Iron in PDB 5lo9: Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form

The structure of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form, PDB code: 5lo9 was solved by J.A.Brito, J.M.Kurth, J.Reuter, A.Flegler, T.Koch, T.Franke, E.Klein, S.Rowe, J.N.Butt, 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)	113.13 / 2.75
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	159.753, 159.753, 393.086, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 19.8

The structure of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

The binding sites of Iron atom in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form (pdb code 5lo9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form, PDB code: 5lo9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:56.6 occ:1.00 FE A:HEC1001 0.0 56.6 1.0 ND A:HEC1001 2.1 43.3 1.0 NB A:HEC1001 2.1 45.6 1.0 NC A:HEC1001 2.1 45.6 1.0 NA A:HEC1001 2.1 43.6 1.0 NE2 A:HIS25 2.1 46.8 1.0 SD A:MET65 2.3 50.6 1.0 CE1 A:HIS25 3.0 48.8 1.0 C4D A:HEC1001 3.1 39.1 1.0 C1D A:HEC1001 3.1 45.2 1.0 C1C A:HEC1001 3.1 45.6 1.0 C1B A:HEC1001 3.1 43.7 1.0 C4B A:HEC1001 3.1 43.4 1.0 C4C A:HEC1001 3.1 47.6 1.0 C1A A:HEC1001 3.1 42.5 1.0 C4A A:HEC1001 3.1 38.0 1.0 CD2 A:HIS25 3.2 50.0 1.0 CE A:MET65 3.4 43.9 1.0 CHA A:HEC1001 3.5 36.1 1.0 CHC A:HEC1001 3.5 47.0 1.0 CHD A:HEC1001 3.5 44.1 1.0 CHB A:HEC1001 3.5 41.8 1.0 CG A:MET65 3.6 52.6 1.0 ND1 A:HIS25 4.2 51.8 1.0 CG A:HIS25 4.3 49.4 1.0 C2D A:HEC1001 4.4 45.9 1.0 CB A:MET65 4.4 52.9 1.0 C2B A:HEC1001 4.4 39.0 1.0 C2C A:HEC1001 4.4 45.0 1.0 C3B A:HEC1001 4.4 43.6 1.0 C3D A:HEC1001 4.4 39.2 1.0 C3C A:HEC1001 4.4 47.8 1.0 C3A A:HEC1001 4.4 36.5 1.0 C2A A:HEC1001 4.4 42.4 1.0

Iron binding site 2 out of 8 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:44.8 occ:1.00 FE A:HEC1002 0.0 44.8 1.0 NE2 A:HIS125 2.1 43.1 1.0 ND A:HEC1002 2.1 34.3 1.0 NC A:HEC1002 2.1 34.7 1.0 NB A:HEC1002 2.1 34.4 1.0 NA A:HEC1002 2.1 42.5 1.0 SD A:MET167 2.4 38.4 1.0 CE1 A:HIS125 3.0 43.2 1.0 C1D A:HEC1002 3.1 32.1 1.0 C1C A:HEC1002 3.1 33.5 1.0 C4C A:HEC1002 3.1 33.6 1.0 C4D A:HEC1002 3.1 38.7 1.0 CD2 A:HIS125 3.1 38.3 1.0 C1A A:HEC1002 3.1 32.2 1.0 C4B A:HEC1002 3.1 33.6 1.0 C4A A:HEC1002 3.1 44.0 1.0 C1B A:HEC1002 3.1 35.5 1.0 CG A:MET167 3.4 39.9 1.0 CE A:MET167 3.4 40.0 1.0 CHD A:HEC1002 3.5 37.0 1.0 CHA A:HEC1002 3.5 35.4 1.0 CHC A:HEC1002 3.5 32.2 1.0 CHB A:HEC1002 3.5 32.9 1.0 ND1 A:HIS125 4.2 39.5 1.0 CG A:HIS125 4.2 42.9 1.0 C2D A:HEC1002 4.4 29.4 1.0 C2C A:HEC1002 4.4 35.0 1.0 C2A A:HEC1002 4.4 36.8 1.0 C3B A:HEC1002 4.4 35.0 1.0 C3A A:HEC1002 4.4 45.7 1.0 C3D A:HEC1002 4.4 28.9 1.0 C3C A:HEC1002 4.4 32.7 1.0 C2B A:HEC1002 4.4 35.4 1.0 CB A:MET167 4.8 39.8 1.0

