Iron in PDB 4wq8: Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak

All present enzymatic activity of Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak:
1.8.2.2;

The structure of Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak, PDB code: 4wq8 was solved by J.A.Brito, K.Denkmann, I.A.C.Pereira, C.Dahl, M.Archer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.42 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.030, 70.125, 57.723, 90.00, 129.20, 90.00
R / Rfree (%)	13.8 / 16.5

The structure of Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Iron atom in the Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak (pdb code 4wq8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak, PDB code: 4wq8:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:12.2 occ:0.57 FE A:HEC1001 0.0 12.2 0.6 FE A:HEC1001 0.0 11.9 0.4 NB A:HEC1001 2.1 9.8 0.6 NC A:HEC1001 2.1 9.8 0.6 NB A:HEC1001 2.1 11.3 0.4 ND A:HEC1001 2.1 10.7 0.4 NC A:HEC1001 2.1 10.4 0.4 NE2 A:HIS53 2.1 12.4 1.0 ND A:HEC1001 2.1 10.0 0.6 NA A:HEC1001 2.1 10.6 0.6 NA A:HEC1001 2.1 11.1 0.4 SD A:CSS96 2.2 12.9 0.4 CE1 A:HIS53 2.9 12.0 1.0 C4B A:HEC1001 3.0 9.5 0.6 C4B A:HEC1001 3.0 11.6 0.4 C1D A:HEC1001 3.0 11.5 0.4 C1B A:HEC1001 3.0 9.8 0.6 C4C A:HEC1001 3.1 9.9 0.6 C1C A:HEC1001 3.1 9.5 0.6 C1D A:HEC1001 3.1 11.2 0.6 C4C A:HEC1001 3.1 10.5 0.4 C1B A:HEC1001 3.1 11.7 0.4 C4A A:HEC1001 3.1 11.1 0.6 C1C A:HEC1001 3.1 10.2 0.4 C4D A:HEC1001 3.1 11.2 0.6 C4D A:HEC1001 3.1 11.7 0.4 C4A A:HEC1001 3.1 11.7 0.4 C1A A:HEC1001 3.1 10.8 0.6 C1A A:HEC1001 3.1 11.5 0.4 CD2 A:HIS53 3.2 12.9 1.0 SG A:CSS96 3.4 18.3 0.6 CHD A:HEC1001 3.5 11.4 0.4 CHB A:HEC1001 3.5 11.5 0.6 CHC A:HEC1001 3.5 11.3 0.6 CHD A:HEC1001 3.5 11.7 0.6 CHC A:HEC1001 3.5 12.6 0.4 SG A:CSS96 3.5 19.3 0.4 CHB A:HEC1001 3.5 12.3 0.4 CHA A:HEC1001 3.5 12.4 0.6 CHA A:HEC1001 3.5 12.3 0.4 OD1 A:CSS96 3.7 19.2 0.6 CB A:CSS96 4.0 14.7 0.6 ND1 A:HIS53 4.1 11.4 1.0 CG A:HIS53 4.2 11.1 1.0 CB A:CSS96 4.3 17.3 0.4 C3B A:HEC1001 4.3 11.2 0.6 C3B A:HEC1001 4.3 13.2 0.4 C2B A:HEC1001 4.3 12.3 0.6 C2D A:HEC1001 4.3 13.4 0.4 C3C A:HEC1001 4.3 11.3 0.6 OD2 A:CSS96 4.3 19.5 0.6 C2D A:HEC1001 4.3 13.0 0.6 C2B A:HEC1001 4.4 13.1 0.4 C2C A:HEC1001 4.4 11.9 0.6 C3A A:HEC1001 4.4 13.3 0.6 C3D A:HEC1001 4.4 14.0 0.4 C3C A:HEC1001 4.4 12.1 0.4 C3D A:HEC1001 4.4 13.0 0.6 C2C A:HEC1001 4.4 11.7 0.4 C2A A:HEC1001 4.4 13.6 0.6 C3A A:HEC1001 4.4 13.3 0.4 C2A A:HEC1001 4.4 12.8 0.4

