Iron in PDB 3sid: Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy

The structure of Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy, PDB code: 3sid 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)	30.74 / 1.40
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	82.009, 82.009, 46.440, 90.00, 90.00, 120.00
R / Rfree (%)	11.5 / 15.6

The binding sites of Iron atom in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy (pdb code 3sid). 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, Azide Adduct at 50% Occupancy, PDB code: 3sid:
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, Azide Adduct at 50% Occupancy


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, Azide Adduct at 50% Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:9.0 occ:1.00 OE2 A:GLU71 2.0 9.9 1.0 OE1 A:GLU162 2.0 9.6 1.0 N3 A:AZI300 2.2 8.7 0.5 OE2 A:GLU128 2.2 8.5 1.0 O A:HOH183 2.2 11.8 0.5 ND1 A:HIS165 2.2 9.1 1.0 OE1 A:GLU128 2.3 8.5 1.0 CD A:GLU128 2.6 7.6 1.0 N2 A:AZI300 2.9 9.9 0.5 CD A:GLU71 2.9 8.5 1.0 CD A:GLU162 3.0 8.9 1.0 CE1 A:HIS165 3.1 9.6 1.0 OE1 A:GLU71 3.3 12.0 1.0 CG A:HIS165 3.3 7.5 1.0 OE2 A:GLU162 3.5 9.6 1.0 FE A:FE201 3.5 11.1 1.0 CB A:HIS165 3.7 7.8 1.0 N1 A:AZI300 3.9 11.5 0.5 CG A:GLU128 4.1 8.2 1.0 OE1 A:GLU131 4.1 13.6 0.5 CG2 A:ILE67 4.2 11.9 1.0 CG A:GLU162 4.2 8.6 1.0 CA A:GLU162 4.3 7.9 1.0 NE2 A:HIS165 4.3 8.5 1.0 CG A:GLU71 4.3 8.8 1.0 CD2 A:HIS165 4.4 8.5 1.0 CB A:GLU162 4.4 8.5 1.0 CE1 A:HIS74 4.4 12.3 1.0 CE2 A:TYR45 4.6 11.6 1.0 OH A:TYR45 4.6 14.1 1.0 OE1 A:GLU40 4.7 13.3 1.0 CD A:GLU131 4.8 11.2 0.5 O A:HOH204 4.8 12.1 0.5 OE2 A:GLU131 4.9 14.4 0.5 CB A:GLU128 5.0 8.6 1.0 CZ A:TYR45 5.0 12.5 1.0 O A:GLU162 5.0 9.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy


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, Azide Adduct at 50% Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:11.1 occ:1.00 O A:HOH204 1.9 12.1 0.5 OE2 A:GLU37 2.0 8.8 0.5 N3 A:AZI300 2.0 8.7 0.5 O A:HOH183 2.0 11.8 0.5 OE1 A:GLU40 2.1 13.3 1.0 OE1 A:GLU71 2.1 12.0 1.0 OE2 A:GLU162 2.1 9.6 1.0 OE1 A:GLU37 2.2 11.1 0.5 OE2 A:GLU131 2.3 14.4 0.5 N2 A:AZI300 2.7 9.9 0.5 CD A:GLU37 2.9 9.3 0.5 CD A:GLU71 3.0 8.5 1.0 CD A:GLU37 3.1 10.6 0.5 CD A:GLU40 3.1 12.7 1.0 CD A:GLU162 3.1 8.9 1.0 CD A:GLU131 3.1 11.2 0.5 OE1 A:GLU37 3.2 13.1 0.5 OE2 A:GLU37 3.2 14.1 0.5 OE1 A:GLU131 3.4 13.6 0.5 OE1 A:GLU162 3.4 9.6 1.0 OE2 A:GLU40 3.5 17.1 1.0 FE A:FE200 3.5 9.0 1.0 OE2 A:GLU71 3.5 9.9 1.0 N1 A:AZI300 3.7 11.5 0.5 CG A:GLU71 4.2 8.8 1.0 ND1 A:HIS74 4.2 11.0 1.0 CG A:GLU37 4.2 9.4 0.5 CG A:GLU162 4.4 8.6 1.0 CG A:GLU131 4.4 9.6 0.5 CG A:GLU40 4.5 10.6 1.0 CG A:GLU37 4.5 8.7 0.5 CE1 A:HIS74 4.6 12.3 1.0 CB A:GLU71 4.7 9.5 1.0 OE1 A:GLU128 4.8 8.5 1.0 CB A:GLU40 4.8 10.1 1.0 CE2 A:TYR136 4.8 14.7 1.0 CA A:GLU37 4.9 9.9 0.5 CA A:GLU37 4.9 9.8 0.5 CB A:GLU37 4.9 9.6 0.5 OE2 A:GLU128 4.9 8.5 1.0 CG A:GLU131 5.0 9.4 0.5

