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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 in the Reduced State, PDB code: 3fye was solved by L.Qin, D.A.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.613, 131.472, 176.192, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.1

Other elements in 3fye:

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

Copper binding site 1 out of 6 in 3fye

Go back to Copper Binding Sites List in 3fye
Copper binding site 1 out of 6 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu570

b:36.0
occ:1.00
NE2 A:HIS334 2.0 35.9 1.0
ND1 A:HIS284 2.1 32.8 1.0
NE2 A:HIS333 2.1 38.1 1.0
CD2 A:HIS334 2.9 33.8 1.0
CE1 A:HIS334 2.9 34.4 1.0
CE1 A:HIS333 3.0 37.8 1.0
CG A:HIS284 3.0 33.2 1.0
CE1 A:HIS284 3.1 33.6 1.0
CD2 A:HIS333 3.2 36.8 1.0
O A:HOH601 3.2 55.7 1.0
CB A:HIS284 3.3 32.2 1.0
CA A:HIS284 3.9 33.1 1.0
ND1 A:HIS334 4.0 33.9 1.0
CG A:HIS334 4.0 33.8 1.0
ND1 A:HIS333 4.1 38.8 1.0
CD2 A:HIS284 4.2 33.3 1.0
NE2 A:HIS284 4.2 35.2 1.0
CG A:HIS333 4.2 36.5 1.0
N A:HIS284 4.7 32.7 1.0
CG2 A:VAL330 4.8 36.7 1.0
C1A A:HEA568 4.9 34.0 1.0
NA A:HEA568 4.9 34.8 1.0
O A:HOH602 4.9 50.9 1.0
ND A:HEA568 5.0 32.2 1.0

Copper binding site 2 out of 6 in 3fye

Go back to Copper Binding Sites List in 3fye
Copper binding site 2 out of 6 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu3

b:29.2
occ:1.00
ND1 B:HIS260 2.1 22.8 1.0
SG B:CYS252 2.3 28.6 1.0
SG B:CYS256 2.3 29.1 1.0
CU B:CU14 2.6 29.3 1.0
O B:GLU254 2.6 27.8 1.0
CE1 B:HIS260 2.9 23.2 1.0
CG B:HIS260 3.1 25.0 1.0
CB B:CYS252 3.3 28.3 1.0
CB B:CYS256 3.5 27.9 1.0
CA B:HIS260 3.5 25.4 1.0
CB B:HIS260 3.5 25.0 1.0
C B:GLU254 3.6 26.9 1.0
N B:CYS256 3.7 27.8 1.0
O B:HIS260 3.9 25.6 1.0
O B:CYS252 4.0 26.9 1.0
NE2 B:HIS260 4.1 26.7 1.0
C B:CYS252 4.1 28.1 1.0
N B:GLU254 4.2 28.0 1.0
CA B:LEU255 4.2 27.0 1.0
CD2 B:HIS260 4.2 23.2 1.0
C B:HIS260 4.2 25.2 1.0
CA B:CYS256 4.2 28.4 1.0
C B:LEU255 4.2 27.2 1.0
ND1 B:HIS217 4.3 25.3 1.0
N B:LEU255 4.3 26.9 1.0
CA B:CYS252 4.3 28.1 1.0
SD B:MET263 4.5 27.3 1.0
CA B:GLU254 4.5 27.5 1.0
CG B:MET263 4.7 27.3 1.0
N B:SER253 4.7 27.2 1.0
N B:HIS260 4.8 26.1 1.0
CA B:HIS217 4.9 27.9 1.0

Copper binding site 3 out of 6 in 3fye

Go back to Copper Binding Sites List in 3fye
Copper binding site 3 out of 6 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu4

b:29.3
occ:1.00
ND1 B:HIS217 2.1 25.3 1.0
SG B:CYS252 2.3 28.6 1.0
SG B:CYS256 2.4 29.1 1.0
SD B:MET263 2.4 27.3 1.0
CU B:CU13 2.6 29.2 1.0
CE1 B:HIS217 2.9 23.2 1.0
CE B:MET263 2.9 23.8 1.0
CG B:HIS217 3.2 26.2 1.0
CB B:CYS256 3.4 27.9 1.0
CB B:CYS252 3.5 28.3 1.0
CG B:MET263 3.5 27.3 1.0
CB B:HIS217 3.6 27.1 1.0
NE2 B:HIS217 4.1 24.2 1.0
CA B:HIS217 4.2 27.9 1.0
CD2 B:HIS217 4.3 26.0 1.0
O B:GLU254 4.4 27.8 1.0
CD1 B:TRP143 4.5 29.7 1.0
ND1 B:HIS260 4.6 22.8 1.0
O B:TYR141 4.7 30.7 1.0
CA B:HIS260 4.7 25.4 1.0
CA B:CYS256 4.8 28.4 1.0
CA B:CYS252 4.9 28.1 1.0
CB B:MET263 4.9 27.3 1.0

