Iron in PDB 8bqg: W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 Min

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 Min, PDB code: 8bqg 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)	94.93 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.537, 122.778, 148.985, 90, 90, 90
R / Rfree (%)	19.3 / 24.3

The structure of W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min (pdb code 8bqg). 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 1 Min, PDB code: 8bqg:
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 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:26.4 occ:1.00 FE1 A:SF41103 0.0 26.4 1.0 S2 A:SF41103 2.3 25.5 1.0 S4 A:SF41103 2.3 25.1 1.0 SG A:CYS53 2.3 24.9 1.0 S3 A:SF41103 2.3 26.7 1.0 FE3 A:SF41103 2.7 26.3 1.0 FE2 A:SF41103 2.7 26.1 1.0 FE4 A:SF41103 2.8 25.8 1.0 CB A:CYS53 3.3 24.8 1.0 N A:CYS53 3.7 25.9 1.0 CA A:CYS53 3.9 24.1 1.0 S1 A:SF41103 3.9 25.8 1.0 CB A:VAL55 4.1 24.0 1.0 O A:CYS53 4.1 25.7 1.0 C A:CYS53 4.1 29.0 1.0 CG2 A:VAL55 4.2 24.9 1.0 CD A:PRO234 4.5 23.6 1.0 N A:VAL55 4.6 23.0 1.0 SG A:CYS50 4.7 26.7 1.0 SG A:CYS88 4.7 26.9 1.0 SG A:CYS57 4.7 27.3 1.0 C A:TYR52 4.9 28.2 1.0 N A:ALA54 4.9 27.8 1.0 CA A:VAL55 4.9 22.1 1.0 CB A:TYR52 5.0 28.3 1.0 CG1 A:VAL55 5.0 23.2 1.0

Iron binding site 2 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:26.1 occ:1.00 FE2 A:SF41103 0.0 26.1 1.0 SG A:CYS57 2.2 27.3 1.0 S3 A:SF41103 2.3 26.7 1.0 S4 A:SF41103 2.3 25.1 1.0 S1 A:SF41103 2.3 25.8 1.0 FE3 A:SF41103 2.7 26.3 1.0 FE4 A:SF41103 2.7 25.8 1.0 FE1 A:SF41103 2.7 26.4 1.0 CB A:CYS57 3.1 24.2 1.0 S2 A:SF41103 3.8 25.5 1.0 N A:CYS57 4.2 25.1 1.0 CA A:CYS57 4.2 26.4 1.0 CB A:VAL55 4.3 24.0 1.0 CD1 A:ILE235 4.3 24.0 1.0 CG1 A:VAL55 4.3 23.2 1.0 CB A:ILE235 4.4 25.4 1.0 CG1 A:ILE235 4.4 23.8 1.0 SG A:CYS50 4.6 26.7 1.0 CB A:CYS50 4.6 26.3 1.0 SG A:CYS53 4.8 24.9 1.0 SG A:CYS88 4.9 26.9 1.0 CG2 A:VAL55 4.9 24.9 1.0 CD2 A:LEU87 5.0 25.4 1.0

Iron binding site 3 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:26.3 occ:1.00 FE3 A:SF41103 0.0 26.3 1.0 SG A:CYS50 2.2 26.7 1.0 S2 A:SF41103 2.2 25.5 1.0 S4 A:SF41103 2.3 25.1 1.0 S1 A:SF41103 2.3 25.8 1.0 FE2 A:SF41103 2.7 26.1 1.0 FE4 A:SF41103 2.7 25.8 1.0 FE1 A:SF41103 2.7 26.4 1.0 CB A:CYS50 3.1 26.3 1.0 S3 A:SF41103 3.8 26.7 1.0 CB A:TYR52 4.2 28.3 1.0 CA A:GLY91 4.2 25.1 1.0 N A:GLY91 4.3 25.8 1.0 N A:CYS53 4.3 25.9 1.0 CB A:CYS57 4.5 24.2 1.0 CA A:CYS50 4.5 25.9 1.0 SG A:CYS88 4.6 26.9 1.0 SG A:CYS57 4.6 27.3 1.0 N A:TYR52 4.8 27.6 1.0 CA A:TYR52 4.9 29.3 1.0 SG A:CYS53 4.9 24.9 1.0 CD2 A:TYR52 4.9 28.0 1.0 O A:CYS53 5.0 25.7 1.0