Iron binding site 3 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy


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, Azide Adduct at 50% Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:10.9 occ:1.00 OE1 B:GLU37 2.0 8.4 0.5 O B:HOH198 2.0 12.2 0.5 O B:HOH181 2.0 11.3 0.5 OE1 B:GLU71 2.1 12.1 1.0 N1 B:AZI300 2.1 7.8 0.5 OE2 B:GLU162 2.1 10.3 1.0 OE1 B:GLU40 2.1 13.6 1.0 OE1 B:GLU131 2.2 13.8 0.5 OE1 B:GLU37 2.3 11.4 0.5 N2 B:AZI300 2.7 10.1 0.5 CD B:GLU37 2.9 9.8 0.5 CD B:GLU71 3.0 9.1 1.0 CD B:GLU37 3.0 11.0 0.5 CD B:GLU162 3.1 10.1 1.0 CD B:GLU131 3.1 12.3 0.5 CD B:GLU40 3.1 13.0 1.0 OE2 B:GLU37 3.2 13.7 0.5 OE2 B:GLU37 3.2 12.8 0.5 OE2 B:GLU131 3.4 14.4 0.5 OE1 B:GLU162 3.4 9.0 1.0 OE2 B:GLU40 3.5 16.6 1.0 FE B:FE201 3.5 9.0 1.0 OE2 B:GLU71 3.5 10.5 1.0 N3 B:AZI300 3.7 10.7 0.5 CG B:GLU71 4.2 9.2 1.0 ND1 B:HIS74 4.2 10.7 1.0 CG B:GLU37 4.3 9.7 0.5 CG B:GLU162 4.4 8.7 1.0 CG B:GLU37 4.5 9.2 0.5 CG B:GLU40 4.5 10.2 1.0 CG B:GLU131 4.5 9.3 0.5 CE1 B:HIS74 4.6 10.8 1.0 CB B:GLU71 4.7 9.2 1.0 OE1 B:GLU128 4.8 8.4 1.0 CA B:GLU37 4.8 10.4 0.5 CE2 B:TYR136 4.8 14.9 1.0 CB B:GLU40 4.8 10.4 1.0 OE2 B:GLU128 4.9 9.4 1.0 CG B:GLU131 5.0 10.6 0.5 CB B:GLU37 5.0 9.9 0.5 CA B:GLU37 5.0 9.4 0.5 CB B:GLU37 5.0 9.6 0.5

Iron binding site 4 out of 4 in the Crystal Structure of Oxidized Symerythrin From Cyanophora Paradoxa, Azide Adduct at 50% Occupancy


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, Azide Adduct at 50% Occupancy within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:9.0 occ:1.00 OE2 B:GLU71 2.0 10.5 1.0 OE1 B:GLU162 2.0 9.0 1.0 N1 B:AZI300 2.1 7.8 0.5 O B:HOH181 2.2 11.3 0.5 OE2 B:GLU128 2.2 9.4 1.0 ND1 B:HIS165 2.2 8.8 1.0 OE1 B:GLU128 2.3 8.4 1.0 CD B:GLU128 2.6 7.7 1.0 N2 B:AZI300 2.9 10.1 0.5 CD B:GLU71 2.9 9.1 1.0 CD B:GLU162 3.0 10.1 1.0 CE1 B:HIS165 3.1 10.0 1.0 OE1 B:GLU71 3.2 12.1 1.0 CG B:HIS165 3.3 7.9 1.0 OE2 B:GLU162 3.5 10.3 1.0 FE B:FE200 3.5 10.9 1.0 CB B:HIS165 3.7 8.8 1.0 N3 B:AZI300 3.9 10.7 0.5 OE2 B:GLU131 4.1 14.4 0.5 CG B:GLU128 4.1 7.6 1.0 CG2 B:ILE67 4.2 11.4 1.0 CG B:GLU162 4.2 8.7 1.0 CA B:GLU162 4.3 7.1 1.0 NE2 B:HIS165 4.3 8.6 1.0 CG B:GLU71 4.3 9.2 1.0 CB B:GLU162 4.4 9.0 1.0 CD2 B:HIS165 4.4 8.9 1.0 CE1 B:HIS74 4.4 10.8 1.0 CE2 B:TYR45 4.5 11.8 1.0 OH B:TYR45 4.6 14.8 1.0 OE1 B:GLU40 4.7 13.6 1.0 OE1 B:GLU131 4.8 13.8 0.5 CD B:GLU131 4.8 12.3 0.5 O B:HOH198 4.9 12.2 0.5 CB B:GLU128 4.9 8.9 1.0 CZ B:TYR45 5.0 12.3 1.0

R.B.Cooley, D.J.Arp, P.A.Karplus. Symerythrin Structures at Atomic Resolution and the Origins of Rubrerythrins and the Ferritin-Like Superfamily. J.Mol.Biol. V. 413 177 2011.
ISSN: ISSN 0022-2836
PubMed: 21872605
DOI: 10.1016/J.JMB.2011.08.019