Iron binding site 3 out of 8 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:47.0 occ:1.00 FE A:HEC1003 0.0 47.0 1.0 NA A:HEC1003 2.1 36.8 1.0 ND A:HEC1003 2.1 43.6 1.0 NB A:HEC1003 2.1 37.1 1.0 NC A:HEC1003 2.1 43.7 1.0 NE2 A:HIS291 2.2 35.3 1.0 SG A:CYS330 3.0 60.9 1.0 C1D A:HEC1003 3.0 36.7 1.0 C4C A:HEC1003 3.0 32.0 1.0 CE1 A:HIS291 3.1 38.9 1.0 C1A A:HEC1003 3.1 39.0 1.0 C4A A:HEC1003 3.1 34.8 1.0 C1B A:HEC1003 3.1 37.1 1.0 C4B A:HEC1003 3.1 31.8 1.0 C1C A:HEC1003 3.1 37.0 1.0 C4D A:HEC1003 3.1 42.1 1.0 S2 A:THJ1008 3.2 58.6 0.7 CD2 A:HIS291 3.3 36.9 1.0 CHD A:HEC1003 3.4 35.0 1.0 CHB A:HEC1003 3.5 33.0 1.0 CHA A:HEC1003 3.5 38.9 1.0 CHC A:HEC1003 3.5 34.1 1.0 ND1 A:HIS291 4.2 37.9 1.0 C2D A:HEC1003 4.4 40.6 1.0 C3C A:HEC1003 4.4 35.2 1.0 C3A A:HEC1003 4.4 31.8 1.0 C2B A:HEC1003 4.4 30.6 1.0 CB A:CYS330 4.4 47.5 1.0 C2A A:HEC1003 4.4 37.4 1.0 C3B A:HEC1003 4.4 34.5 1.0 CG A:HIS291 4.4 36.5 1.0 C2C A:HEC1003 4.4 31.1 1.0 C3D A:HEC1003 4.4 40.9 1.0 S1 A:THJ1008 5.0 0.6 0.7

Iron binding site 4 out of 8 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1004 b:45.3 occ:1.00 FE A:HEC1004 0.0 45.3 1.0 NB A:HEC1004 2.1 37.0 1.0 NE2 A:HIS406 2.1 42.5 1.0 NA A:HEC1004 2.1 36.4 1.0 ND A:HEC1004 2.1 40.0 1.0 NC A:HEC1004 2.1 44.9 1.0 SD A:MET450 2.3 39.4 1.0 CE1 A:HIS406 3.0 44.7 1.0 C4B A:HEC1004 3.0 37.8 1.0 C1C A:HEC1004 3.1 36.5 1.0 C4A A:HEC1004 3.1 36.0 1.0 C1B A:HEC1004 3.1 35.8 1.0 C4D A:HEC1004 3.1 34.1 1.0 C1A A:HEC1004 3.1 34.7 1.0 C1D A:HEC1004 3.1 38.5 1.0 C4C A:HEC1004 3.1 42.6 1.0 CD2 A:HIS406 3.1 47.0 1.0 CG A:MET450 3.4 36.0 1.0 CE A:MET450 3.4 39.6 1.0 CHC A:HEC1004 3.5 36.7 1.0 CHA A:HEC1004 3.5 32.2 1.0 CHB A:HEC1004 3.5 38.1 1.0 CHD A:HEC1004 3.5 35.7 1.0 ND1 A:HIS406 4.2 40.1 1.0 CG A:HIS406 4.2 36.0 1.0 CB A:MET450 4.3 34.4 1.0 C3B A:HEC1004 4.4 40.6 1.0 C2B A:HEC1004 4.4 33.4 1.0 C3D A:HEC1004 4.4 34.1 1.0 C2A A:HEC1004 4.4 32.8 1.0 C2C A:HEC1004 4.4 35.4 1.0 C2D A:HEC1004 4.4 36.7 1.0 C3A A:HEC1004 4.4 35.0 1.0 C3C A:HEC1004 4.4 35.0 1.0