Iron binding site 4 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1103 b:25.8 occ:1.00 FE4 A:SF41103 0.0 25.8 1.0 SG A:CYS88 2.2 26.9 1.0 S1 A:SF41103 2.3 25.8 1.0 S3 A:SF41103 2.3 26.7 1.0 S2 A:SF41103 2.3 25.5 1.0 FE3 A:SF41103 2.7 26.3 1.0 FE2 A:SF41103 2.7 26.1 1.0 FE1 A:SF41103 2.8 26.4 1.0 CB A:CYS88 3.2 29.6 1.0 N A:CYS88 3.9 29.3 1.0 S4 A:SF41103 3.9 25.1 1.0 CA A:CYS88 4.1 28.4 1.0 CD A:PRO234 4.3 23.6 1.0 N A:GLY91 4.4 25.8 1.0 NZ A:LYS90 4.4 25.6 1.0 CG A:PRO234 4.6 21.9 1.0 C A:CYS88 4.6 27.3 1.0 CD1 A:ILE235 4.7 24.0 1.0 SG A:CYS53 4.7 24.9 1.0 O A:CYS88 4.8 28.9 1.0 SG A:CYS50 4.8 26.7 1.0 SG A:CYS57 4.8 27.3 1.0 CB A:LYS90 4.9 25.9 1.0 CB A:PRO234 5.0 22.5 1.0 CA A:GLY91 5.0 25.1 1.0

Iron binding site 5 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:28.7 occ:1.00 FE1 B:SF4301 0.0 28.7 1.0 S3 B:SF4301 2.3 28.2 1.0 S4 B:SF4301 2.3 28.5 1.0 SG B:CYS157 2.3 30.3 1.0 S2 B:SF4301 2.3 28.4 1.0 FE2 B:SF4301 2.7 27.9 1.0 FE3 B:SF4301 2.7 28.2 1.0 FE4 B:SF4301 2.8 28.7 1.0 CB B:CYS157 3.2 28.3 1.0 CA B:CYS157 3.7 27.2 1.0 S1 B:SF4301 3.9 29.0 1.0 CD B:PRO158 4.0 28.9 1.0 CB B:THR161 4.1 27.4 1.0 OG1 B:THR159 4.1 26.8 1.0 CG B:MET162 4.3 36.3 1.0 C B:CYS157 4.5 26.8 1.0 OG1 B:THR161 4.5 25.5 1.0 N B:PRO158 4.5 28.5 1.0 SG B:CYS15 4.6 27.5 1.0 CG2 B:THR161 4.6 27.7 1.0 SG B:CYS18 4.7 29.5 1.0 N B:MET162 4.9 36.1 1.0 N B:CYS157 5.0 28.7 1.0 N B:THR159 5.0 29.2 1.0

Iron binding site 6 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.9 occ:1.00 FE2 B:SF4301 0.0 27.9 1.0 SG B:CYS18 2.2 29.5 1.0 S3 B:SF4301 2.3 28.2 1.0 S1 B:SF4301 2.3 29.0 1.0 S4 B:SF4301 2.3 28.5 1.0 FE1 B:SF4301 2.7 28.7 1.0 FE4 B:SF4301 2.7 28.7 1.0 FE3 B:SF4301 2.8 28.2 1.0 CB B:CYS18 3.2 31.8 1.0 N B:CYS18 3.9 28.1 1.0 S2 B:SF4301 3.9 28.4 1.0 CA B:CYS18 4.2 27.4 1.0 CG B:PRO71 4.5 33.8 1.0 N B:GLY17 4.6 28.0 1.0 CB B:PRO71 4.7 31.9 1.0 N B:ARG16 4.7 26.1 1.0 SG B:CYS15 4.7 27.5 1.0 CA B:ARG16 4.7 27.7 1.0 CG2 B:VAL53 4.8 31.4 1.0 SG B:CYS157 4.8 30.3 1.0 SG B:CYS12 4.8 26.1 1.0 C B:ARG16 4.9 27.3 1.0

Iron binding site 7 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:28.2 occ:1.00 FE3 B:SF4301 0.0 28.2 1.0 S2 B:SF4301 2.2 28.4 1.0 S1 B:SF4301 2.3 29.0 1.0 S4 B:SF4301 2.3 28.5 1.0 SG B:CYS15 2.3 27.5 1.0 FE4 B:SF4301 2.7 28.7 1.0 FE1 B:SF4301 2.7 28.7 1.0 FE2 B:SF4301 2.8 27.9 1.0 N B:CYS15 3.4 26.7 1.0 CB B:CYS15 3.6 24.7 1.0 N B:ARG16 3.7 26.1 1.0 S3 B:SF4301 3.9 28.2 1.0 CA B:CYS15 3.9 24.7 1.0 N B:GLY17 4.2 28.0 1.0 CD B:PRO158 4.2 28.9 1.0 C B:CYS15 4.2 27.2 1.0 OG1 B:THR13 4.3 25.0 1.0 C B:ALA14 4.4 25.6 1.0 N B:ALA14 4.5 25.4 1.0 CA B:ARG16 4.6 27.7 1.0 SG B:CYS18 4.6 29.5 1.0 CA B:ALA14 4.6 24.6 1.0 SG B:CYS12 4.7 26.1 1.0 SG B:CYS157 4.7 30.3 1.0 CG B:PRO158 4.8 30.0 1.0 C B:ARG16 4.8 27.3 1.0 N B:THR13 4.9 28.0 1.0 N B:CYS18 4.9 28.1 1.0 CA B:GLY17 4.9 27.8 1.0