Copper binding site 4 out of 6 in 3fye

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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 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 in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu570

b:42.1
occ:1.00
NE2 C:HIS334 2.0 42.1 1.0
ND1 C:HIS284 2.0 43.5 1.0
NE2 C:HIS333 2.1 39.9 1.0
CD2 C:HIS334 2.9 41.3 1.0
CG C:HIS284 3.0 42.9 1.0
CE1 C:HIS334 3.0 41.6 1.0
CE1 C:HIS333 3.0 40.8 1.0
CE1 C:HIS284 3.1 42.0 1.0
CD2 C:HIS333 3.2 39.5 1.0
CB C:HIS284 3.2 41.7 1.0
O C:HOH1601 3.3 48.2 1.0
CA C:HIS284 4.0 41.6 1.0
CG C:HIS334 4.0 40.5 1.0
ND1 C:HIS334 4.1 41.2 1.0
CD2 C:HIS284 4.1 43.2 1.0
ND1 C:HIS333 4.2 40.3 1.0
NE2 C:HIS284 4.2 42.9 1.0
CG C:HIS333 4.3 40.4 1.0
O C:HOH1602 4.7 56.6 1.0
N C:HIS284 4.8 40.8 1.0
CG2 C:VAL330 4.8 44.6 1.0
C1A C:HEA568 4.9 37.8 1.0
NA C:HEA568 4.9 39.9 1.0
CG2 C:VAL287 5.0 38.1 1.0
ND C:HEA568 5.0 36.3 1.0

Copper binding site 5 out of 6 in 3fye

Go back to Copper Binding Sites List in 3fye
Copper binding site 5 out of 6 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu3

b:35.9
occ:1.00
ND1 D:HIS260 2.1 32.9 1.0
SG D:CYS252 2.3 32.5 1.0
SG D:CYS256 2.3 34.8 1.0
CU D:CU14 2.6 35.1 1.0
O D:GLU254 2.7 35.1 1.0
CE1 D:HIS260 2.9 33.4 1.0
CB D:CYS252 3.2 32.6 1.0
CG D:HIS260 3.2 33.4 1.0
CB D:CYS256 3.4 35.0 1.0
CA D:HIS260 3.6 34.1 1.0
CB D:HIS260 3.6 34.1 1.0
C D:GLU254 3.6 34.7 1.0
N D:CYS256 3.7 34.8 1.0
O D:HIS260 3.9 33.2 1.0
NE2 D:HIS260 4.1 31.5 1.0
C D:CYS252 4.1 33.0 1.0
N D:GLU254 4.2 33.7 1.0
C D:HIS260 4.2 33.8 1.0
O D:CYS252 4.2 32.6 1.0
CD2 D:HIS260 4.2 33.1 1.0
CA D:CYS256 4.2 34.5 1.0
ND1 D:HIS217 4.2 32.3 1.0
CA D:CYS252 4.3 32.6 1.0
CA D:LEU255 4.3 34.6 1.0
C D:LEU255 4.3 34.6 1.0
N D:LEU255 4.3 34.4 1.0
SD D:MET263 4.4 35.9 1.0
N D:SER253 4.5 33.3 1.0
CA D:GLU254 4.6 34.4 1.0
CG D:MET263 4.7 34.6 1.0
N D:HIS260 4.7 35.1 1.0
CA D:HIS217 4.8 34.0 1.0

Copper binding site 6 out of 6 in 3fye

Go back to Copper Binding Sites List in 3fye
Copper binding site 6 out of 6 in the Catalytic Core Subunits (I and II) of 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 Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu4

b:35.1
occ:1.00
ND1 D:HIS217 2.1 32.3 1.0
SG D:CYS252 2.4 32.5 1.0
SD D:MET263 2.4 35.9 1.0
SG D:CYS256 2.4 34.8 1.0
CU D:CU13 2.6 35.9 1.0
CE1 D:HIS217 3.0 32.1 1.0
CE D:MET263 3.0 30.4 1.0
CG D:HIS217 3.2 32.5 1.0
CB D:CYS256 3.4 35.0 1.0
CB D:CYS252 3.4 32.6 1.0
CG D:MET263 3.5 34.6 1.0
CB D:HIS217 3.6 33.7 1.0
NE2 D:HIS217 4.1 30.9 1.0
CA D:HIS217 4.1 34.0 1.0
CD2 D:HIS217 4.2 30.8 1.0
O D:GLU254 4.4 35.1 1.0
CD1 D:TRP143 4.4 39.5 1.0
ND1 D:HIS260 4.6 32.9 1.0
O D:TYR141 4.6 38.6 1.0
CA D:HIS260 4.7 34.1 1.0
CA D:CYS256 4.8 34.5 1.0
CA D:CYS252 4.8 32.6 1.0
CB D:MET263 4.9 36.1 1.0

Reference:

L.Qin, J.Liu, D.Mills, D.A.Proshlyakov, C.Hiser, S.Ferguson-Miller. Redox Dependent Conformational Changes in Cytochrome C Oxidase Suggest A Gating Mechanism For Proton Uptake. Biochemistry V. 48 5121 2009.
ISSN: ISSN 0006-2960
PubMed: 19397279
DOI: 10.1021/BI9001387
Page generated: Sun Dec 13 11:09:46 2020

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