Iron in PDB 1e5d: Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas

The structure of Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas, PDB code: 1e5d was solved by C.Frazao, G.Silva, C.M.Gomes, P.Matias, R.Coelho, L.Sieker, S.Macedo, M.Y.Liu, S.Oliveira, M.Teixeira, A.V.Xavier, C.Rodrigues-Pousada, M.A.Carrondo, J.Le Gall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.240, 101.250, 90.800, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 24.8

The binding sites of Iron atom in the Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas (pdb code 1e5d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas, PDB code: 1e5d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:11.8 occ:1.00 FE1 A:FEO404 0.0 11.8 1.0 O A:FEO404 1.7 24.1 1.0 NE2 A:HIS226 2.0 8.0 1.0 OD1 A:ASP165 2.1 21.9 1.0 OD2 A:ASP83 2.3 18.8 1.0 O A:HOH2044 2.4 23.7 1.0 O1 A:OXY405 2.6 13.9 1.0 CG A:ASP165 2.9 14.4 1.0 CE1 A:HIS226 2.9 9.6 1.0 OD2 A:ASP165 3.0 15.5 1.0 CD2 A:HIS226 3.1 10.8 1.0 CG A:ASP83 3.2 14.1 1.0 OD1 A:ASP83 3.3 13.7 1.0 FE2 A:FEO404 3.4 15.5 1.0 O2 A:OXY405 3.7 15.5 1.0 ND1 A:HIS226 4.1 8.8 1.0 CG A:HIS226 4.2 8.9 1.0 OD2 A:ASP225 4.2 19.6 1.0 CB A:ASP165 4.3 8.8 1.0 OH A:TYR193 4.4 47.2 1.0 CB A:ASP225 4.4 18.0 1.0 CD2 A:HIS79 4.5 15.0 1.0 NE2 A:HIS79 4.5 14.9 1.0 CE1 A:HIS24 4.6 29.3 1.0 CB A:ASP83 4.6 11.6 1.0 CG A:ASP225 4.8 20.1 1.0 OE1 A:GLU81 4.8 28.6 1.0 CD A:GLU81 4.8 19.8 1.0 CA A:ASP165 4.9 10.8 1.0

Iron binding site 2 out of 4 in the Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:15.5 occ:1.00 FE2 A:FEO404 0.0 15.5 1.0 OD2 A:ASP165 1.9 15.5 1.0 OE1 A:GLU81 2.0 28.6 1.0 NE2 A:HIS146 2.1 24.1 1.0 NE2 A:HIS79 2.1 14.9 1.0 O A:FEO404 2.3 24.1 1.0 O1 A:OXY405 2.7 13.9 1.0 CD A:GLU81 2.9 19.8 1.0 CE1 A:HIS146 2.9 21.5 1.0 CG A:ASP165 3.1 14.4 1.0 O2 A:OXY405 3.1 15.5 1.0 CD2 A:HIS79 3.1 15.0 1.0 CE1 A:HIS79 3.1 19.5 1.0 CD2 A:HIS146 3.2 19.9 1.0 FE1 A:FEO404 3.4 11.8 1.0 OE2 A:GLU81 3.5 21.7 1.0 OD1 A:ASP165 3.6 21.9 1.0 CG A:GLU81 3.8 17.1 1.0 CB A:GLU81 3.9 11.2 1.0 ND1 A:HIS146 4.1 13.3 1.0 CB A:ASP165 4.2 8.8 1.0 OD1 A:ASP83 4.2 13.7 1.0 ND1 A:HIS79 4.2 19.3 1.0 CG A:HIS146 4.3 15.3 1.0 CG A:HIS79 4.3 19.4 1.0 O A:HOH2030 4.5 12.6 1.0 OH A:TYR193 4.8 47.2 1.0 O A:HOH2044 4.8 23.7 1.0 CD1 A:ILE197 4.8 35.6 1.0 OD2 A:ASP83 4.9 18.8 1.0

