Iron in PDB 1yv1: Fully Reduced State of Nigerythrin (All Ferrous)

The structure of Fully Reduced State of Nigerythrin (All Ferrous), PDB code: 1yv1 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)	23.72 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.773, 72.907, 118.905, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 20.6

The binding sites of Iron atom in the Fully Reduced State of Nigerythrin (All Ferrous) (pdb code 1yv1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Fully Reduced State of Nigerythrin (All Ferrous), PDB code: 1yv1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Fully Reduced State of Nigerythrin (All Ferrous)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fully Reduced State of Nigerythrin (All Ferrous) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:8.2 occ:1.00 OE2 A:GLU149 2.0 7.5 1.0 OE1 A:GLU73 2.1 9.1 1.0 ND1 A:HIS76 2.2 8.6 1.0 OE1 A:GLU40 2.3 9.6 1.0 OE2 A:GLU40 2.3 9.8 1.0 O A:HOH304 2.4 16.8 1.0 CD A:GLU40 2.6 9.8 1.0 CD A:GLU149 2.9 7.2 1.0 CE1 A:HIS76 3.0 8.5 1.0 OE1 A:GLU149 3.1 7.4 1.0 CD A:GLU73 3.2 9.0 1.0 CG A:HIS76 3.3 8.7 1.0 CB A:HIS76 3.7 9.0 1.0 OE2 A:GLU73 3.8 9.0 1.0 O A:HOH356 3.9 14.7 1.0 FE A:FE2302 3.9 8.5 1.0 CA A:GLU73 4.1 9.1 1.0 CG A:GLU40 4.1 9.8 1.0 NE2 A:HIS76 4.2 8.4 1.0 CG A:GLU73 4.2 9.0 1.0 CB A:GLU73 4.2 9.0 1.0 CD2 A:HIS76 4.3 8.6 1.0 CG A:GLU149 4.3 6.9 1.0 OH A:TYR123 4.6 6.8 1.0 OE2 A:GLU118 4.7 9.9 1.0 CB A:GLU40 4.8 9.9 1.0 CE1 A:TYR123 4.9 6.6 1.0 N A:GLU73 4.9 8.8 1.0 O A:GLU73 4.9 9.3 1.0 CB A:ALA145 5.0 7.1 1.0

Iron binding site 2 out of 6 in the Fully Reduced State of Nigerythrin (All Ferrous)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fully Reduced State of Nigerythrin (All Ferrous) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:8.5 occ:1.00 OE2 A:GLU73 2.0 9.0 1.0 OE1 A:GLU149 2.1 7.4 1.0 OE1 A:GLU115 2.2 6.9 1.0 ND1 A:HIS152 2.3 6.4 1.0 O A:HOH356 2.3 14.7 1.0 OE2 A:GLU115 2.4 7.2 1.0 CD A:GLU115 2.6 7.1 1.0 CD A:GLU73 3.0 9.0 1.0 CE1 A:HIS152 3.1 6.4 1.0 CD A:GLU149 3.2 7.2 1.0 OE1 A:GLU73 3.2 9.1 1.0 CG A:HIS152 3.4 6.3 1.0 OE2 A:GLU149 3.8 7.5 1.0 CB A:HIS152 3.8 6.3 1.0 O A:HOH304 3.8 16.8 1.0 FE A:FE2301 3.9 8.2 1.0 CA A:GLU149 4.1 6.1 1.0 OE2 A:GLU118 4.1 9.9 1.0 CG A:GLU115 4.1 7.0 1.0 CG2 A:THR69 4.2 7.9 1.0 CB A:GLU149 4.3 6.3 1.0 NE2 A:HIS152 4.3 6.4 1.0 CG A:GLU149 4.3 6.9 1.0 CG A:GLU73 4.4 9.0 1.0 CD2 A:HIS152 4.4 6.4 1.0 CE1 A:TYR47 4.4 8.4 1.0 OH A:TYR47 4.6 8.6 1.0 N A:GLU149 4.8 6.1 1.0 CE1 A:HIS76 4.8 8.5 1.0 CB A:GLU115 4.9 7.0 1.0 O A:GLU149 4.9 5.9 1.0

Iron binding site 3 out of 6 in the Fully Reduced State of Nigerythrin (All Ferrous)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fully Reduced State of Nigerythrin (All Ferrous) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:8.4 occ:1.00 SG A:CYS192 2.3 11.4 1.0 SG A:CYS177 2.3 8.6 1.0 SG A:CYS189 2.3 10.6 1.0 SG A:CYS174 2.3 8.8 1.0 CB A:CYS189 3.2 11.7 1.0 CB A:CYS174 3.3 9.1 1.0 CB A:CYS177 3.5 8.8 1.0 CB A:CYS192 3.5 12.1 1.0 N A:CYS177 3.8 9.0 1.0 N A:CYS192 3.8 12.0 1.0 CA A:CYS192 4.2 12.3 1.0 CA A:CYS177 4.2 8.8 1.0 CB A:TYR179 4.3 9.2 1.0 CB A:ARG194 4.3 15.0 1.0 CB A:ILE176 4.5 9.5 1.0 CB A:ILE191 4.5 11.5 1.0 CA A:CYS189 4.7 11.9 1.0 C A:ILE176 4.7 9.2 1.0 CA A:CYS174 4.7 9.3 1.0 C A:ILE191 4.7 11.8 1.0 C A:CYS192 4.8 12.7 1.0 N A:TYR179 4.9 8.9 1.0 C A:CYS177 4.9 8.8 1.0 N A:ARG194 4.9 14.4 1.0 CG2 A:ILE191 4.9 11.5 1.0 N A:GLY178 4.9 8.8 1.0 CA A:ILE176 4.9 9.3 1.0 N A:PHE193 5.0 13.2 1.0 N A:ILE176 5.0 9.3 1.0

