Copper in PDB 3hb3: High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase

All present enzymatic activity of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase:
1.9.3.1;

The structure of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase, PDB code: 3hb3 was solved by J.Koepke, H.Angerer, G.Peng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.403, 150.473, 157.185, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 28

The structure of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Iron	(Fe)	2 atoms
Calcium	(Ca)	1 atom

The binding sites of Copper atom in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase (pdb code 3hb3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase, PDB code: 3hb3:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu561 b:43.4 occ:1.00 O2 A:PEO576 1.9 32.9 1.0 ND1 A:HIS276 2.0 44.1 1.0 NE2 A:HIS326 2.0 44.2 1.0 NE2 A:HIS325 2.0 45.5 1.0 CE1 A:HIS326 2.8 38.1 1.0 CE1 A:HIS276 2.8 42.0 1.0 O1 A:PEO576 2.9 17.5 1.0 CE1 A:HIS325 2.9 42.7 1.0 CD2 A:HIS326 3.1 37.3 1.0 CD2 A:HIS325 3.1 45.2 1.0 CG A:HIS276 3.2 37.2 1.0 CB A:HIS276 3.6 34.9 1.0 ND1 A:HIS326 3.9 37.1 1.0 NE2 A:HIS276 4.0 43.4 1.0 CA A:HIS276 4.0 35.4 1.0 CG A:HIS326 4.1 37.8 1.0 ND1 A:HIS325 4.1 37.0 1.0 CD2 A:HIS276 4.2 36.9 1.0 CG A:HIS325 4.2 41.3 1.0 NA A:HEA560 4.4 34.7 1.0 C1A A:HEA560 4.6 34.6 1.0 FE A:HEA560 4.6 26.6 1.0 C4A A:HEA560 4.7 34.9 1.0 N A:HIS276 4.8 35.8 1.0 ND A:HEA560 4.9 38.8 1.0 CG2 A:VAL279 4.9 33.2 1.0 CHA A:HEA560 4.9 36.2 1.0 O A:GLY275 5.0 37.6 1.0

Copper binding site 2 out of 3 in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu270 b:35.3 occ:1.00 O B:GLU218 2.0 32.6 1.0 ND1 B:HIS224 2.0 38.3 1.0 SG B:CYS220 2.3 32.3 1.0 SG B:CYS216 2.3 29.4 1.0 CU B:CU1271 2.7 32.2 1.0 CE1 B:HIS224 2.8 34.4 1.0 CG B:HIS224 3.2 37.6 1.0 C B:GLU218 3.2 31.1 1.0 CB B:CYS216 3.3 22.1 1.0 CA B:HIS224 3.6 30.9 1.0 CB B:CYS220 3.6 28.9 1.0 CB B:HIS224 3.7 31.3 1.0 O B:HIS224 3.8 28.7 1.0 N B:CYS220 3.9 30.3 1.0 NE2 B:HIS224 4.0 32.6 1.0 N B:LEU219 4.0 30.3 1.0 N B:GLU218 4.1 28.0 1.0 C B:HIS224 4.1 26.9 1.0 C B:CYS216 4.2 24.8 1.0 CD2 B:HIS224 4.2 34.6 1.0 CA B:LEU219 4.2 29.8 1.0 SD B:MET227 4.2 31.5 1.0 O B:CYS216 4.3 23.8 1.0 ND1 B:HIS181 4.3 19.3 1.0 CA B:GLU218 4.3 28.5 1.0 CA B:CYS216 4.3 24.3 1.0 C B:LEU219 4.4 28.5 1.0 CA B:CYS220 4.4 32.0 1.0 N B:SER217 4.4 25.6 1.0 CB B:HIS181 4.7 25.9 1.0 N B:HIS224 4.7 34.1 1.0 CA B:HIS181 4.9 24.4 1.0 CG B:HIS181 5.0 26.7 1.0

Copper binding site 3 out of 3 in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu271 b:32.2 occ:1.00 ND1 B:HIS181 2.0 19.3 1.0 SD B:MET227 2.4 31.5 1.0 SG B:CYS220 2.5 32.3 1.0 SG B:CYS216 2.5 29.4 1.0 CE B:MET227 2.6 17.8 1.0 CU B:CU1270 2.7 35.3 1.0 CG B:HIS181 2.9 26.7 1.0 CE1 B:HIS181 3.0 24.2 1.0 CB B:HIS181 3.2 25.9 1.0 CB B:CYS220 3.4 28.9 1.0 CB B:CYS216 3.6 22.1 1.0 O B:GLU218 3.7 32.6 1.0 CG B:MET227 4.0 21.5 1.0 NE2 B:HIS181 4.1 25.9 1.0 CD2 B:HIS181 4.1 24.0 1.0 CA B:HIS181 4.2 24.4 1.0 CD1 B:TRP121 4.4 40.6 1.0 ND1 B:HIS224 4.7 38.3 1.0 CB B:MET227 4.8 18.0 1.0 O B:HIS119 4.8 25.6 1.0 CA B:CYS220 4.8 32.0 1.0 CA B:HIS224 4.9 30.9 1.0 O B:ILE180 4.9 29.4 1.0

J.Koepke, E.Olkhova, H.Angerer, H.Muller, G.Peng, H.Michel. High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase: New Insights Into the Active Site and the Proton Transfer Pathways Biochim.Biophys.Acta V.1787 635 2009.
ISSN: ISSN 0006-3002
PubMed: 19374884
DOI: 10.1016/J.BBABIO.2009.04.003