Iron in PDB 3qhb: Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa

The structure of Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, PDB code: 3qhb was solved by R.B.Cooley, D.J.Arp, P.A.Karplus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.60 / 1.20
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	81.593, 81.593, 46.277, 90.00, 90.00, 120.00
R / Rfree (%)	10.1 / 12.5

The binding sites of Iron atom in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa (pdb code 3qhb). 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 Oxidized Symerythrin From Cyanophora Paradoxa, PDB code: 3qhb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa


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 Oxidized Symerythrin From Cyanophora Paradoxa within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe182 b:6.0 occ:1.00 OE2 A:GLU71 2.0 7.4 1.0 OE2 A:GLU162 2.0 6.2 1.0 O A:HOH190 2.2 7.1 1.0 OE2 A:GLU128 2.2 6.4 1.0 ND1 A:HIS165 2.2 5.9 1.0 OE1 A:GLU128 2.2 5.9 1.0 CD A:GLU128 2.5 5.7 1.0 CD A:GLU162 3.0 6.0 1.0 CD A:GLU71 3.0 6.5 1.0 CE1 A:HIS165 3.1 6.3 1.0 OE1 A:GLU71 3.3 8.5 1.0 CG A:HIS165 3.3 4.8 1.0 OE1 A:GLU162 3.4 7.7 1.0 FE A:FE181 3.6 7.5 1.0 CB A:HIS165 3.7 6.2 1.0 CG A:GLU128 4.0 6.5 1.0 OE1 A:GLU131 4.1 10.1 1.0 CG2 A:ILE67 4.2 9.1 1.0 CG A:GLU162 4.2 6.3 1.0 OE2 A:GLU40 4.3 8.3 0.5 NE2 A:HIS165 4.3 6.9 1.0 CA A:GLU162 4.3 6.1 1.0 CG A:GLU71 4.3 6.3 1.0 CD2 A:HIS165 4.4 6.4 1.0 CB A:GLU162 4.4 5.8 1.0 CE1 A:HIS74 4.5 7.8 1.0 CE2 A:TYR45 4.6 9.5 1.0 OH A:TYR45 4.6 11.5 1.0 OE1 A:GLU40 4.7 8.0 0.5 CD A:GLU131 4.8 8.7 1.0 OE2 A:GLU131 4.8 9.1 1.0 OE1 A:GLU40 4.9 9.1 0.5 CB A:GLU128 4.9 6.1 1.0 CD A:GLU40 5.0 7.5 0.5

Iron binding site 2 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa


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 Oxidized Symerythrin From Cyanophora Paradoxa within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe181 b:7.5 occ:1.00 OE1 A:GLU40 1.9 8.0 0.5 OE2 A:GLU37 2.0 9.7 1.0 O A:HOH190 2.1 7.1 1.0 OE2 A:GLU131 2.1 9.1 1.0 OE1 A:GLU71 2.1 8.5 1.0 OE1 A:GLU162 2.1 7.7 1.0 OE1 A:GLU40 2.2 9.1 0.5 CD A:GLU40 3.0 7.5 0.5 CD A:GLU37 3.0 8.3 1.0 CD A:GLU131 3.0 8.7 1.0 CD A:GLU71 3.1 6.5 1.0 CD A:GLU162 3.1 6.0 1.0 OE1 A:GLU37 3.2 15.9 1.0 OE2 A:GLU40 3.3 8.3 0.5 OE1 A:GLU131 3.3 10.1 1.0 CD A:GLU40 3.3 8.4 0.5 OE2 A:GLU162 3.5 6.2 1.0 FE A:FE182 3.6 6.0 1.0 OE2 A:GLU71 3.6 7.4 1.0 OE2 A:GLU40 3.7 9.6 0.5 O A:HOH400 4.0 11.7 0.3 CG A:GLU71 4.3 6.3 1.0 CG A:GLU40 4.3 5.7 0.5 CG A:GLU37 4.3 7.8 1.0 OH A:TYR136 4.3 11.7 0.7 O A:HOH341 4.4 8.5 0.5 CG A:GLU131 4.4 7.2 1.0 CG A:GLU162 4.4 6.3 1.0 ND1 A:HIS74 4.4 7.5 1.0 CE2 A:TYR136 4.4 7.0 0.7 CG A:GLU40 4.6 6.0 0.5 OE1 A:GLU128 4.7 5.9 1.0 O A:HOH316 4.7 13.8 0.5 CB A:GLU40 4.8 5.7 0.5 CB A:GLU71 4.8 6.7 1.0 CB A:GLU40 4.9 6.1 0.5 CZ A:TYR136 4.9 9.8 0.7 CA A:GLU37 4.9 7.0 1.0 CE1 A:HIS74 4.9 7.8 1.0 OE2 A:GLU128 4.9 6.4 1.0 CE2 A:TYR136 5.0 12.2 0.3 CB A:GLU37 5.0 7.2 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa


