Iron in PDB 1yuz: Partially Reduced State of Nigerythrin

The structure of Partially Reduced State of Nigerythrin, PDB code: 1yuz was solved by R.B.Iyer, R.Silaghi-Dumitrescu, D.M.Kurtz, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.60 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.666, 72.315, 119.020, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 20.8

The binding sites of Iron atom in the Partially Reduced State of Nigerythrin (pdb code 1yuz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Partially Reduced State of Nigerythrin, PDB code: 1yuz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Partially Reduced State of Nigerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Partially Reduced State of Nigerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:11.1 occ:1.00 OE2 A:GLU149 1.9 11.4 1.0 O A:HOH471 2.0 13.7 1.0 OE1 A:GLU40 2.1 11.7 1.0 OE1 A:GLU118 2.2 13.8 1.0 OE1 A:GLU73 2.2 10.6 1.0 OE2 A:GLU40 2.3 11.1 1.0 CD A:GLU40 2.5 11.5 1.0 CD A:GLU149 2.9 10.1 1.0 CD A:GLU118 3.0 13.1 1.0 CD A:GLU73 3.1 10.4 1.0 OE2 A:GLU118 3.2 14.7 1.0 OE1 A:GLU149 3.4 10.2 1.0 FE A:FE2302 3.4 8.5 1.0 OE2 A:GLU73 3.5 10.4 1.0 ND1 A:HIS76 4.0 10.1 1.0 CG A:GLU40 4.0 11.6 1.0 CG A:GLU73 4.2 10.3 1.0 CG A:GLU149 4.2 9.4 1.0 O A:HOH521 4.3 31.0 1.0 CG A:GLU118 4.4 12.1 1.0 OE1 A:GLU115 4.5 8.5 1.0 CE1 A:TYR123 4.5 9.4 1.0 CE1 A:HIS76 4.5 9.8 1.0 OH A:TYR123 4.6 9.8 1.0 CB A:ALA43 4.6 12.2 1.0 CB A:GLU118 4.7 10.5 1.0 CB A:GLU73 4.7 10.2 1.0 CB A:GLU40 4.8 11.7 1.0 OE2 A:GLU115 4.9 8.8 1.0 CA A:GLU40 4.9 11.8 1.0

Iron binding site 2 out of 6 in the Partially Reduced State of Nigerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Partially Reduced State of Nigerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:8.5 occ:1.00 OE2 A:GLU73 2.0 10.4 1.0 OE1 A:GLU149 2.1 10.2 1.0 OE1 A:GLU115 2.1 8.5 1.0 ND1 A:HIS152 2.2 8.0 1.0 O A:HOH471 2.3 13.7 1.0 OE2 A:GLU115 2.3 8.8 1.0 CD A:GLU115 2.5 8.4 1.0 CD A:GLU73 2.9 10.4 1.0 CD A:GLU149 3.0 10.1 1.0 CE1 A:HIS152 3.0 8.1 1.0 OE1 A:GLU73 3.3 10.6 1.0 CG A:HIS152 3.3 7.8 1.0 OE2 A:GLU149 3.4 11.4 1.0 FE A:FE301 3.4 11.1 1.0 CB A:HIS152 3.8 7.7 1.0 CG A:GLU115 4.0 8.3 1.0 CA A:GLU149 4.1 8.3 1.0 CG A:GLU149 4.2 9.4 1.0 CG2 A:THR69 4.2 9.2 1.0 NE2 A:HIS152 4.2 8.0 1.0 CG A:GLU73 4.3 10.3 1.0 CB A:GLU149 4.3 8.7 1.0 CD2 A:HIS152 4.4 7.9 1.0 CE1 A:TYR47 4.5 10.3 1.0 OH A:TYR47 4.6 11.0 1.0 CE1 A:HIS76 4.7 9.8 1.0 N A:GLU149 4.8 8.3 1.0 OE2 A:GLU118 4.8 14.7 1.0 CB A:GLU115 4.8 8.3 1.0 O A:GLU149 4.9 8.0 1.0 OE1 A:GLU118 4.9 13.8 1.0 ND1 A:HIS76 5.0 10.1 1.0

Iron binding site 3 out of 6 in the Partially Reduced State of Nigerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Partially Reduced State of Nigerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:11.8 occ:1.00 SG A:CYS192 2.2 14.2 1.0 SG A:CYS177 2.3 12.4 1.0 SG A:CYS174 2.3 12.2 1.0 SG A:CYS189 2.4 12.4 1.0 CB A:CYS174 3.2 12.4 1.0 CB A:CYS189 3.3 13.5 1.0 CB A:CYS177 3.3 12.8 1.0 CB A:CYS192 3.4 14.5 1.0 N A:CYS192 3.8 14.3 1.0 N A:CYS177 4.0 13.2 1.0 CA A:CYS192 4.1 14.6 1.0 CA A:CYS177 4.2 12.9 1.0 CB A:TYR179 4.3 11.4 1.0 CB A:ILE191 4.5 13.8 1.0 CG1 A:ILE176 4.5 13.6 1.0 C A:CYS177 4.6 12.6 1.0 CA A:CYS174 4.7 12.6 1.0 CB A:ARG194 4.7 16.6 1.0 CA A:CYS189 4.7 13.8 1.0 C A:ILE191 4.7 14.1 1.0 C A:CYS192 4.8 15.0 1.0 O A:CYS177 4.8 12.8 1.0 C A:ILE176 4.9 13.5 1.0 N A:PHE193 4.9 15.4 1.0 CG2 A:ILE191 4.9 13.8 1.0 N A:ARG194 5.0 16.2 1.0 N A:TYR179 5.0 11.3 1.0

Iron binding site 4 out of 6 in the Partially Reduced State of Nigerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Partially Reduced State of Nigerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:10.0 occ:1.00 O B:HOH501 2.0 13.3 1.0 OE2 B:GLU149 2.0 11.0 1.0 OE1 B:GLU118 2.1 12.8 1.0 OE1 B:GLU40 2.1 10.2 1.0 OE1 B:GLU73 2.2 9.9 1.0 OE2 B:GLU40 2.3 10.0 1.0 CD B:GLU40 2.5 10.1 1.0 CD B:GLU149 3.0 9.7 1.0 CD B:GLU118 3.0 12.2 1.0 CD B:GLU73 3.1 9.6 1.0 OE2 B:GLU118 3.3 13.8 1.0 OE1 B:GLU149 3.3 9.9 1.0 FE B:FE2302 3.5 8.1 1.0 OE2 B:GLU73 3.5 9.8 1.0 ND1 B:HIS76 4.0 9.2 1.0 CG B:GLU40 4.0 10.1 1.0 O B:HOH482 4.1 46.7 1.0 CG B:GLU73 4.2 9.3 1.0 CG B:GLU149 4.3 9.0 1.0 CG B:GLU118 4.4 11.2 1.0 CE1 B:TYR123 4.5 7.9 1.0 CE1 B:HIS76 4.5 9.1 1.0 OE1 B:GLU115 4.6 8.0 1.0 OH B:TYR123 4.6 8.0 1.0 CB B:ALA43 4.6 9.9 1.0 CB B:GLU118 4.7 9.7 1.0 CB B:GLU73 4.8 9.0 1.0 CB B:GLU40 4.8 10.0 1.0 OE2 B:GLU115 4.9 8.0 1.0 CA B:GLU40 5.0 10.1 1.0

Iron binding site 5 out of 6 in the Partially Reduced State of Nigerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Partially Reduced State of Nigerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:8.1 occ:1.00 OE1 B:GLU149 2.0 9.9 1.0 OE2 B:GLU73 2.0 9.8 1.0 OE1 B:GLU115 2.2 8.0 1.0 ND1 B:HIS152 2.2 7.1 1.0 O B:HOH501 2.3 13.3 1.0 OE2 B:GLU115 2.3 8.0 1.0 CD B:GLU115 2.5 7.8 1.0 CD B:GLU73 3.0 9.6 1.0 CD B:GLU149 3.0 9.7 1.0 CE1 B:HIS152 3.0 7.2 1.0 OE1 B:GLU73 3.3 9.9 1.0 CG B:HIS152 3.3 7.0 1.0 FE B:FE301 3.5 10.0 1.0 OE2 B:GLU149 3.5 11.0 1.0 CB B:HIS152 3.8 6.9 1.0 CA B:GLU149 4.1 7.6 1.0 CG B:GLU115 4.1 7.8 1.0 CG2 B:THR69 4.1 8.3 1.0 CG B:GLU149 4.2 9.0 1.0 NE2 B:HIS152 4.2 7.1 1.0 CB B:GLU149 4.3 8.2 1.0 CG B:GLU73 4.3 9.3 1.0 CD2 B:HIS152 4.4 7.1 1.0 CE1 B:TYR47 4.5 9.2 1.0 OH B:TYR47 4.6 9.8 1.0 CE1 B:HIS76 4.6 9.1 1.0 OE1 B:GLU118 4.7 12.8 1.0 N B:GLU149 4.8 7.5 1.0 CB B:GLU115 4.9 7.7 1.0 O B:GLU149 4.9 7.4 1.0 ND1 B:HIS76 5.0 9.2 1.0

Iron binding site 6 out of 6 in the Partially Reduced State of Nigerythrin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Partially Reduced State of Nigerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:8.9 occ:1.00 SG B:CYS192 2.3 10.2 1.0 SG B:CYS177 2.3 9.7 1.0 SG B:CYS174 2.3 9.6 1.0 SG B:CYS189 2.3 9.1 1.0 CB B:CYS174 3.2 10.3 1.0 CB B:CYS189 3.2 9.9 1.0 CB B:CYS177 3.4 10.4 1.0 CB B:CYS192 3.4 10.9 1.0 N B:CYS192 3.8 10.7 1.0 N B:CYS177 4.0 10.8 1.0 CA B:CYS192 4.1 11.0 1.0 CA B:CYS177 4.2 10.6 1.0 CB B:TYR179 4.4 9.3 1.0 CB B:ILE191 4.4 10.3 1.0 CG1 B:ILE176 4.5 11.4 1.0 CA B:CYS174 4.6 10.7 1.0 C B:CYS177 4.6 10.5 1.0 C B:ILE191 4.7 10.6 1.0 CA B:CYS189 4.7 10.2 1.0 C B:CYS192 4.8 11.4 1.0 O B:CYS177 4.8 10.8 1.0 CB B:ARG194 4.8 13.6 1.0 CG2 B:ILE191 4.9 10.3 1.0 C B:ILE176 4.9 11.1 1.0 N B:PHE193 4.9 11.7 1.0 CA B:ILE191 4.9 10.3 1.0 N B:ARG194 5.0 12.8 1.0 N B:ILE191 5.0 10.1 1.0

R.B.Iyer, R.Silaghi-Dumitrescu, D.M.Kurtz, W.N.Lanzilotta. High-Resolution Crystal Structures of Desulfovibrio Vulgaris (Hildenborough) Nigerythrin: Facile, Redox-Dependent Iron Movement, Domain Interface Variability, and Peroxidase Activity in the Rubrerythrins. J.Biol.Inorg.Chem. V. 10 407 2005.
ISSN: ISSN 0949-8257
PubMed: 15895271
DOI: 10.1007/S00775-005-0650-8