Iron binding site 2 out of 3 in the Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:11.9 occ:0.43 FE A:HEC1001 0.0 11.9 0.4 FE A:HEC1001 0.0 12.2 0.6 NE2 A:HIS53 2.0 12.4 1.0 NB A:HEC1001 2.0 9.8 0.6 NB A:HEC1001 2.1 11.3 0.4 NC A:HEC1001 2.1 9.8 0.6 NA A:HEC1001 2.1 10.6 0.6 NC A:HEC1001 2.1 10.4 0.4 ND A:HEC1001 2.1 10.7 0.4 ND A:HEC1001 2.1 10.0 0.6 NA A:HEC1001 2.1 11.1 0.4 SD A:CSS96 2.2 12.9 0.4 CE1 A:HIS53 2.9 12.0 1.0 C4B A:HEC1001 3.0 9.5 0.6 C4B A:HEC1001 3.0 11.6 0.4 C1B A:HEC1001 3.0 9.8 0.6 C1B A:HEC1001 3.1 11.7 0.4 C1D A:HEC1001 3.1 11.5 0.4 C1C A:HEC1001 3.1 9.5 0.6 C4A A:HEC1001 3.1 11.1 0.6 C4C A:HEC1001 3.1 9.9 0.6 C1C A:HEC1001 3.1 10.2 0.4 C4C A:HEC1001 3.1 10.5 0.4 C1D A:HEC1001 3.1 11.2 0.6 C4A A:HEC1001 3.1 11.7 0.4 C4D A:HEC1001 3.1 11.2 0.6 C4D A:HEC1001 3.1 11.7 0.4 C1A A:HEC1001 3.1 10.8 0.6 C1A A:HEC1001 3.1 11.5 0.4 CD2 A:HIS53 3.1 12.9 1.0 SG A:CSS96 3.4 18.3 0.6 CHB A:HEC1001 3.5 11.5 0.6 CHC A:HEC1001 3.5 11.3 0.6 CHC A:HEC1001 3.5 12.6 0.4 CHD A:HEC1001 3.5 11.4 0.4 CHB A:HEC1001 3.5 12.3 0.4 CHD A:HEC1001 3.5 11.7 0.6 SG A:CSS96 3.5 19.3 0.4 CHA A:HEC1001 3.5 12.4 0.6 CHA A:HEC1001 3.5 12.3 0.4 OD1 A:CSS96 3.8 19.2 0.6 CB A:CSS96 4.0 14.7 0.6 ND1 A:HIS53 4.1 11.4 1.0 CG A:HIS53 4.2 11.1 1.0 C3B A:HEC1001 4.3 11.2 0.6 C2B A:HEC1001 4.3 12.3 0.6 C3B A:HEC1001 4.3 13.2 0.4 CB A:CSS96 4.3 17.3 0.4 C2B A:HEC1001 4.3 13.1 0.4 C3C A:HEC1001 4.4 11.3 0.6 C2D A:HEC1001 4.4 13.4 0.4 C2C A:HEC1001 4.4 11.9 0.6 C2D A:HEC1001 4.4 13.0 0.6 C3A A:HEC1001 4.4 13.3 0.6 OD2 A:CSS96 4.4 19.5 0.6 C3A A:HEC1001 4.4 13.3 0.4 C3D A:HEC1001 4.4 14.0 0.4 C2C A:HEC1001 4.4 11.7 0.4 C3C A:HEC1001 4.4 12.1 0.4 C3D A:HEC1001 4.4 13.0 0.6 C2A A:HEC1001 4.4 13.6 0.6 C2A A:HEC1001 4.4 12.8 0.4

Iron binding site 3 out of 3 in the Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum - Tetrathionate Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:12.9 occ:1.00 FE A:HEC1002 0.0 12.9 1.0 NE2 A:HIS164 2.0 12.1 1.0 NB A:HEC1002 2.0 11.6 1.0 ND A:HEC1002 2.1 11.3 1.0 NA A:HEC1002 2.1 11.9 1.0 NC A:HEC1002 2.1 12.0 1.0 NZ A:LYS208 2.1 11.4 1.0 CD2 A:HIS164 3.0 11.7 1.0 CE1 A:HIS164 3.0 10.6 1.0 C1B A:HEC1002 3.0 13.8 1.0 C4A A:HEC1002 3.0 12.8 1.0 C4D A:HEC1002 3.0 12.5 1.0 C4B A:HEC1002 3.0 12.7 1.0 C1D A:HEC1002 3.0 12.5 1.0 C4C A:HEC1002 3.0 13.1 1.0 C1C A:HEC1002 3.1 14.2 1.0 C1A A:HEC1002 3.1 13.7 1.0 CE A:LYS208 3.1 20.5 1.0 CHB A:HEC1002 3.4 13.3 1.0 CHD A:HEC1002 3.5 13.3 1.0 CHA A:HEC1002 3.5 13.0 1.0 CHC A:HEC1002 3.5 13.0 1.0 ND1 A:HIS164 4.1 12.6 1.0 CG A:HIS164 4.1 11.2 1.0 C2B A:HEC1002 4.3 12.6 1.0 C3D A:HEC1002 4.3 12.9 1.0 C3B A:HEC1002 4.3 12.3 1.0 C3A A:HEC1002 4.3 13.7 1.0 C2D A:HEC1002 4.3 16.0 1.0 C2A A:HEC1002 4.3 13.2 1.0 C2C A:HEC1002 4.3 15.1 1.0 C3C A:HEC1002 4.3 15.9 1.0 CD A:LYS208 4.4 26.3 1.0 O A:HOH1319 4.4 33.5 1.0

J.A.Brito, K.Denkmann, I.A.C.Pereira, C.Dahl, M.Archer. Thiosulfate Dehydrogenase (Tsda) From Allochromatium Vinosum: Structural and Functional Insights Into Thiosulfate Oxidation J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.623397