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Copper in PDB 3om3: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation in the Reduced State

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation in the Reduced State:
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 in the Reduced State, PDB code: 3om3 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) 40.46 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.650, 132.365, 178.006, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 22.9

Other elements in 3om3:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with K362M Mutation in the Reduced State 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 in the Reduced State (pdb code 3om3). 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 in the Reduced State, PDB code: 3om3:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3om3

Go back to Copper Binding Sites List in 3om3
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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu5

b:48.0
occ:1.00
NE2 A:HIS334 2.1 49.3 1.0
NE2 A:HIS333 2.1 48.1 1.0
ND1 A:HIS284 2.2 45.8 1.0
CE1 A:HIS333 2.8 47.6 1.0
CE1 A:HIS334 3.0 48.8 1.0
CD2 A:HIS334 3.0 48.7 1.0
CG A:HIS284 3.0 44.6 1.0
CE1 A:HIS284 3.2 45.6 1.0
CD2 A:HIS333 3.3 48.0 1.0
CB A:HIS284 3.3 44.1 1.0
CA A:HIS284 4.0 43.9 1.0
ND1 A:HIS333 4.0 48.0 1.0
ND1 A:HIS334 4.1 47.7 1.0
CG A:HIS334 4.1 48.1 1.0
CD2 A:HIS284 4.2 44.5 1.0
NE2 A:HIS284 4.2 45.4 1.0
CG A:HIS333 4.3 47.6 1.0
N A:HIS284 4.8 44.0 1.0
ND A:HEA2 4.8 44.0 1.0
NA A:HEA2 4.9 47.7 1.0
C1A A:HEA2 4.9 47.2 1.0
CG2 A:VAL287 4.9 41.2 1.0
CG2 A:VAL330 5.0 48.8 1.0
C4D A:HEA2 5.0 45.3 1.0

Copper binding site 2 out of 6 in 3om3

Go back to Copper Binding Sites List in 3om3
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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu287

b:37.0
occ:1.00
ND1 B:HIS260 2.0 32.5 1.0
SG B:CYS252 2.3 35.6 1.0
SG B:CYS256 2.3 35.7 1.0
CU B:CU1288 2.6 34.7 1.0
O B:GLU254 2.7 35.8 1.0
CE1 B:HIS260 2.8 31.7 1.0
CG B:HIS260 3.1 33.5 1.0
CB B:CYS256 3.3 34.6 1.0
CB B:CYS252 3.3 34.2 1.0
CB B:HIS260 3.6 34.0 1.0
CA B:HIS260 3.6 34.1 1.0
C B:GLU254 3.6 35.2 1.0
N B:CYS256 3.7 34.9 1.0
O B:HIS260 4.0 33.9 1.0
NE2 B:HIS260 4.0 30.6 1.0
CD2 B:HIS260 4.1 31.8 1.0
C B:CYS252 4.1 35.0 1.0
CA B:CYS256 4.1 35.1 1.0
N B:GLU254 4.1 35.6 1.0
O B:CYS252 4.1 34.6 1.0
CA B:LEU255 4.2 34.0 1.0
C B:LEU255 4.2 34.3 1.0
C B:HIS260 4.2 34.0 1.0
N B:LEU255 4.3 34.5 1.0
ND1 B:HIS217 4.3 32.7 1.0
CA B:CYS252 4.3 34.7 1.0
SD B:MET263 4.4 35.8 1.0
CA B:GLU254 4.6 35.4 1.0
N B:SER253 4.6 35.0 1.0
CG B:MET263 4.7 35.5 1.0
N B:HIS260 4.8 34.6 1.0
CA B:HIS217 4.9 34.7 1.0
C B:CYS256 5.0 35.4 1.0

Copper binding site 3 out of 6 in 3om3

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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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu288

b:34.7
occ:1.00
ND1 B:HIS217 2.1 32.7 1.0
SG B:CYS252 2.3 35.6 1.0
SG B:CYS256 2.3 35.7 1.0
SD B:MET263 2.4 35.8 1.0
CU B:CU1287 2.6 37.0 1.0
CE1 B:HIS217 3.0 31.8 1.0
CE B:MET263 3.0 32.2 1.0
CG B:HIS217 3.2 33.5 1.0
CB B:CYS256 3.3 34.6 1.0
CB B:CYS252 3.4 34.2 1.0
CG B:MET263 3.5 35.5 1.0
CB B:HIS217 3.6 34.1 1.0
NE2 B:HIS217 4.2 33.5 1.0
CA B:HIS217 4.2 34.7 1.0
CD2 B:HIS217 4.3 32.2 1.0
O B:GLU254 4.4 35.8 1.0
ND1 B:HIS260 4.5 32.5 1.0
CD1 B:TRP143 4.5 33.4 1.0
CA B:CYS256 4.7 35.1 1.0
CA B:HIS260 4.8 34.1 1.0
CA B:CYS252 4.8 34.7 1.0
O B:TYR141 4.8 35.9 1.0
CB B:MET263 4.9 35.5 1.0
O B:ILE216 4.9 34.9 1.0
CZ2 B:TRP145 5.0 34.5 1.0

