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Copper in PDB 3oma: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation:
1.9.3.1;

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation, PDB code: 3oma was solved by J.Liu, L.Qin, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.019, 131.579, 176.626, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.9

Other elements in 3oma:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 4 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation (pdb code 3oma). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation, PDB code: 3oma:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3oma

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Copper binding site 1 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu5

b:35.2
occ:1.00
 NE2 A:HIS333 2.0 37.7 1.0
NE2 A:HIS334 2.1 37.8 1.0
ND1 A:HIS284 2.1 37.1 1.0
O A:OH706 2.4 36.1 1.0
CE1 A:HIS333 2.9 39.1 1.0
O A:HOH727 2.9 32.8 1.0
CG A:HIS284 3.0 36.2 1.0
CE1 A:HIS334 3.0 35.8 1.0
CD2 A:HIS334 3.0 36.1 1.0
CD2 A:HIS333 3.1 36.7 1.0
CE1 A:HIS284 3.1 36.8 1.0
CB A:HIS284 3.2 35.3 1.0
CA A:HIS284 3.8 35.9 1.0
ND1 A:HIS333 4.1 37.8 1.0
ND1 A:HIS334 4.1 35.3 1.0
CG A:HIS334 4.1 36.6 1.0
CD2 A:HIS284 4.1 37.5 1.0
CG A:HIS333 4.2 35.8 1.0
NE2 A:HIS284 4.2 36.8 1.0
NA A:HEA2 4.5 31.6 1.0
N A:HIS284 4.6 35.7 1.0
C1A A:HEA2 4.6 32.5 1.0
C4A A:HEA2 4.7 32.1 1.0
O A:HOH806 4.8 49.2 1.0
C2A A:HEA2 4.9 34.4 1.0
C3A A:HEA2 5.0 33.5 1.0
FE A:HEA2 5.0 32.2 1.0

Copper binding site 2 out of 6 in 3oma

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Copper binding site 2 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu287

b:28.0
occ:1.00
 ND1 B:HIS260 2.1 26.4 1.0
SG B:CYS252 2.2 27.3 1.0
SG B:CYS256 2.3 26.5 1.0
CU B:CU1288 2.6 27.9 1.0
O B:GLU254 2.6 27.7 1.0
CE1 B:HIS260 2.9 24.5 1.0
CG B:HIS260 3.2 26.2 1.0
CB B:CYS252 3.3 26.7 1.0
CB B:CYS256 3.4 27.4 1.0
C B:GLU254 3.5 27.5 1.0
CA B:HIS260 3.6 25.9 1.0
CB B:HIS260 3.7 25.4 1.0
N B:CYS256 3.7 27.7 1.0
O B:HIS260 4.0 25.3 1.0
NE2 B:HIS260 4.0 27.2 1.0
N B:GLU254 4.1 27.9 1.0
CA B:LEU255 4.1 27.6 1.0
C B:CYS252 4.2 27.2 1.0
O B:CYS252 4.2 26.9 1.0
CD2 B:HIS260 4.2 26.0 1.0
CA B:CYS256 4.2 27.5 1.0
N B:LEU255 4.2 27.3 1.0
C B:LEU255 4.2 27.9 1.0
ND1 B:HIS217 4.2 27.7 1.0
C B:HIS260 4.3 25.4 1.0
CA B:CYS252 4.3 27.0 1.0
CA B:GLU254 4.5 27.8 1.0
SD B:MET263 4.5 26.8 1.0
N B:SER253 4.6 27.7 1.0
CG B:MET263 4.8 25.7 1.0
N B:HIS260 4.8 26.1 1.0
CA B:HIS217 5.0 27.7 1.0

Copper binding site 3 out of 6 in 3oma

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Copper binding site 3 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu288

b:27.9
occ:1.00
 ND1 B:HIS217 2.1 27.7 1.0
SG B:CYS252 2.3 27.3 1.0
SG B:CYS256 2.3 26.5 1.0
SD B:MET263 2.5 26.8 1.0
CU B:CU287 2.6 28.0 1.0
CE1 B:HIS217 2.9 25.5 1.0
CE B:MET263 3.1 22.6 1.0
CG B:HIS217 3.3 27.0 1.0
CB B:CYS256 3.3 27.4 1.0
CB B:CYS252 3.4 26.7 1.0
CG B:MET263 3.5 25.7 1.0
CB B:HIS217 3.7 27.0 1.0
NE2 B:HIS217 4.1 26.4 1.0
O B:GLU254 4.3 27.7 1.0
CA B:HIS217 4.3 27.7 1.0
CD2 B:HIS217 4.3 25.6 1.0
CD1 B:TRP143 4.5 27.9 1.0
ND1 B:HIS260 4.5 26.4 1.0
O B:TYR141 4.6 29.4 1.0
CA B:HIS260 4.7 25.9 1.0
CA B:CYS256 4.7 27.5 1.0
CA B:CYS252 4.8 27.0 1.0
CB B:MET263 4.9 26.9 1.0