Iron binding site 5 out of 8 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1001 b:70.1 occ:1.00 FE B:HEC1001 0.0 70.1 1.0 ND B:HEC1001 2.1 63.2 1.0 NB B:HEC1001 2.1 76.7 1.0 NA B:HEC1001 2.1 71.7 1.0 NE2 B:HIS25 2.1 59.6 1.0 NC B:HEC1001 2.1 75.1 1.0 SD B:MET65 2.3 59.1 1.0 CE1 B:HIS25 2.9 60.5 1.0 C4D B:HEC1001 3.1 58.9 1.0 C1D B:HEC1001 3.1 62.7 1.0 C1A B:HEC1001 3.1 61.8 1.0 C1B B:HEC1001 3.1 71.6 1.0 C4B B:HEC1001 3.1 73.0 1.0 C4A B:HEC1001 3.1 64.0 1.0 C1C B:HEC1001 3.1 68.8 1.0 C4C B:HEC1001 3.1 64.0 1.0 CD2 B:HIS25 3.2 50.2 1.0 CE B:MET65 3.4 64.7 1.0 CHA B:HEC1001 3.5 61.0 1.0 CHC B:HEC1001 3.5 74.6 1.0 CHB B:HEC1001 3.5 68.0 1.0 CG B:MET65 3.5 58.2 1.0 CHD B:HEC1001 3.5 63.5 1.0 ND1 B:HIS25 4.1 59.0 1.0 CB B:MET65 4.3 64.6 1.0 CG B:HIS25 4.3 49.3 1.0 C2D B:HEC1001 4.4 59.7 1.0 C3D B:HEC1001 4.4 57.9 1.0 C3B B:HEC1001 4.4 65.8 1.0 C2B B:HEC1001 4.4 69.9 1.0 C2A B:HEC1001 4.4 60.0 1.0 C3A B:HEC1001 4.4 60.0 1.0 C2C B:HEC1001 4.4 69.0 1.0 C3C B:HEC1001 4.4 70.2 1.0

Iron binding site 6 out of 8 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1002 b:62.6 occ:1.00 FE B:HEC1002 0.0 62.6 1.0 NB B:HEC1002 2.1 59.9 1.0 ND B:HEC1002 2.1 55.3 1.0 NA B:HEC1002 2.1 52.4 1.0 NE2 B:HIS125 2.1 51.0 1.0 NC B:HEC1002 2.1 53.5 1.0 SD B:MET167 2.3 53.2 1.0 CE1 B:HIS125 2.9 54.6 1.0 C4D B:HEC1002 3.1 52.4 1.0 C4B B:HEC1002 3.1 53.1 1.0 C1A B:HEC1002 3.1 57.5 1.0 C1C B:HEC1002 3.1 46.0 1.0 C1D B:HEC1002 3.1 48.9 1.0 C1B B:HEC1002 3.1 56.8 1.0 C4A B:HEC1002 3.1 52.0 1.0 C4C B:HEC1002 3.1 50.7 1.0 CG B:MET167 3.2 51.6 1.0 CD2 B:HIS125 3.2 46.1 1.0 CE B:MET167 3.4 51.6 1.0 CHC B:HEC1002 3.5 53.3 1.0 CHA B:HEC1002 3.5 57.0 1.0 CHB B:HEC1002 3.5 55.6 1.0 CHD B:HEC1002 3.5 50.6 1.0 ND1 B:HIS125 4.1 50.0 1.0 CG B:HIS125 4.3 47.8 1.0 C3D B:HEC1002 4.4 49.5 1.0 C2D B:HEC1002 4.4 56.3 1.0 C3B B:HEC1002 4.4 55.4 1.0 C2C B:HEC1002 4.4 40.3 1.0 C2A B:HEC1002 4.4 53.7 1.0 C2B B:HEC1002 4.4 55.6 1.0 C3A B:HEC1002 4.4 48.5 1.0 C3C B:HEC1002 4.4 44.7 1.0 CB B:MET167 4.6 52.0 1.0

