Copper in PDB 5weh: Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

Enzymatic activity of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

All present enzymatic activity of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State:
1.9.3.1;

Protein crystallography data

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh was solved by J.Liu, F.Ferguson-Miller, Q.Ling, C.Hiser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.45 / 3.45
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 339.221, 339.221, 89.199, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 26.2

Other elements in 5weh:

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State (pdb code 5weh). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5weh

Go back to Copper Binding Sites List in 5weh
Copper binding site 1 out of 6 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:81.6
occ:1.00
 ND1 A:HIS284 2.4 79.5 1.0
NE2 A:HIS333 2.4 89.4 1.0
NE2 A:HIS334 2.4 97.5 1.0
CD2 A:HIS334 3.0 92.7 1.0
CE1 A:HIS333 3.0 87.2 1.0
CG A:HIS284 3.3 81.8 1.0
CD2 A:HIS333 3.3 95.0 1.0
CE1 A:HIS284 3.4 89.4 1.0
CB A:HIS284 3.4 64.2 1.0
CE1 A:HIS334 3.4 99.6 1.0
ND1 A:HIS333 4.1 90.8 1.0
CG A:HIS334 4.1 98.4 1.0
CA A:HIS284 4.1 92.2 1.0
CG A:HIS333 4.2 98.0 1.0
ND1 A:HIS334 4.3 0.1 1.0
CD2 A:HIS284 4.4 87.2 1.0
NE2 A:HIS284 4.5 89.9 1.0
N A:HIS284 4.7 75.7 1.0
O A:TRP331 4.7 78.1 1.0
O A:VAL330 4.9 98.4 1.0

Copper binding site 2 out of 6 in 5weh

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Copper binding site 2 out of 6 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu604

b:94.1
occ:1.00
 ND1 G:HIS284 2.1 0.7 1.0
NE2 G:HIS333 2.4 0.7 1.0
CE1 G:HIS334 2.7 0.1 1.0
CE1 G:HIS284 2.8 0.3 1.0
NE2 G:HIS334 3.0 0.6 1.0
CE1 G:HIS333 3.2 97.8 1.0
CG G:HIS284 3.3 0.5 1.0
CD2 G:HIS333 3.3 0.4 1.0
ND1 G:HIS334 3.6 0.7 1.0
CB G:HIS284 3.8 97.5 1.0
NE2 G:HIS284 4.0 0.7 1.0
CD2 G:HIS334 4.1 0.1 1.0
NA G:HEA603 4.2 0.7 1.0
CD2 G:HIS284 4.2 0.9 1.0
ND1 G:HIS333 4.3 0.1 1.0
C1A G:HEA603 4.3 0.4 1.0
CG G:HIS333 4.4 0.1 1.0
CG G:HIS334 4.4 0.4 1.0
CA G:HIS284 4.4 87.7 1.0
FE G:HEA603 4.4 0.5 1.0
C4D G:HEA603 4.7 0.7 1.0
CG2 G:VAL287 4.7 98.8 1.0
ND G:HEA603 4.7 99.4 1.0
C4A G:HEA603 4.7 0.3 1.0
CHA G:HEA603 4.8 0.4 1.0
C2A G:HEA603 5.0 0.4 1.0

Copper binding site 3 out of 6 in 5weh

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Copper binding site 3 out of 6 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu301

b:1.0
occ:1.00
 ND1 B:HIS260 2.3 91.2 1.0
CU B:CU1302 2.3 0.8 1.0
O B:GLU254 2.6 0.5 1.0
SG B:CYS252 2.9 0.5 1.0
SG B:CYS256 2.9 95.7 1.0
CE1 B:HIS260 3.0 88.5 1.0
CB B:CYS256 3.3 81.9 1.0
CB B:CYS252 3.4 78.9 1.0
CG B:HIS260 3.5 91.2 1.0
C B:GLU254 3.6 96.5 1.0
O B:HIS260 3.8 97.5 1.0
N B:CYS256 3.9 83.8 1.0
CB B:HIS260 4.0 99.2 1.0
N B:GLU254 4.0 91.5 1.0
CA B:HIS260 4.1 96.9 1.0
CA B:CYS256 4.2 70.0 1.0
C B:CYS252 4.3 97.4 1.0
NE2 B:HIS260 4.3 94.5 1.0
O B:CYS252 4.4 1.0 1.0
C B:HIS260 4.4 0.1 1.0
ND1 B:HIS217 4.4 98.7 1.0
C B:LEU255 4.4 0.2 1.0
CA B:GLU254 4.4 90.8 1.0
CA B:CYS252 4.5 86.7 1.0
N B:LEU255 4.5 96.5 1.0
SD B:MET263 4.5 0.2 1.0
CD2 B:HIS260 4.5 95.0 1.0
CA B:LEU255 4.5 95.9 1.0
N B:SER253 4.6 97.0 1.0
CG B:MET263 4.7 0.3 1.0
CA B:HIS217 4.7 93.6 1.0
O B:ILE216 4.9 91.6 1.0
CB B:HIS217 5.0 98.7 1.0

