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Copper in PDB 3omn: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A Mutation in the Reduced State

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A 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 D132A Mutation in the Reduced State, PDB code: 3omn 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) 42.70 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.670, 132.033, 176.286, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 21.9

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 D132A Mutation in the Reduced State (pdb code 3omn). 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 D132A Mutation in the Reduced State, PDB code: 3omn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3omn

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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 D132A 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 D132A Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu5

b:37.3
occ:1.00
NE2 A:HIS334 2.0 34.6 1.0
ND1 A:HIS284 2.2 32.5 1.0
NE2 A:HIS333 2.3 37.6 1.0
O A:OH802 2.6 8.4 0.4
O A:HOH701 2.6 31.0 0.6
O A:HOH701 2.8 12.9 0.4
CD2 A:HIS334 3.0 32.3 1.0
CE1 A:HIS334 3.0 31.8 1.0
CE1 A:HIS333 3.1 38.4 1.0
CE1 A:HIS284 3.1 32.3 1.0
CG A:HIS284 3.2 31.8 1.0
CD2 A:HIS333 3.3 35.3 1.0
CB A:HIS284 3.5 30.6 1.0
CA A:HIS284 4.0 30.9 1.0
ND1 A:HIS334 4.0 31.4 1.0
CG A:HIS334 4.1 31.8 1.0
NE2 A:HIS284 4.2 32.4 1.0
ND1 A:HIS333 4.2 37.2 1.0
CD2 A:HIS284 4.3 32.4 1.0
CG A:HIS333 4.4 34.7 1.0
NA A:HEA2 4.5 21.3 0.4
C1A A:HEA2 4.7 21.8 0.4
C4A A:HEA2 4.7 22.4 0.4
ND A:HEA2 4.7 33.9 0.6
N A:HIS284 4.7 31.0 1.0
FE A:HEA2 4.8 22.1 0.4
C1A A:HEA2 4.8 33.6 0.6
C4D A:HEA2 4.9 33.5 0.6
NA A:HEA2 4.9 33.2 0.6
CG2 A:VAL330 5.0 35.3 1.0
CG2 A:VAL287 5.0 30.9 1.0
C3A A:HEA2 5.0 22.8 0.4
C2A A:HEA2 5.0 22.4 0.4

Copper binding site 2 out of 6 in 3omn

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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 D132A 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 D132A Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu287

b:25.6
occ:1.00
ND1 B:HIS260 2.1 25.0 1.0
SG B:CYS252 2.2 24.6 1.0
SG B:CYS256 2.3 25.4 1.0
CU B:CU1288 2.6 26.0 1.0
O B:GLU254 2.6 24.5 1.0
CE1 B:HIS260 2.9 24.7 1.0
CG B:HIS260 3.2 25.2 1.0
CB B:CYS252 3.3 24.6 1.0
CB B:CYS256 3.5 25.9 1.0
C B:GLU254 3.6 24.9 1.0
CA B:HIS260 3.6 24.5 1.0
CB B:HIS260 3.6 24.2 1.0
N B:CYS256 3.7 25.5 1.0
O B:HIS260 3.9 24.3 1.0
NE2 B:HIS260 4.1 25.2 1.0
N B:GLU254 4.1 25.6 1.0
C B:CYS252 4.1 25.2 1.0
O B:CYS252 4.1 25.0 1.0
CA B:LEU255 4.2 24.8 1.0
CD2 B:HIS260 4.2 23.5 1.0
C B:HIS260 4.2 24.3 1.0
CA B:CYS256 4.2 25.8 1.0
C B:LEU255 4.2 25.1 1.0
N B:LEU255 4.3 24.9 1.0
ND1 B:HIS217 4.3 24.6 1.0
CA B:CYS252 4.4 24.9 1.0
CA B:GLU254 4.5 25.6 1.0
SD B:MET263 4.5 23.2 1.0
N B:SER253 4.6 25.2 1.0
CG B:MET263 4.8 23.0 1.0
N B:HIS260 4.8 25.1 1.0
CA B:HIS217 4.9 25.6 1.0

Copper binding site 3 out of 6 in 3omn

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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 D132A 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 D132A Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu288

b:26.0
occ:1.00
ND1 B:HIS217 2.1 24.6 1.0
SG B:CYS252 2.3 24.6 1.0
SG B:CYS256 2.4 25.4 1.0
SD B:MET263 2.4 23.2 1.0
CU B:CU1287 2.6 25.6 1.0
CE B:MET263 2.9 17.6 1.0
CE1 B:HIS217 3.0 23.6 1.0
CG B:HIS217 3.2 23.7 1.0
CB B:CYS256 3.4 25.9 1.0
CB B:CYS252 3.5 24.6 1.0
CG B:MET263 3.5 23.0 1.0
CB B:HIS217 3.6 24.8 1.0
NE2 B:HIS217 4.1 25.2 1.0
CA B:HIS217 4.2 25.6 1.0
CD2 B:HIS217 4.3 23.4 1.0
O B:GLU254 4.3 24.5 1.0
CD1 B:TRP143 4.5 26.8 1.0
ND1 B:HIS260 4.5 25.0 1.0
O B:TYR141 4.7 27.3 1.0
CA B:HIS260 4.7 24.5 1.0
CA B:CYS256 4.8 25.8 1.0
CA B:CYS252 4.9 24.9 1.0
CB B:MET263 4.9 24.2 1.0

