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

Enzymatic activity of 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;

Protein crystallography data

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

Copper Binding Sites:

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 3hb3

Go back to Copper Binding Sites List in 3hb3
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 3hb3

Go back to Copper Binding Sites List in 3hb3
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 3hb3

Go back to Copper Binding Sites List in 3hb3
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

Reference:

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
Page generated: Thu Sep 3 17:17:40 2020
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