Copper binding site 4 out of 6 in 5weh

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Copper binding site 4 out of 6 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu302

b:0.8
occ:1.00
 CU B:CU1301 2.3 1.0 1.0
ND1 B:HIS217 2.4 98.7 1.0
SD B:MET263 2.6 0.2 1.0
SG B:CYS256 2.7 95.7 1.0
SG B:CYS252 2.8 0.5 1.0
CB B:CYS256 3.3 81.9 1.0
CE B:MET263 3.3 0.8 1.0
CE1 B:HIS217 3.4 0.4 1.0
CG B:HIS217 3.4 98.1 1.0
CG B:MET263 3.6 0.3 1.0
CB B:CYS252 3.6 78.9 1.0
CB B:HIS217 3.7 98.7 1.0
CA B:HIS217 4.1 93.6 1.0
O B:GLU254 4.3 0.5 1.0
NE2 B:HIS217 4.5 1.0 1.0
ND1 B:HIS260 4.5 91.2 1.0
CD2 B:HIS217 4.5 98.5 1.0
CA B:CYS256 4.7 70.0 1.0
O B:HIS260 4.9 97.5 1.0
O B:TYR141 5.0 93.8 1.0
CB B:MET263 5.0 0.6 1.0
N B:SER218 5.0 98.4 1.0

Copper binding site 5 out of 6 in 5weh

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Copper binding site 5 out of 6 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu301

b:0.0
occ:1.00
 ND1 H:HIS217 2.4 0.1 1.0
CU H:CU1302 2.4 0.6 1.0
SG H:CYS252 2.7 0.0 1.0
SG H:CYS256 2.8 0.5 1.0
SD H:MET263 3.0 0.5 1.0
CB H:CYS256 3.1 0.4 1.0
CG H:HIS217 3.2 0.7 1.0
CB H:HIS217 3.3 1.0 1.0
CE1 H:HIS217 3.4 0.5 1.0
CE H:MET263 3.6 0.1 1.0
CA H:HIS217 3.6 0.9 1.0
CB H:CYS252 3.7 0.8 1.0
O H:GLU254 3.8 0.9 1.0
CG H:MET263 4.1 0.2 1.0
CD2 H:HIS217 4.3 0.6 1.0
NE2 H:HIS217 4.4 0.6 1.0
O H:ILE216 4.5 0.4 1.0
CA H:CYS256 4.5 0.4 1.0
CD2 H:HIS260 4.5 0.0 1.0
N H:SER218 4.5 0.4 1.0
N H:HIS217 4.6 1.0 1.0
C H:HIS217 4.6 0.5 1.0
N H:CYS256 4.8 0.7 1.0
C H:ILE216 5.0 0.8 1.0
C H:GLU254 5.0 0.3 1.0

Copper binding site 6 out of 6 in 5weh

Go back to Copper Binding Sites List in 5weh
Copper binding site 6 out of 6 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu302

b:0.6
occ:1.00
 CU H:CU1301 2.4 0.0 1.0
CD2 H:HIS260 2.5 0.0 1.0
SG H:CYS256 2.9 0.5 1.0
O H:HIS260 3.0 0.1 1.0
SG H:CYS252 3.0 0.0 1.0
CB H:CYS252 3.1 0.8 1.0
CG H:HIS260 3.2 0.5 1.0
O H:GLU254 3.4 0.9 1.0
CA H:HIS260 3.4 0.8 1.0
NE2 H:HIS260 3.5 0.1 1.0
CB H:HIS260 3.6 0.6 1.0
C H:HIS260 3.6 0.4 1.0
SD H:MET263 3.8 0.5 1.0
CB H:CYS256 3.8 0.4 1.0
CG H:MET263 3.9 0.2 1.0
O H:CYS252 4.2 0.1 1.0
C H:CYS252 4.2 0.5 1.0
CA H:CYS252 4.2 0.4 1.0
N H:CYS256 4.4 0.7 1.0
C H:GLU254 4.4 0.3 1.0
ND1 H:HIS260 4.4 0.4 1.0
CE1 H:HIS260 4.5 0.6 1.0
N H:GLU254 4.6 0.4 1.0
ND1 H:HIS217 4.7 0.1 1.0
N H:HIS260 4.7 0.5 1.0
CA H:CYS256 4.7 0.4 1.0
N H:SER253 4.8 0.8 1.0
CE H:MET263 4.8 0.1 1.0
OH G:TYR483 4.9 0.5 1.0
O H:SER259 4.9 0.8 1.0
N H:ALA261 5.0 0.1 1.0

Reference:

J.Liu, C.Hiser, S.Ferguson-Miller. Role of Conformational Change and K-Path Ligands in Controlling Cytochrome C Oxidase Activity. Biochem. Soc. Trans. V. 45 1087 2017.
ISSN: ISSN 1470-8752
PubMed: 28842531
DOI: 10.1042/BST20160138
Page generated: Sun Dec 13 11:20:06 2020

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