Copper binding site 4 out of 6 in 3omn

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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 D132A 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 D132A Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu553

b:45.1
occ:1.00
NE2 C:HIS334 2.0 40.8 1.0
ND1 C:HIS284 2.2 43.8 1.0
NE2 C:HIS333 2.3 40.4 1.0
O C:OH802 2.4 21.9 0.4
O C:HOH701 2.7 10.1 0.4
CE1 C:HIS334 2.9 39.8 1.0
CD2 C:HIS334 3.0 38.6 1.0
CG C:HIS284 3.1 43.1 1.0
CE1 C:HIS333 3.1 40.0 1.0
CE1 C:HIS284 3.2 44.1 1.0
CD2 C:HIS333 3.3 39.1 1.0
CB C:HIS284 3.4 42.0 1.0
CA C:HIS284 4.0 41.7 1.0
ND1 C:HIS334 4.0 39.3 1.0
CG C:HIS334 4.1 38.9 1.0
CD2 C:HIS284 4.2 44.2 1.0
NE2 C:HIS284 4.2 43.5 1.0
ND1 C:HIS333 4.3 39.7 1.0
CG C:HIS333 4.4 39.1 1.0
NA C:HEA2 4.5 28.6 0.4
C4A C:HEA2 4.6 28.6 0.4
FE C:HEA2 4.7 27.4 0.4
C1A C:HEA2 4.7 27.9 0.4
ND C:HEA2 4.7 39.3 0.6
N C:HIS284 4.8 41.4 1.0
CG2 C:VAL287 4.8 40.1 1.0
C1A C:HEA2 4.8 39.4 0.6
C4D C:HEA2 4.8 39.5 0.6
NB C:HEA2 4.9 29.5 0.4
NA C:HEA2 4.9 39.8 0.6
C3A C:HEA2 4.9 28.1 0.4
C2A C:HEA2 4.9 28.5 0.4
CHB C:HEA2 5.0 28.9 0.4

Copper binding site 5 out of 6 in 3omn

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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 D132A 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 D132A Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu286

b:33.6
occ:1.00
ND1 D:HIS260 2.0 32.0 1.0
SG D:CYS256 2.3 32.6 1.0
SG D:CYS252 2.3 30.2 1.0
CU D:CU1287 2.6 32.8 1.0
O D:GLU254 2.6 32.9 1.0
CE1 D:HIS260 2.9 31.6 1.0
CG D:HIS260 3.2 31.6 1.0
CB D:CYS252 3.2 29.8 1.0
CB D:CYS256 3.4 32.7 1.0
C D:GLU254 3.6 32.4 1.0
CA D:HIS260 3.6 32.1 1.0
CB D:HIS260 3.7 31.9 1.0
N D:CYS256 3.7 33.0 1.0
O D:HIS260 3.9 31.9 1.0
NE2 D:HIS260 4.0 31.5 1.0
N D:GLU254 4.1 31.7 1.0
C D:CYS252 4.1 30.4 1.0
O D:CYS252 4.2 30.0 1.0
CD2 D:HIS260 4.2 31.7 1.0
CA D:CYS256 4.2 32.8 1.0
C D:HIS260 4.2 32.1 1.0
ND1 D:HIS217 4.2 29.0 1.0
CA D:LEU255 4.3 32.9 1.0
C D:LEU255 4.3 32.5 1.0
CA D:CYS252 4.3 30.3 1.0
N D:LEU255 4.3 32.4 1.0
CA D:GLU254 4.5 32.1 1.0
SD D:MET263 4.5 34.0 1.0
N D:SER253 4.5 30.9 1.0
CG D:MET263 4.7 32.5 1.0
N D:HIS260 4.8 33.0 1.0
CA D:HIS217 4.9 31.9 1.0

Copper binding site 6 out of 6 in 3omn

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Copper binding site 6 out of 6 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with D132A 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 D132A Mutation in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu287

b:32.8
occ:1.00
ND1 D:HIS217 2.0 29.0 1.0
SG D:CYS256 2.3 32.6 1.0
SG D:CYS252 2.3 30.2 1.0
SD D:MET263 2.4 34.0 1.0
CU D:CU1286 2.6 33.6 1.0
CE1 D:HIS217 2.9 29.4 1.0
CE D:MET263 3.0 30.0 1.0
CG D:HIS217 3.1 30.1 1.0
CB D:CYS256 3.3 32.7 1.0
CG D:MET263 3.4 32.5 1.0
CB D:CYS252 3.4 29.8 1.0
CB D:HIS217 3.5 32.0 1.0
NE2 D:HIS217 4.1 27.2 1.0
CA D:HIS217 4.2 31.9 1.0
CD2 D:HIS217 4.2 27.4 1.0
O D:GLU254 4.3 32.9 1.0
CD1 D:TRP143 4.4 36.7 1.0
ND1 D:HIS260 4.6 32.0 1.0
O D:TYR141 4.7 35.9 1.0
CA D:CYS256 4.7 32.8 1.0
CA D:HIS260 4.8 32.1 1.0
CB D:MET263 4.8 32.6 1.0
CA D:CYS252 4.8 30.3 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: Fri Sep 4 08:13:11 2020
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