Copper in PDB 5djq: The Structure of CBB3 Cytochrome Oxidase.

All present enzymatic activity of The Structure of CBB3 Cytochrome Oxidase.:
1.9.3.1;

The structure of The Structure of CBB3 Cytochrome Oxidase., PDB code: 5djq was solved by S.Buschmann, E.Warkentin, H.Xie, M.Kohlstaedt, J.D.Langer, U.Ermler, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.98 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	136.475, 279.933, 175.192, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.3

The structure of The Structure of CBB3 Cytochrome Oxidase. also contains other interesting chemical elements:

Iron	(Fe)	24 atoms
Calcium	(Ca)	8 atoms

The binding sites of Copper atom in the The Structure of CBB3 Cytochrome Oxidase. (pdb code 5djq). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the The Structure of CBB3 Cytochrome Oxidase., PDB code: 5djq:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu503 b:0.4 occ:1.00 NE2 A:HIS257 2.0 49.3 1.0 NE2 A:HIS258 2.1 88.5 1.0 ND1 A:HIS207 2.1 78.5 1.0 O2 A:PEO505 2.1 74.6 1.0 CE1 A:HIS257 2.7 65.4 1.0 CG A:HIS207 2.7 73.7 1.0 CB A:HIS207 2.9 68.9 1.0 CD2 A:HIS258 2.9 81.2 1.0 CE1 A:HIS258 3.0 87.3 1.0 O1 A:PEO505 3.1 74.1 1.0 CE1 A:HIS207 3.2 86.5 1.0 CD2 A:HIS257 3.2 65.2 1.0 CA A:HIS207 3.6 71.8 1.0 ND1 A:HIS257 3.9 66.4 1.0 NA A:HEM501 3.9 64.6 1.0 CD2 A:HIS207 4.0 76.5 1.0 CG A:HIS258 4.0 65.7 1.0 ND1 A:HIS258 4.0 69.0 1.0 C4A A:HEM501 4.1 66.3 1.0 NE2 A:HIS207 4.1 78.2 1.0 CG A:HIS257 4.1 65.0 1.0 CHB A:HEM501 4.3 72.1 1.0 O A:ALA254 4.4 67.7 1.0 C1A A:HEM501 4.5 58.0 1.0 N A:HIS207 4.6 71.7 1.0 C1B A:HEM501 4.6 66.7 1.0 FE A:HEM501 4.7 59.2 1.0 C A:HIS207 4.7 75.3 1.0 C3A A:HEM501 4.8 63.5 1.0 NB A:HEM501 4.9 60.7 1.0 O A:HIS207 4.9 80.9 1.0 C2A A:HEM501 5.0 55.3 1.0

Copper binding site 2 out of 4 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu503 b:0.9 occ:1.00 NE2 D:HIS258 2.1 0.2 1.0 ND1 D:HIS207 2.1 0.9 1.0 NE2 D:HIS257 2.1 0.6 1.0 O2 D:PEO506 2.1 0.9 1.0 CG D:HIS207 2.7 0.3 1.0 CE1 D:HIS257 2.7 0.4 1.0 CB D:HIS207 2.8 0.3 1.0 O1 D:PEO506 2.8 0.4 1.0 CD2 D:HIS258 2.9 0.1 1.0 CE1 D:HIS258 3.0 0.9 1.0 CE1 D:HIS207 3.2 0.3 1.0 CD2 D:HIS257 3.2 0.2 1.0 CA D:HIS207 3.6 0.1 1.0 NA D:HEM501 3.9 0.7 1.0 ND1 D:HIS257 3.9 0.4 1.0 CD2 D:HIS207 3.9 0.1 1.0 CG D:HIS258 4.0 0.5 1.0 ND1 D:HIS258 4.0 0.8 1.0 C4A D:HEM501 4.1 0.4 1.0 NE2 D:HIS207 4.1 0.5 1.0 CG D:HIS257 4.2 0.7 1.0 CHB D:HEM501 4.3 1.0 1.0 O D:ALA254 4.4 0.6 1.0 C1A D:HEM501 4.5 0.3 1.0 N D:HIS207 4.5 0.2 1.0 FE D:HEM501 4.6 0.2 1.0 C D:HIS207 4.7 0.6 1.0 C1B D:HEM501 4.7 0.1 1.0 C3A D:HEM501 4.8 0.6 1.0 O D:HIS207 4.9 0.3 1.0 NB D:HEM501 5.0 0.8 1.0

