 1.0 CB B:CYS121 4.9 54.7 1.0 CE1 B:PHE105 4.9 46.1 1.0

G.Vilela-Alves, R.R.Manuel, A.R.Oliveira, I.C.Pereira, M.J.Romao, C.Mota. Tracking W-Formate Dehydrogenase Structural Changes During Catalysis and Enzyme Reoxidation. Int J Mol Sci V. 24 2022.
ISSN: ESSN 1422-0067
PubMed: 36613918
DOI: 10.3390/IJMS24010476