Iron binding site 7 out of 8 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1003 b:50.6 occ:1.00 FE B:HEC1003 0.0 50.6 1.0 NB B:HEC1003 2.1 45.2 1.0 NC B:HEC1003 2.1 51.2 1.0 NA B:HEC1003 2.1 50.1 1.0 ND B:HEC1003 2.1 41.4 1.0 NE2 B:HIS291 2.1 33.7 1.0 CE1 B:HIS291 2.8 36.7 1.0 SG B:CYS330 2.9 54.3 1.0 C4B B:HEC1003 3.1 42.2 1.0 C1C B:HEC1003 3.1 41.8 1.0 C1B B:HEC1003 3.1 37.0 1.0 C1D B:HEC1003 3.1 38.1 1.0 C4C B:HEC1003 3.1 37.7 1.0 C4A B:HEC1003 3.1 38.7 1.0 C1A B:HEC1003 3.1 45.0 1.0 C4D B:HEC1003 3.1 45.1 1.0 S2 B:THJ1006 3.2 55.3 0.7 CD2 B:HIS291 3.4 40.2 1.0 CHC B:HEC1003 3.5 38.0 1.0 CHD B:HEC1003 3.5 39.3 1.0 CHB B:HEC1003 3.5 31.8 1.0 CHA B:HEC1003 3.5 47.1 1.0 ND1 B:HIS291 4.1 36.5 1.0 CG B:HIS291 4.3 36.5 1.0 CB B:CYS330 4.4 44.7 1.0 C2C B:HEC1003 4.4 35.1 1.0 C2B B:HEC1003 4.4 36.2 1.0 C3B B:HEC1003 4.4 31.0 1.0 C2D B:HEC1003 4.4 41.5 1.0 C3A B:HEC1003 4.4 34.1 1.0 C2A B:HEC1003 4.4 39.7 1.0 C3C B:HEC1003 4.4 34.3 1.0 C3D B:HEC1003 4.4 44.1 1.0 OG B:SER334 4.9 44.9 1.0

Iron binding site 8 out of 8 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1004 b:52.6 occ:1.00 FE B:HEC1004 0.0 52.6 1.0 NC B:HEC1004 2.1 51.2 1.0 NE2 B:HIS406 2.1 36.6 1.0 NB B:HEC1004 2.1 47.4 1.0 ND B:HEC1004 2.1 40.5 1.0 NA B:HEC1004 2.1 54.7 1.0 SD B:MET450 2.3 46.4 1.0 C1C B:HEC1004 3.1 44.4 1.0 CD2 B:HIS406 3.1 49.9 1.0 C4C B:HEC1004 3.1 47.3 1.0 C4D B:HEC1004 3.1 43.3 1.0 C4B B:HEC1004 3.1 48.2 1.0 CE1 B:HIS406 3.1 45.7 1.0 C1A B:HEC1004 3.1 38.8 1.0 C1B B:HEC1004 3.1 45.3 1.0 C1D B:HEC1004 3.1 40.1 1.0 C4A B:HEC1004 3.1 44.0 1.0 CE B:MET450 3.3 50.2 1.0 CG B:MET450 3.4 39.4 1.0 CHA B:HEC1004 3.5 43.9 1.0 CHC B:HEC1004 3.5 52.0 1.0 CHD B:HEC1004 3.5 48.9 1.0 CHB B:HEC1004 3.5 40.7 1.0 ND1 B:HIS406 4.2 43.4 1.0 CG B:HIS406 4.2 46.6 1.0 CB B:MET450 4.3 44.9 1.0 C2C B:HEC1004 4.4 48.1 1.0 C3C B:HEC1004 4.4 42.5 1.0 C3A B:HEC1004 4.4 37.9 1.0 C2A B:HEC1004 4.4 37.6 1.0 C3B B:HEC1004 4.4 48.3 1.0 C2B B:HEC1004 4.4 44.7 1.0 C3D B:HEC1004 4.4 47.4 1.0 C2D B:HEC1004 4.4 47.8 1.0

J.M.Kurth, J.A.Brito, J.Reuter, A.Flegler, T.Koch, T.Franke, E.M.Klein, S.F.Rowe, J.N.Butt, K.Denkmann, I.A.Pereira, M.Archer, C.Dahl. Electron Accepting Units of the Diheme Cytochrome C Tsda, A Bifunctional Thiosulfate Dehydrogenase/Tetrathionate Reductase. J.Biol.Chem. V. 291 24804 2016.
ISSN: ESSN 1083-351X
PubMed: 27694441
DOI: 10.1074/JBC.M116.753863