Copper in PDB 3ziy: Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution

All present enzymatic activity of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution:
1.7.2.1;

The structure of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution, PDB code: 3ziy was solved by S.V.Antonyuk, C.Han, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.76 / 1.01
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	128.177, 128.177, 86.314, 90.00, 90.00, 120.00
R / Rfree (%)	10.9 / 12.2

The structure of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Copper atom in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution (pdb code 3ziy). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution, PDB code: 3ziy:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:7.2 occ:1.00 ND1 A:HIS94 2.0 6.8 1.0 ND1 A:HIS143 2.1 6.5 1.0 SG A:CYS135 2.2 7.1 1.0 SD A:MET148 2.6 7.1 1.0 HB3 A:HIS143 2.9 6.4 1.0 CE1 A:HIS143 2.9 6.6 1.0 CE1 A:HIS94 3.0 7.2 1.0 CG A:HIS94 3.1 6.8 1.0 CG A:HIS143 3.1 6.4 1.0 HA A:HIS94 3.1 6.8 1.0 HE1 A:HIS143 3.1 6.0 1.0 HE1 A:HIS94 3.1 7.0 1.0 HB3 A:HIS94 3.1 6.6 1.0 HE2 A:MET148 3.2 8.3 1.0 HB2 A:CYS135 3.2 6.6 1.0 CB A:CYS135 3.2 6.7 1.0 HB3 A:CYS135 3.4 6.7 1.0 CE A:MET148 3.4 8.7 1.0 CB A:HIS94 3.5 7.0 1.0 CB A:HIS143 3.5 6.5 1.0 HB A:THR137 3.5 7.5 1.0 HE3 A:MET148 3.7 9.0 1.0 CA A:HIS94 3.8 7.0 1.0 H A:ASN95 3.9 6.6 1.0 HE3 A:TRP61 3.9 6.8 1.0 HG1 A:THR137 3.9 8.0 0.0 O A:PRO93 4.0 7.5 1.0 NE2 A:HIS143 4.1 7.1 1.0 HB2 A:HIS143 4.1 6.7 1.0 NE2 A:HIS94 4.1 7.3 1.0 CG A:MET148 4.1 7.1 1.0 CD2 A:HIS143 4.2 6.6 1.0 CD2 A:HIS94 4.2 6.9 1.0 HE1 A:MET148 4.3 8.8 1.0 OG1 A:THR137 4.3 7.9 1.0 CB A:THR137 4.3 7.0 1.0 HG3 A:MET148 4.4 7.4 1.0 HB2 A:HIS94 4.4 6.3 1.0 HA A:HIS143 4.4 6.0 1.0 HB3 A:MET148 4.4 6.4 1.0 HB2 A:MET148 4.5 6.4 1.0 CE3 A:TRP61 4.6 6.8 1.0 N A:ASN95 4.6 6.7 1.0 H A:THR137 4.6 6.9 1.0 CA A:HIS143 4.6 6.2 1.0 CA A:CYS135 4.6 5.9 1.0 CB A:MET148 4.6 6.3 1.0 HG22 A:THR137 4.7 8.3 1.0 HZ3 A:TRP61 4.8 7.6 1.0 N A:HIS94 4.8 7.1 1.0 C A:HIS94 4.8 7.4 1.0 HA A:CYS135 4.8 5.7 1.0 HB3 A:TRP61 4.8 6.9 1.0 HG2 A:MET148 4.8 7.2 1.0 C A:PRO93 4.8 7.1 1.0 HE2 A:HIS143 4.8 6.3 1.0 HE2 A:HIS94 4.9 7.6 1.0 HG12 A:VAL45 4.9 8.6 1.0

Copper binding site 2 out of 2 in the Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii at 1.01 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:7.6 occ:1.00 NE2 A:HIS99 2.0 6.9 1.0 NE2 A:HIS134 2.0 6.6 1.0 O A:HOH2282 2.1 9.1 1.0 O A:HOH2384 2.5 12.8 0.5 CD2 A:HIS134 2.9 6.5 1.0 CE1 A:HIS99 3.0 7.0 1.0 CD2 A:HIS99 3.0 6.5 1.0 HD2 A:HIS134 3.1 5.9 1.0 CE1 A:HIS134 3.1 6.6 1.0 HE1 A:HIS99 3.1 6.1 1.0 HD2 A:HIS99 3.3 6.5 1.0 HE1 A:HIS134 3.3 6.5 1.0 O A:HOH2806 3.6 16.7 0.5 OD2 A:ASP97 3.9 7.2 1.0 ND1 A:HIS99 4.1 6.9 1.0 CG A:HIS134 4.1 5.7 1.0 ND1 A:HIS134 4.2 6.4 1.0 CG A:HIS99 4.2 6.4 1.0 CG A:ASP97 4.5 6.5 1.0 HB3 A:ASP97 4.8 6.3 1.0 HA3 A:GLY269 4.9 6.2 1.0 OD1 A:ASP97 4.9 7.4 1.0 HD1 A:HIS99 4.9 7.1 1.0 HD1 A:HIS134 4.9 6.5 1.0 HG13 A:VAL132 5.0 6.0 1.0

S.V.Antonyuk, C.Han, R.R.Eady, S.S.Hasnain. Structures of Protein-Protein Complexes Involved in Electron Transfer. Nature V. 496 123 2013.
ISSN: ESSN 1476-4687
PubMed: 23535590
DOI: 10.1038/NATURE11996