Iron binding site 3 out of 4 in the Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:13.0 occ:1.00 FE1 B:FEO404 0.0 13.0 1.0 O B:FEO404 1.8 24.1 1.0 NE2 B:HIS226 2.0 8.4 1.0 OD1 B:ASP165 2.1 21.8 1.0 OD2 B:ASP83 2.3 18.8 1.0 O B:HOH2018 2.6 23.8 1.0 O1 B:OXY405 2.6 14.3 1.0 CG B:ASP165 2.9 14.4 1.0 CE1 B:HIS226 2.9 9.7 1.0 OD2 B:ASP165 3.0 15.3 1.0 CD2 B:HIS226 3.1 10.8 1.0 CG B:ASP83 3.2 14.1 1.0 OD1 B:ASP83 3.3 13.6 1.0 FE2 B:FEO404 3.4 16.1 1.0 O2 B:OXY405 3.5 15.6 1.0 ND1 B:HIS226 4.1 8.8 1.0 OH B:TYR193 4.2 47.1 1.0 CG B:HIS226 4.2 8.8 1.0 CB B:ASP165 4.3 8.9 1.0 OD2 B:ASP225 4.5 19.7 1.0 CE1 B:HIS24 4.5 29.3 1.0 CB B:ASP225 4.6 18.0 1.0 CD2 B:HIS79 4.6 15.1 1.0 CB B:ASP83 4.6 11.6 1.0 NE2 B:HIS79 4.6 15.0 1.0 OE1 B:GLU81 4.9 28.5 1.0 CD B:GLU81 4.9 19.8 1.0 CA B:ASP165 4.9 10.9 1.0 OE2 B:GLU81 4.9 21.7 1.0 ND1 B:HIS24 4.9 29.3 1.0 CZ B:PHE23 5.0 19.7 1.0

Iron binding site 4 out of 4 in the Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rubredoxin Oxygen:Oxidoreductase (Roo) From Anaerobe Desulfovibrio Gigas within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:16.1 occ:1.00 FE2 B:FEO404 0.0 16.1 1.0 OD2 B:ASP165 1.9 15.3 1.0 OE1 B:GLU81 2.0 28.5 1.0 NE2 B:HIS146 2.1 24.2 1.0 NE2 B:HIS79 2.1 15.0 1.0 O B:FEO404 2.3 24.1 1.0 CD B:GLU81 2.9 19.8 1.0 CE1 B:HIS146 2.9 21.5 1.0 CG B:ASP165 3.1 14.4 1.0 O2 B:OXY405 3.1 15.6 1.0 CD2 B:HIS79 3.1 15.1 1.0 CE1 B:HIS79 3.1 19.5 1.0 CD2 B:HIS146 3.2 20.0 1.0 O1 B:OXY405 3.3 14.3 1.0 FE1 B:FEO404 3.4 13.0 1.0 OE2 B:GLU81 3.4 21.7 1.0 OD1 B:ASP165 3.6 21.8 1.0 CB B:GLU81 3.8 11.2 1.0 CG B:GLU81 3.9 17.3 1.0 ND1 B:HIS146 4.1 13.3 1.0 OD1 B:ASP83 4.2 13.6 1.0 CB B:ASP165 4.2 8.9 1.0 ND1 B:HIS79 4.2 19.3 1.0 CG B:HIS146 4.3 15.3 1.0 CG B:HIS79 4.3 19.4 1.0 O B:HOH2029 4.5 12.7 1.0 CD1 B:ILE197 4.8 35.6 1.0 OH B:TYR193 4.9 47.1 1.0 OD2 B:ASP83 4.9 18.8 1.0 CG B:ASP83 5.0 14.1 1.0

C.Frazao, G.Silva, C.M.Gomes, P.Matias, R.Coelho, L.Sieker, S.Macedo, M.Y.Liu, S.Oliveira, M.Teixeira, A.V.Xavier, C.Rodrigues-Pousada, M.A.Carrondo, J.Le Gall. Structure of A Dioxygen Reduction Enzyme From Desulfovibrio Gigas Nat.Struct.Biol. V. 7 1041 2000.
ISSN: ISSN 1072-8368
PubMed: 11062560
DOI: 10.1038/80961