Copper binding site 3 out of 4 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ G:Cu503 b:74.7 occ:1.00 NE2 G:HIS257 2.1 71.2 1.0 NE2 G:HIS258 2.1 0.1 1.0 ND1 G:HIS207 2.1 83.2 1.0 O2 G:PEO505 2.1 80.0 1.0 CE1 G:HIS257 2.7 77.6 1.0 CG G:HIS207 2.8 71.5 1.0 O1 G:PEO505 2.9 83.2 1.0 CD2 G:HIS258 2.9 98.1 1.0 CB G:HIS207 3.0 65.6 1.0 CE1 G:HIS258 3.0 95.5 1.0 CE1 G:HIS207 3.2 86.1 1.0 CD2 G:HIS257 3.2 81.9 1.0 CA G:HIS207 3.7 71.2 1.0 NA G:HEM501 3.8 83.4 1.0 ND1 G:HIS257 3.9 81.3 1.0 C4A G:HEM501 4.0 85.9 1.0 CD2 G:HIS207 4.0 73.4 1.0 CG G:HIS258 4.0 89.1 1.0 ND1 G:HIS258 4.0 88.4 1.0 NE2 G:HIS207 4.2 79.2 1.0 CG G:HIS257 4.2 87.6 1.0 CHB G:HEM501 4.2 83.4 1.0 C1A G:HEM501 4.4 73.0 1.0 O G:ALA254 4.4 98.1 1.0 FE G:HEM501 4.5 67.0 1.0 C1B G:HEM501 4.6 75.5 1.0 N G:HIS207 4.7 75.2 1.0 C3A G:HEM501 4.8 78.5 1.0 C G:HIS207 4.8 78.5 1.0 NB G:HEM501 4.9 72.6 1.0 CHA G:HEM501 4.9 66.4 1.0 C2A G:HEM501 5.0 76.3 1.0 O G:HIS207 5.0 81.5 1.0

Copper binding site 4 out of 4 in the The Structure of CBB3 Cytochrome Oxidase.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of The Structure of CBB3 Cytochrome Oxidase. within 5.0Å range: probe atom residue distance (Å) B Occ K:Cu503 b:0.6 occ:1.00 NE2 K:HIS257 2.1 1.0 1.0 ND1 K:HIS207 2.1 0.0 1.0 NE2 K:HIS258 2.1 0.8 1.0 O2 K:PEO507 2.1 0.2 1.0 O1 K:PEO507 2.6 0.3 1.0 CE1 K:HIS257 2.7 0.1 1.0 CG K:HIS207 2.8 0.9 1.0 CE1 K:HIS258 2.9 0.1 1.0 CB K:HIS207 3.0 0.5 1.0 CD2 K:HIS258 3.0 0.9 1.0 CE1 K:HIS207 3.2 0.1 1.0 CD2 K:HIS257 3.3 0.6 1.0 CA K:HIS207 3.7 1.0 1.0 NA K:HEM501 3.7 0.4 1.0 ND1 K:HIS257 3.9 0.1 1.0 C4A K:HEM501 4.0 0.9 1.0 ND1 K:HIS258 4.0 0.2 1.0 CG K:HIS258 4.0 0.6 1.0 CD2 K:HIS207 4.0 0.2 1.0 CHB K:HEM501 4.2 0.3 1.0 NE2 K:HIS207 4.2 0.9 1.0 CG K:HIS257 4.2 0.5 1.0 C1A K:HEM501 4.3 0.0 1.0 FE K:HEM501 4.4 0.8 1.0 C1B K:HEM501 4.6 0.4 1.0 O K:ALA254 4.6 0.9 1.0 N K:HIS207 4.6 1.0 1.0 C3A K:HEM501 4.7 0.1 1.0 C K:HIS207 4.7 0.5 1.0 NB K:HEM501 4.8 0.4 1.0 CHA K:HEM501 4.8 0.5 1.0 ND K:HEM501 4.8 0.2 1.0 C4D K:HEM501 4.9 1.0 1.0 C2A K:HEM501 4.9 0.6 1.0 O K:HIS207 4.9 0.7 1.0

S.Buschmann, E.Warkentin, H.Xie, J.D.Langer, U.Ermler, H.Michel. The Structure of CBB3 Cytochrome Oxidase Provides Insights Into Proton Pumping. Science V. 329 327 2010.
ISSN: ESSN 1095-9203
PubMed: 20576851
DOI: 10.1126/SCIENCE.1187303