Copper binding site 4 out of 6 in 3oma

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Copper binding site 4 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu553

b:42.4
occ:1.00
 ND1 C:HIS284 2.1 45.4 1.0
NE2 C:HIS334 2.1 38.5 1.0
NE2 C:HIS333 2.1 39.8 1.0
O C:OH706 2.3 48.3 1.0
O C:HOH556 3.0 33.9 1.0
CD2 C:HIS334 3.0 37.5 1.0
CG C:HIS284 3.0 43.7 1.0
CE1 C:HIS284 3.1 44.6 1.0
CE1 C:HIS333 3.1 39.8 1.0
CE1 C:HIS334 3.1 37.6 1.0
CD2 C:HIS333 3.2 38.9 1.0
CB C:HIS284 3.3 42.1 1.0
CA C:HIS284 3.9 42.1 1.0
ND1 C:HIS334 4.1 38.6 1.0
CG C:HIS334 4.1 38.3 1.0
CD2 C:HIS284 4.1 45.1 1.0
NE2 C:HIS284 4.2 44.6 1.0
ND1 C:HIS333 4.2 38.7 1.0
CG C:HIS333 4.3 39.1 1.0
NA C:HEA2 4.5 36.6 1.0
C1A C:HEA2 4.6 37.0 1.0
C4A C:HEA2 4.7 38.0 1.0
N C:HIS284 4.7 41.7 1.0
C2A C:HEA2 4.9 37.2 1.0
FE C:HEA2 4.9 34.6 1.0
C3A C:HEA2 4.9 36.8 1.0

Copper binding site 5 out of 6 in 3oma

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Copper binding site 5 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu286

b:35.7
occ:1.00
 ND1 D:HIS260 2.0 35.0 1.0
SG D:CYS252 2.3 32.1 1.0
SG D:CYS256 2.3 33.1 1.0
CU D:CU1287 2.6 35.2 1.0
O D:GLU254 2.6 35.1 1.0
CE1 D:HIS260 2.8 35.0 1.0
CG D:HIS260 3.1 34.5 1.0
CB D:CYS252 3.3 32.5 1.0
CB D:CYS256 3.4 34.2 1.0
C D:GLU254 3.6 35.1 1.0
CA D:HIS260 3.6 34.8 1.0
CB D:HIS260 3.6 35.0 1.0
N D:CYS256 3.7 34.7 1.0
O D:HIS260 3.9 34.2 1.0
NE2 D:HIS260 4.0 35.7 1.0
N D:GLU254 4.1 34.8 1.0
CD2 D:HIS260 4.1 34.3 1.0
C D:CYS252 4.2 33.6 1.0
C D:HIS260 4.2 34.6 1.0
CA D:CYS256 4.2 34.5 1.0
CA D:LEU255 4.3 34.6 1.0
C D:LEU255 4.3 34.4 1.0
N D:LEU255 4.3 34.8 1.0
O D:CYS252 4.3 33.7 1.0
ND1 D:HIS217 4.3 32.5 1.0
CA D:CYS252 4.3 33.2 1.0
SD D:MET263 4.5 34.8 1.0
N D:SER253 4.5 34.1 1.0
CA D:GLU254 4.5 35.1 1.0
CG D:MET263 4.7 34.3 1.0
N D:HIS260 4.8 35.6 1.0
CA D:HIS217 4.9 34.6 1.0

Copper binding site 6 out of 6 in 3oma

Go back to Copper Binding Sites List in 3oma
Copper binding site 6 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu287

b:35.2
occ:1.00
 ND1 D:HIS217 2.2 32.5 1.0
SG D:CYS256 2.3 33.1 1.0
SD D:MET263 2.4 34.8 1.0
SG D:CYS252 2.4 32.1 1.0
CU D:CU286 2.6 35.7 1.0
CE1 D:HIS217 3.1 33.1 1.0
CE D:MET263 3.1 31.4 1.0
CG D:HIS217 3.2 33.5 1.0
CB D:CYS256 3.3 34.2 1.0
CG D:MET263 3.4 34.3 1.0
CB D:CYS252 3.5 32.5 1.0
CB D:HIS217 3.6 34.9 1.0
NE2 D:HIS217 4.2 32.8 1.0
CA D:HIS217 4.3 34.6 1.0
O D:GLU254 4.3 35.1 1.0
CD2 D:HIS217 4.3 30.2 1.0
ND1 D:HIS260 4.5 35.0 1.0
CD1 D:TRP143 4.5 41.1 1.0
O D:TYR141 4.7 38.2 1.0
CA D:HIS260 4.8 34.8 1.0
CA D:CYS256 4.8 34.5 1.0
CA D:CYS252 4.9 33.2 1.0
CB D:MET263 4.9 34.6 1.0
CZ2 D:TRP145 5.0 36.6 1.0

Reference:

J.Liu, L.Qin, S.Ferguson-Miller. Crystallographic and Online Spectral Evidence For Role of Conformational Change and Conserved Water in Cytochrome Oxidase Proton Pump. Proc.Natl.Acad.Sci.Usa V. 108 1284 2011.
ISSN: ISSN 0027-8424
PubMed: 21205904
DOI: 10.1073/PNAS.1012846108
Page generated: Mon Jul 14 02:33:28 2025

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