Iron in PDB 2i7f: Sphingomonas Yanoikuyae B1 Ferredoxin

The structure of Sphingomonas Yanoikuyae B1 Ferredoxin, PDB code: 2i7f was solved by S.Ramaswamy, E.N.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.50 / 1.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.064, 62.064, 238.436, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 24

The binding sites of Iron atom in the Sphingomonas Yanoikuyae B1 Ferredoxin (pdb code 2i7f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Sphingomonas Yanoikuyae B1 Ferredoxin, PDB code: 2i7f:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Sphingomonas Yanoikuyae B1 Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sphingomonas Yanoikuyae B1 Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:17.8 occ:1.00 FE1 A:FES501 0.0 17.8 1.0 ND1 A:HIS67 2.1 15.4 1.0 S1 A:FES501 2.2 19.9 1.0 S2 A:FES501 2.2 19.1 1.0 ND1 A:HIS47 2.2 16.9 1.0 FE2 A:FES501 2.8 18.6 1.0 CE1 A:HIS67 2.9 18.4 1.0 CE1 A:HIS47 3.2 16.8 1.0 CG A:HIS47 3.2 14.9 1.0 CG A:HIS67 3.3 17.1 1.0 CB A:HIS47 3.5 15.3 1.0 CB A:HIS67 3.8 17.4 1.0 NE2 A:HIS67 4.1 16.9 1.0 CB A:PHE66 4.1 16.2 1.0 CG A:PRO82 4.2 18.6 1.0 C A:HIS47 4.3 16.0 1.0 O A:PHE66 4.3 16.5 1.0 NE2 A:HIS47 4.3 16.0 1.0 CD2 A:HIS67 4.3 18.1 1.0 CD2 A:HIS47 4.3 18.0 1.0 N A:GLY48 4.3 16.2 1.0 SG A:CYS45 4.5 14.6 1.0 CA A:HIS47 4.5 15.5 1.0 SG A:CYS64 4.5 15.9 1.0 C A:PHE66 4.5 16.7 1.0 O A:HOH534 4.5 28.3 1.0 O A:HIS47 4.6 15.6 1.0 CA A:GLY48 4.9 16.1 1.0 CA A:HIS67 5.0 16.8 1.0

Iron binding site 2 out of 4 in the Sphingomonas Yanoikuyae B1 Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sphingomonas Yanoikuyae B1 Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:18.6 occ:1.00 FE2 A:FES501 0.0 18.6 1.0 S1 A:FES501 2.2 19.9 1.0 SG A:CYS64 2.2 15.9 1.0 S2 A:FES501 2.2 19.1 1.0 SG A:CYS45 2.3 14.6 1.0 FE1 A:FES501 2.8 17.8 1.0 CB A:CYS64 3.1 16.4 1.0 CB A:CYS45 3.2 16.3 1.0 CB A:HIS47 4.1 15.3 1.0 O A:PHE66 4.2 16.5 1.0 N A:GLY48 4.4 16.2 1.0 ND1 A:HIS47 4.5 16.9 1.0 SG A:CYS83 4.5 20.7 1.0 ND1 A:HIS67 4.5 15.4 1.0 CA A:CYS45 4.6 16.0 1.0 CA A:CYS64 4.6 16.6 1.0 CB A:PHE66 4.6 16.2 1.0 CB A:ALA50 4.7 15.1 1.0 CG A:HIS47 4.8 14.9 1.0 N A:HIS47 4.8 15.7 1.0 CA A:HIS47 4.8 15.5 1.0 C A:HIS47 4.9 16.0 1.0 C A:PHE66 4.9 16.7 1.0 N A:PHE66 5.0 17.0 1.0

Iron binding site 3 out of 4 in the Sphingomonas Yanoikuyae B1 Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sphingomonas Yanoikuyae B1 Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:18.9 occ:1.00 FE1 B:FES502 0.0 18.9 1.0 ND1 B:HIS67 2.0 19.2 1.0 ND1 B:HIS47 2.2 15.1 1.0 S2 B:FES502 2.2 17.7 1.0 S1 B:FES502 2.2 17.4 1.0 FE2 B:FES502 2.7 17.3 1.0 CE1 B:HIS67 2.8 23.5 1.0 CE1 B:HIS47 3.1 15.2 1.0 CG B:HIS67 3.1 21.1 1.0 CG B:HIS47 3.2 14.9 1.0 CB B:HIS47 3.5 14.6 1.0 CB B:HIS67 3.6 20.9 1.0 NE2 B:HIS67 4.0 21.1 1.0 CG B:PRO82 4.0 16.4 1.0 CB B:PHE66 4.1 19.8 1.0 CD2 B:HIS67 4.2 21.6 1.0 NE2 B:HIS47 4.2 13.8 1.0 O B:PHE66 4.2 20.3 1.0 CD2 B:HIS47 4.3 14.0 1.0 C B:HIS47 4.3 16.7 1.0 SG B:CYS45 4.4 16.6 1.0 N B:GLY48 4.5 17.0 1.0 O B:HOH555 4.5 22.1 1.0 CA B:HIS47 4.5 15.6 1.0 SG B:CYS64 4.5 15.4 1.0 C B:PHE66 4.5 19.8 1.0 O B:HIS47 4.6 15.4 1.0 CD B:PRO82 4.8 16.5 1.0 CA B:HIS67 4.9 19.9 1.0 N B:HIS67 4.9 20.4 1.0 CA B:GLY48 4.9 17.4 1.0

Iron binding site 4 out of 4 in the Sphingomonas Yanoikuyae B1 Ferredoxin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sphingomonas Yanoikuyae B1 Ferredoxin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe502 b:17.3 occ:1.00 FE2 B:FES502 0.0 17.3 1.0 S1 B:FES502 2.2 17.4 1.0 S2 B:FES502 2.2 17.7 1.0 SG B:CYS45 2.3 16.6 1.0 SG B:CYS64 2.3 15.4 1.0 FE1 B:FES502 2.7 18.9 1.0 CB B:CYS64 3.2 17.8 1.0 CB B:CYS45 3.3 16.6 1.0 O B:PHE66 4.2 20.3 1.0 CB B:HIS47 4.2 14.6 1.0 ND1 B:HIS67 4.4 19.2 1.0 ND1 B:HIS47 4.4 15.1 1.0 CB B:PHE66 4.5 19.8 1.0 N B:GLY48 4.6 17.0 1.0 CB B:ALA50 4.6 15.3 1.0 CA B:CYS64 4.7 18.2 1.0 SG B:CYS83 4.7 19.9 1.0 CA B:CYS45 4.7 16.8 1.0 CG B:HIS47 4.8 14.9 1.0 N B:HIS47 4.8 15.0 1.0 C B:PHE66 4.9 19.8 1.0 CA B:HIS47 4.9 15.6 1.0 C B:HIS47 4.9 16.7 1.0

D.J.Ferraro, E.N.Brown, C.L.Yu, R.E.Parales, D.T.Gibson, S.Ramaswamy. Structural Investigations of the Ferredoxin and Terminal Oxygenase Components of the Biphenyl 2,3-Dioxygenase From Sphingobium Yanoikuyae B1. Bmc Struct.Biol. V. 7 10 2007.
ISSN: ESSN 1472-6807
PubMed: 17349044
DOI: 10.1186/1472-6807-7-10