Atomistry » Copper » PDB 3mnd-3qjo » 3oma
Atomistry »
  Copper »
    PDB 3mnd-3qjo »
      3oma »

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

Go back to Copper Binding Sites List in 3oma
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

Go back to Copper Binding Sites List in 3oma
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

Go back to Copper Binding Sites List in 3oma
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

Go back to Copper Binding Sites List in 3oma
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

Go back to Copper Binding Sites List in 3oma
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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy