Iron in PDB 2e4p: Crystal Structure of BPHA3 (Oxidized Form)

The structure of Crystal Structure of BPHA3 (Oxidized Form), PDB code: 2e4p was solved by M.Senda, S.Kishigami, S.Kimura, T.Ishida, M.Fukuda, T.Senda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.65 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	26.294, 144.113, 61.176, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.4

The binding sites of Iron atom in the Crystal Structure of BPHA3 (Oxidized Form) (pdb code 2e4p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of BPHA3 (Oxidized Form), PDB code: 2e4p:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of BPHA3 (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of BPHA3 (Oxidized Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:13.1 occ:1.00 FE1 A:FES1001 0.0 13.1 1.0 S2 A:FES1001 2.2 16.1 1.0 S1 A:FES1001 2.2 15.3 1.0 SG A:CYS63 2.3 16.8 1.0 SG A:CYS43 2.3 12.5 1.0 FE2 A:FES1001 2.8 16.7 1.0 CB A:CYS63 3.1 16.6 1.0 CB A:CYS43 3.2 12.5 1.0 CB A:HIS45 4.1 15.4 1.0 N A:GLY46 4.4 17.1 1.0 ND1 A:HIS45 4.5 16.9 1.0 CA A:CYS63 4.6 16.8 1.0 CA A:CYS43 4.7 12.5 1.0 ND1 A:HIS66 4.7 16.9 1.0 N A:HIS66 4.7 17.5 1.0 CB A:LEU65 4.8 17.7 1.0 CG A:HIS45 4.8 16.2 1.0 N A:HIS45 4.8 14.8 1.0 CA A:HIS45 4.8 16.0 1.0 CB A:TRP48 4.8 16.8 1.0 C A:HIS45 4.9 16.4 1.0 C A:CYS63 5.0 17.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of BPHA3 (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of BPHA3 (Oxidized Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:16.7 occ:1.00 FE2 A:FES1001 0.0 16.7 1.0 S1 A:FES1001 2.2 15.3 1.0 ND1 A:HIS45 2.2 16.9 1.0 S2 A:FES1001 2.2 16.1 1.0 ND1 A:HIS66 2.3 16.9 1.0 FE1 A:FES1001 2.8 13.1 1.0 CG A:HIS66 3.1 17.4 1.0 CG A:HIS45 3.2 16.2 1.0 CE1 A:HIS45 3.2 18.0 1.0 CB A:HIS66 3.3 17.9 1.0 CE1 A:HIS66 3.3 17.0 1.0 CB A:HIS45 3.4 15.4 1.0 N A:HIS66 4.1 17.5 1.0 C A:HIS45 4.2 16.4 1.0 NE2 A:HIS45 4.3 16.7 1.0 CA A:HIS66 4.3 17.6 1.0 CD2 A:HIS45 4.3 17.4 1.0 CD2 A:HIS66 4.3 16.6 1.0 N A:GLY46 4.3 17.1 1.0 NE2 A:HIS66 4.4 15.7 1.0 CA A:HIS45 4.4 16.0 1.0 SG A:CYS43 4.4 12.5 1.0 SG A:CYS63 4.5 16.8 1.0 O A:HIS45 4.6 17.0 1.0 CB A:LEU65 4.7 17.7 1.0 CG A:PRO81 4.7 17.6 1.0 C A:LEU65 4.9 17.6 1.0 CA A:GLY46 4.9 17.1 1.0 CD A:PRO81 5.0 16.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of BPHA3 (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of BPHA3 (Oxidized Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1001 b:15.1 occ:1.00 FE1 B:FES1001 0.0 15.1 1.0 S1 B:FES1001 2.2 18.1 1.0 S2 B:FES1001 2.2 20.6 1.0 SG B:CYS63 2.2 18.4 1.0 SG B:CYS43 2.4 17.0 1.0 FE2 B:FES1001 2.8 20.8 1.0 CB B:CYS63 3.1 18.7 1.0 CB B:CYS43 3.1 16.9 1.0 CB B:HIS45 4.1 18.0 1.0 N B:GLY46 4.4 19.2 1.0 ND1 B:HIS45 4.5 16.5 1.0 CA B:CYS63 4.6 19.1 1.0 CA B:CYS43 4.6 16.9 1.0 ND1 B:HIS66 4.6 20.4 1.0 CB B:LEU65 4.7 20.7 1.0 N B:HIS66 4.7 19.9 1.0 CB B:TRP48 4.8 20.1 1.0 N B:HIS45 4.8 18.3 1.0 CA B:HIS45 4.8 18.6 1.0 CG B:HIS45 4.8 17.7 1.0 CG B:PRO82 4.8 18.5 1.0 C B:HIS45 4.9 19.1 1.0 C B:CYS63 5.0 19.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of BPHA3 (Oxidized Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of BPHA3 (Oxidized Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1001 b:20.8 occ:1.00 FE2 B:FES1001 0.0 20.8 1.0 ND1 B:HIS45 2.2 16.5 1.0 S1 B:FES1001 2.2 18.1 1.0 S2 B:FES1001 2.2 20.6 1.0 ND1 B:HIS66 2.3 20.4 1.0 FE1 B:FES1001 2.8 15.1 1.0 CG B:HIS45 3.1 17.7 1.0 CG B:HIS66 3.2 20.0 1.0 CE1 B:HIS45 3.2 17.7 1.0 CE1 B:HIS66 3.2 21.1 1.0 CB B:HIS45 3.4 18.0 1.0 CB B:HIS66 3.4 19.5 1.0 N B:HIS66 4.0 19.9 1.0 C B:HIS45 4.2 19.1 1.0 CD2 B:HIS45 4.3 18.0 1.0 NE2 B:HIS45 4.3 17.9 1.0 CA B:HIS66 4.3 19.3 1.0 N B:GLY46 4.3 19.2 1.0 CD2 B:HIS66 4.3 20.1 1.0 NE2 B:HIS66 4.3 19.0 1.0 CA B:HIS45 4.4 18.6 1.0 CG B:PRO81 4.4 16.5 1.0 SG B:CYS43 4.4 17.0 1.0 O B:HIS45 4.5 19.2 1.0 SG B:CYS63 4.5 18.4 1.0 O B:HOH1027 4.6 29.8 1.0 CB B:LEU65 4.6 20.7 1.0 CD2 B:LEU65 4.7 20.5 1.0 CG B:LEU65 4.8 20.1 1.0 CA B:GLY46 4.9 20.2 1.0 C B:LEU65 4.9 20.8 1.0

M.Senda, S.Kishigami, S.Kimura, M.Fukuda, T.Ishida, T.Senda. Molecular Mechanism of the Redox-Dependent Interaction Between Nadh-Dependent Ferredoxin Reductase and Rieske-Type [2FE-2S] Ferredoxin J.Mol.Biol. V. 373 382 2007.
ISSN: ISSN 0022-2836
PubMed: 17850818
DOI: 10.1016/J.JMB.2007.08.002