Iron binding site 8 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:28.7 occ:1.00 FE4 B:SF4301 0.0 28.7 1.0 S1 B:SF4301 2.2 29.0 1.0 S2 B:SF4301 2.3 28.4 1.0 S3 B:SF4301 2.3 28.2 1.0 SG B:CYS12 2.4 26.1 1.0 FE3 B:SF4301 2.7 28.2 1.0 FE2 B:SF4301 2.7 27.9 1.0 FE1 B:SF4301 2.8 28.7 1.0 CB B:CYS12 3.5 21.7 1.0 CA B:CYS12 3.8 25.9 1.0 S4 B:SF4301 3.9 28.5 1.0 N B:ALA14 4.1 25.4 1.0 N B:THR13 4.1 28.0 1.0 CA B:ALA14 4.4 24.6 1.0 C B:CYS12 4.4 25.9 1.0 CG B:PRO71 4.5 33.8 1.0 CG2 B:THR161 4.5 27.7 1.0 OG1 B:THR161 4.5 25.5 1.0 CB B:THR161 4.5 27.4 1.0 SG B:CYS18 4.7 29.5 1.0 N B:CYS15 4.7 26.7 1.0 SG B:CYS157 4.8 30.3 1.0 OG1 B:THR159 5.0 26.8 1.0 SG B:CYS15 5.0 27.5 1.0

Iron binding site 9 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:41.2 occ:1.00 FE1 B:SF4302 0.0 41.2 1.0 SG B:CYS77 2.0 39.2 1.0 S3 B:SF4302 2.2 43.1 1.0 S2 B:SF4302 2.2 40.2 1.0 S4 B:SF4302 2.3 42.6 1.0 FE4 B:SF4302 2.5 42.5 1.0 FE2 B:SF4302 2.7 43.7 1.0 FE3 B:SF4302 2.8 40.2 1.0 CB B:CYS77 3.6 41.3 1.0 S1 B:SF4302 3.8 40.0 1.0 N B:CYS77 4.0 41.1 1.0 CD2 B:TYR123 4.4 40.6 1.0 CA B:CYS77 4.4 43.3 1.0 SG B:CYS121 4.5 48.7 1.0 CD B:PRO81 4.7 48.8 1.0 N B:HIS76 4.7 38.5 1.0 CE2 B:TYR123 4.7 44.4 1.0 SG B:CYS74 4.7 41.0 1.0 N B:ARG75 4.8 32.5 1.0 SG B:CYS82 4.9 48.7 1.0 CD B:PRO122 5.0 40.5 1.0

Iron binding site 10 out of 16 in the W-Formate Dehydrogenase From Desulfovibrio Vulgaris - Soaking with Formate 1 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 1 Min within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:43.7 occ:1.00 FE2 B:SF4302 0.0 43.7 1.0 S4 B:SF4302 2.2 42.6 1.0 S1 B:SF4302 2.3 40.0 1.0 S3 B:SF4302 2.3 43.1 1.0 SG B:CYS82 2.5 48.7 1.0 FE1 B:SF4302 2.7 41.2 1.0 FE4 B:SF4302 2.7 42.5 1.0 FE3 B:SF4302 2.7 40.2 1.0 CB B:CYS82 3.2 51.5 1.0 S2 B:SF4302 3.8 40.2 1.0 N B:CYS82 4.3 52.9 1.0 CA B:CYS82 4.3 47.9 1.0 CG1 B:VAL103 4.3 46.3 1.0 SG B:CYS77 4.5 39.2 1.0 CB B:PRO80 4.6 55.5 1.0 SG B:CYS74 4.7 41.0 1.0 SG B:CYS121 4.8 48.7 1.0 CE B:LYS137 4.9 42.3 1.0 CZ B:PHE105 4.9 42.5 1.0 CE1 B:PHE105 5.0 45.2 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