Copper binding site 4 out of 6 in 3om3

Go back to Copper Binding Sites List in 3om3
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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu553

b:54.8
occ:1.00
NE2 C:HIS334 2.2 55.2 1.0
NE2 C:HIS333 2.2 52.7 1.0
ND1 C:HIS284 2.2 55.2 1.0
CD2 C:HIS334 2.9 54.6 1.0
CE1 C:HIS333 3.0 52.3 1.0
CG C:HIS284 3.0 53.9 1.0
CE1 C:HIS284 3.2 55.1 1.0
CE1 C:HIS334 3.2 55.0 1.0
CB C:HIS284 3.3 52.8 1.0
CD2 C:HIS333 3.3 52.4 1.0
CA C:HIS284 3.9 52.7 1.0
CG C:HIS334 4.1 53.4 1.0
CD2 C:HIS284 4.2 54.4 1.0
ND1 C:HIS333 4.2 53.1 1.0
ND1 C:HIS334 4.2 53.8 1.0
NE2 C:HIS284 4.2 54.8 1.0
CG C:HIS333 4.3 52.8 1.0
N C:HIS284 4.8 52.4 1.0
CG2 C:VAL330 4.9 55.7 1.0
CG2 C:VAL287 4.9 50.5 1.0
C1A C:HEA2 4.9 49.9 1.0
ND C:HEA2 5.0 52.1 1.0
NA C:HEA2 5.0 51.3 1.0

Copper binding site 5 out of 6 in 3om3

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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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu3

b:47.8
occ:1.00
ND1 D:HIS260 2.0 46.2 1.0
SG D:CYS256 2.3 46.5 1.0
SG D:CYS252 2.3 44.1 1.0
CU D:CU1286 2.6 44.1 1.0
O D:GLU254 2.7 46.1 1.0
CE1 D:HIS260 2.8 45.8 1.0
CG D:HIS260 3.1 45.7 1.0
CB D:CYS252 3.3 44.5 1.0
CB D:CYS256 3.4 45.6 1.0
CA D:HIS260 3.6 44.8 1.0
C D:GLU254 3.6 45.8 1.0
CB D:HIS260 3.6 45.1 1.0
N D:CYS256 3.8 45.4 1.0
O D:HIS260 3.8 44.1 1.0
NE2 D:HIS260 4.0 45.0 1.0
C D:HIS260 4.1 44.1 1.0
O D:CYS252 4.1 44.9 1.0
CD2 D:HIS260 4.1 45.7 1.0
C D:CYS252 4.1 45.2 1.0
N D:GLU254 4.2 45.9 1.0
CA D:CYS256 4.2 45.7 1.0
CA D:LEU255 4.3 45.1 1.0
N D:LEU255 4.3 45.3 1.0
C D:LEU255 4.3 45.1 1.0
ND1 D:HIS217 4.3 39.4 1.0
CA D:CYS252 4.3 44.8 1.0
SD D:MET263 4.5 44.4 1.0
CA D:GLU254 4.5 46.0 1.0
N D:SER253 4.6 45.4 1.0
CG D:MET263 4.7 42.6 1.0
N D:HIS260 4.8 45.8 1.0
CA D:HIS217 4.9 44.0 1.0
CB D:HIS217 4.9 43.4 1.0

Copper binding site 6 out of 6 in 3om3

Go back to Copper Binding Sites List in 3om3
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 in the Reduced State


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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu286

b:44.1
occ:1.00
ND1 D:HIS217 2.1 39.4 1.0
SG D:CYS252 2.3 44.1 1.0
SG D:CYS256 2.4 46.5 1.0
SD D:MET263 2.4 44.4 1.0
CU D:CU13 2.6 47.8 1.0
CE1 D:HIS217 3.1 38.7 1.0
CG D:HIS217 3.1 41.0 1.0
CE D:MET263 3.1 41.4 1.0
CB D:CYS256 3.4 45.6 1.0
CB D:HIS217 3.4 43.4 1.0
CB D:CYS252 3.5 44.5 1.0
CG D:MET263 3.5 42.6 1.0
CA D:HIS217 4.1 44.0 1.0
NE2 D:HIS217 4.2 38.5 1.0
CD2 D:HIS217 4.2 38.7 1.0
O D:GLU254 4.3 46.1 1.0
ND1 D:HIS260 4.5 46.2 1.0
CD1 D:TRP143 4.6 48.7 1.0
O D:TYR141 4.7 48.1 1.0
CA D:HIS260 4.8 44.8 1.0
CA D:CYS256 4.8 45.7 1.0
CB D:MET263 4.9 42.6 1.0
CA D:CYS252 4.9 44.8 1.0
CZ2 D:TRP145 4.9 46.2 1.0
O D:HIS260 5.0 44.1 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: Sun Dec 13 11:11:09 2020

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