Iron binding site 4 out of 6 in the Fully Reduced State of Nigerythrin (All Ferrous)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fully Reduced State of Nigerythrin (All Ferrous) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:7.5 occ:1.00 OE2 B:GLU149 2.1 7.1 1.0 OE1 B:GLU73 2.2 7.9 1.0 O B:HOH304 2.2 17.2 1.0 OE1 B:GLU40 2.2 8.9 1.0 OE2 B:GLU40 2.2 8.8 1.0 ND1 B:HIS76 2.3 7.0 1.0 CD B:GLU40 2.5 8.8 1.0 CD B:GLU149 3.0 6.8 1.0 CE1 B:HIS76 3.1 7.0 1.0 CD B:GLU73 3.2 7.8 1.0 OE1 B:GLU149 3.3 6.9 1.0 CG B:HIS76 3.3 7.1 1.0 CB B:HIS76 3.7 7.3 1.0 O B:HOH318 3.9 12.6 1.0 OE2 B:GLU73 3.9 7.9 1.0 FE B:FE2302 4.0 8.1 1.0 CG B:GLU40 4.0 8.7 1.0 CA B:GLU73 4.1 7.6 1.0 CB B:GLU73 4.2 7.7 1.0 CG B:GLU73 4.2 7.7 1.0 NE2 B:HIS76 4.3 6.9 1.0 CG B:GLU149 4.4 6.6 1.0 O B:HOH516 4.4 23.5 1.0 CD2 B:HIS76 4.4 7.0 1.0 OH B:TYR123 4.5 7.1 1.0 CE1 B:TYR123 4.8 6.9 1.0 CB B:GLU40 4.8 8.6 1.0 CB B:ALA145 4.8 6.4 1.0 O B:GLU73 4.9 7.7 1.0 N B:GLU73 4.9 7.4 1.0

Iron binding site 5 out of 6 in the Fully Reduced State of Nigerythrin (All Ferrous)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Fully Reduced State of Nigerythrin (All Ferrous) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:8.1 occ:1.00 OE2 B:GLU73 2.1 7.9 1.0 OE1 B:GLU149 2.1 6.9 1.0 O B:HOH318 2.2 12.6 1.0 ND1 B:HIS152 2.2 5.7 1.0 OE1 B:GLU115 2.2 6.1 1.0 OE2 B:GLU115 2.3 6.4 1.0 CD B:GLU115 2.6 6.4 1.0 CD B:GLU73 3.0 7.8 1.0 CE1 B:HIS152 3.1 5.7 1.0 CD B:GLU149 3.2 6.8 1.0 OE1 B:GLU73 3.2 7.9 1.0 CG B:HIS152 3.4 5.6 1.0 O B:HOH304 3.7 17.2 1.0 CB B:HIS152 3.8 5.5 1.0 OE2 B:GLU149 3.8 7.1 1.0 FE B:FE2301 4.0 7.5 1.0 CA B:GLU149 4.1 5.9 1.0 CG B:GLU115 4.1 6.3 1.0 CG2 B:THR69 4.1 6.8 1.0 OE2 B:GLU118 4.2 10.8 1.0 CB B:GLU149 4.3 6.1 1.0 NE2 B:HIS152 4.3 5.7 1.0 CG B:GLU149 4.3 6.6 1.0 CE1 B:TYR47 4.4 7.0 1.0 CG B:GLU73 4.4 7.7 1.0 CD2 B:HIS152 4.4 5.7 1.0 OH B:TYR47 4.5 7.2 1.0 N B:GLU149 4.8 5.9 1.0 CB B:GLU115 4.9 6.4 1.0 O B:GLU149 4.9 5.7 1.0 CE1 B:HIS76 4.9 7.0 1.0 CZ B:TYR47 5.0 7.0 1.0

Iron binding site 6 out of 6 in the Fully Reduced State of Nigerythrin (All Ferrous)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Fully Reduced State of Nigerythrin (All Ferrous) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:6.9 occ:1.00 SG B:CYS192 2.3 8.8 1.0 SG B:CYS177 2.3 7.0 1.0 SG B:CYS189 2.3 7.7 1.0 SG B:CYS174 2.3 7.4 1.0 CB B:CYS189 3.2 8.9 1.0 CB B:CYS174 3.3 7.9 1.0 CB B:CYS192 3.5 9.3 1.0 CB B:CYS177 3.5 7.4 1.0 N B:CYS192 3.8 9.3 1.0 N B:CYS177 3.8 7.8 1.0 CA B:CYS192 4.2 9.5 1.0 CA B:CYS177 4.2 7.6 1.0 CB B:TYR179 4.3 7.7 1.0 CB B:ILE191 4.5 8.8 1.0 CB B:ARG194 4.5 12.7 1.0 CB B:ILE176 4.5 8.3 1.0 CA B:CYS189 4.7 9.2 1.0 C B:ILE176 4.7 8.0 1.0 CA B:CYS174 4.7 8.1 1.0 C B:ILE191 4.7 9.1 1.0 C B:CYS192 4.8 10.0 1.0 CG2 B:ILE191 4.8 8.9 1.0 N B:ARG194 4.9 11.7 1.0 N B:TYR179 4.9 7.4 1.0 N B:PHE193 4.9 10.4 1.0 C B:CYS177 4.9 7.5 1.0 N B:GLY178 4.9 7.4 1.0 CA B:ILE176 5.0 8.1 1.0 CG B:ARG194 5.0 13.5 1.0 CA B:ILE191 5.0 8.9 1.0 N B:ILE176 5.0 8.2 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