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 Oxidized Symerythrin From Cyanophora Paradoxa within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe182 b:6.0 occ:1.00 OE2 B:GLU71 2.0 7.3 1.0 OE2 B:GLU162 2.0 6.1 1.0 O B:HOH192 2.2 7.3 1.0 ND1 B:HIS165 2.2 5.9 1.0 OE2 B:GLU128 2.2 6.2 1.0 OE1 B:GLU128 2.2 5.8 1.0 CD B:GLU128 2.5 5.9 1.0 CD B:GLU162 3.0 6.2 1.0 CD B:GLU71 3.0 6.7 1.0 CE1 B:HIS165 3.1 6.9 1.0 OE1 B:GLU71 3.3 8.7 1.0 CG B:HIS165 3.3 5.6 1.0 OE1 B:GLU162 3.4 7.3 1.0 FE B:FE181 3.6 7.5 1.0 CB B:HIS165 3.7 6.0 1.0 CG B:GLU128 4.0 6.3 1.0 OE1 B:GLU131 4.1 10.2 1.0 CG2 B:ILE67 4.2 9.0 1.0 CG B:GLU162 4.2 6.1 1.0 CA B:GLU162 4.3 5.7 1.0 OE2 B:GLU40 4.3 8.0 0.5 NE2 B:HIS165 4.3 6.7 1.0 CG B:GLU71 4.3 6.3 1.0 CB B:GLU162 4.4 5.7 1.0 CD2 B:HIS165 4.4 6.7 1.0 CE1 B:HIS74 4.5 7.7 1.0 CE2 B:TYR45 4.6 9.0 1.0 OH B:TYR45 4.6 11.4 1.0 OE1 B:GLU40 4.8 8.1 0.5 OE1 B:GLU40 4.8 9.8 0.5 OE2 B:GLU131 4.8 9.2 1.0 CD B:GLU131 4.8 8.6 1.0 CB B:GLU128 4.9 6.1 1.0 CD B:GLU40 5.0 7.9 0.5

Iron binding site 4 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa


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 Oxidized Symerythrin From Cyanophora Paradoxa within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe181 b:7.5 occ:1.00 OE1 B:GLU40 2.0 8.1 0.5 OE2 B:GLU37 2.0 9.9 1.0 O B:HOH192 2.1 7.3 1.0 OE2 B:GLU131 2.1 9.2 1.0 OE1 B:GLU71 2.1 8.7 1.0 OE1 B:GLU162 2.1 7.3 1.0 OE1 B:GLU40 2.2 9.8 0.5 CD B:GLU40 3.0 7.9 0.5 CD B:GLU37 3.0 7.9 1.0 CD B:GLU131 3.0 8.6 1.0 CD B:GLU71 3.1 6.7 1.0 CD B:GLU162 3.1 6.2 1.0 OE1 B:GLU37 3.2 15.0 1.0 OE2 B:GLU40 3.3 8.0 0.5 OE1 B:GLU131 3.3 10.2 1.0 CD B:GLU40 3.3 8.9 0.5 OE2 B:GLU162 3.5 6.1 1.0 OE2 B:GLU71 3.6 7.3 1.0 FE B:FE182 3.6 6.0 1.0 OE2 B:GLU40 3.7 9.6 0.5 O B:HOH399 4.0 12.5 0.3 CG B:GLU71 4.3 6.3 1.0 CG B:GLU40 4.3 5.4 0.5 CG B:GLU37 4.3 7.2 1.0 OH B:TYR136 4.4 12.1 0.7 O B:HOH340 4.4 8.5 0.5 CG B:GLU131 4.4 7.5 1.0 ND1 B:HIS74 4.4 7.2 1.0 CG B:GLU162 4.4 6.1 1.0 CE2 B:TYR136 4.4 7.4 0.7 CG B:GLU40 4.6 6.2 0.5 OE1 B:GLU128 4.7 5.8 1.0 O B:HOH311 4.8 13.7 0.5 CB B:GLU40 4.8 5.5 0.5 CB B:GLU71 4.8 6.5 1.0 CB B:GLU40 4.9 5.7 0.5 CZ B:TYR136 4.9 9.2 0.7 CE1 B:HIS74 4.9 7.7 1.0 CA B:GLU37 4.9 6.9 1.0 OE2 B:GLU128 5.0 6.2 1.0 CB B:GLU37 5.0 7.3 1.0

R.B.Cooley, T.W.Rhoads, D.J.Arp, P.A.Karplus. A Diiron Protein Autogenerates A Valine-Phenylalanine Cross-Link. Science V. 332 929 2011.
ISSN: ISSN 0036-8075
PubMed: 21596985
DOI: 10.1126/SCIENCE.1205687