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

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

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State Bound with Cyanide:
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 Bound with Cyanide, PDB code: 3fyi 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.344, 131.877, 176.160, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.9

Other elements in 3fyi:

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

Copper binding site 1 out of 6 in 3fyi

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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 in the Reduced State Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu569

b:36.0
occ:1.00
N A:CYN572 1.8 32.3 1.0
NE2 A:HIS334 2.1 33.8 1.0
ND1 A:HIS284 2.1 33.4 1.0
C A:CYN572 2.9 31.7 1.0
NE2 A:HIS333 3.0 39.2 1.0
CE1 A:HIS284 3.0 32.7 1.0
CG A:HIS284 3.0 31.2 1.0
CE1 A:HIS334 3.0 32.5 1.0
CD2 A:HIS334 3.1 31.6 1.0
CB A:HIS284 3.3 29.6 1.0
CE1 A:HIS333 3.7 39.6 1.0
CA A:HIS284 3.8 30.0 1.0
CD2 A:HIS333 4.0 37.2 1.0
CD2 A:HIS284 4.1 33.0 1.0
NE2 A:HIS284 4.1 33.2 1.0
ND1 A:HIS334 4.2 32.7 1.0
CG A:HIS334 4.2 32.8 1.0
CG2 A:VAL287 4.6 29.7 1.0
N A:HIS284 4.6 29.8 1.0
O A:HOH647 4.7 39.9 1.0
ND1 A:HIS333 4.8 38.5 1.0
ND A:HEA568 4.8 26.4 1.0
CG2 A:VAL330 4.9 35.2 1.0
C A:HIS284 4.9 30.5 1.0
O A:HIS284 4.9 30.5 1.0

Copper binding site 2 out of 6 in 3fyi

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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 in the Reduced State Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu3

b:25.8
occ:1.00
ND1 B:HIS260 2.1 22.0 1.0
SG B:CYS252 2.2 24.9 1.0
SG B:CYS256 2.3 24.3 1.0
O B:GLU254 2.5 25.2 1.0
CU B:CU14 2.6 25.6 1.0
CE1 B:HIS260 2.9 21.8 1.0
CG B:HIS260 3.2 22.6 1.0
CB B:CYS252 3.3 24.4 1.0
CB B:CYS256 3.5 25.4 1.0
C B:GLU254 3.5 24.8 1.0
CA B:HIS260 3.6 22.6 1.0
CB B:HIS260 3.6 21.8 1.0
N B:CYS256 3.8 24.4 1.0
O B:HIS260 3.9 22.0 1.0
NE2 B:HIS260 4.1 23.7 1.0
O B:CYS252 4.1 24.2 1.0
N B:GLU254 4.1 25.0 1.0
C B:CYS252 4.1 24.6 1.0
CA B:LEU255 4.2 24.5 1.0
C B:HIS260 4.2 22.1 1.0
CD2 B:HIS260 4.2 21.8 1.0
N B:LEU255 4.2 24.4 1.0
C B:LEU255 4.3 24.3 1.0
CA B:CYS256 4.3 25.0 1.0
ND1 B:HIS217 4.3 21.6 1.0
CA B:CYS252 4.3 24.8 1.0
CA B:GLU254 4.5 24.9 1.0
SD B:MET263 4.5 23.5 1.0
N B:SER253 4.6 24.8 1.0
CG B:MET263 4.7 24.4 1.0
N B:HIS260 4.8 22.9 1.0
CA B:HIS217 4.9 24.6 1.0

Copper binding site 3 out of 6 in 3fyi

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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 in the Reduced State Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu4

b:25.6
occ:1.00
ND1 B:HIS217 2.1 21.6 1.0
SG B:CYS252 2.3 24.9 1.0
SG B:CYS256 2.4 24.3 1.0
SD B:MET263 2.4 23.5 1.0
CU B:CU13 2.6 25.8 1.0
CE1 B:HIS217 3.0 20.3 1.0
CE B:MET263 3.1 21.1 1.0
CG B:HIS217 3.2 23.5 1.0
CB B:CYS256 3.4 25.4 1.0
CG B:MET263 3.5 24.4 1.0
CB B:CYS252 3.5 24.4 1.0
CB B:HIS217 3.6 23.9 1.0
NE2 B:HIS217 4.1 21.9 1.0
CA B:HIS217 4.2 24.6 1.0
CD2 B:HIS217 4.3 22.2 1.0
O B:GLU254 4.3 25.2 1.0
CD1 B:TRP143 4.5 25.9 1.0
ND1 B:HIS260 4.6 22.0 1.0
O B:TYR141 4.6 26.8 1.0
CA B:HIS260 4.7 22.6 1.0
CA B:CYS256 4.8 25.0 1.0
CB B:MET263 4.9 25.5 1.0
CA B:CYS252 4.9 24.8 1.0

Copper binding site 4 out of 6 in 3fyi

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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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu569

b:42.5
occ:1.00
N C:CYN572 1.8 37.9 1.0
NE2 C:HIS334 2.1 39.2 1.0
ND1 C:HIS284 2.3 45.4 1.0
NE2 C:HIS333 2.9 43.4 1.0
C C:CYN572 2.9 36.8 1.0
CD2 C:HIS334 3.0 38.5 1.0
CG C:HIS284 3.1 43.6 1.0
CE1 C:HIS334 3.1 38.7 1.0
CE1 C:HIS284 3.2 45.5 1.0
CB C:HIS284 3.3 41.1 1.0
CE1 C:HIS333 3.6 42.9 1.0
CA C:HIS284 3.9 41.1 1.0
CD2 C:HIS333 3.9 42.0 1.0
CD2 C:HIS284 4.2 45.2 1.0
CG C:HIS334 4.2 38.5 1.0
ND1 C:HIS334 4.2 39.4 1.0
NE2 C:HIS284 4.3 45.3 1.0
CG2 C:VAL287 4.6 41.1 1.0
N C:HIS284 4.7 40.4 1.0
ND1 C:HIS333 4.7 43.7 1.0
O C:HOH1122 4.8 44.1 1.0
ND C:HEA568 4.9 30.6 1.0
CG C:HIS333 4.9 40.7 1.0
C C:HIS284 5.0 41.1 1.0
CG2 C:VAL330 5.0 44.7 1.0
FE C:HEA568 5.0 37.1 1.0

Copper binding site 5 out of 6 in 3fyi

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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 in the Reduced State Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu3

b:33.2
occ:1.00
ND1 D:HIS260 2.0 33.0 1.0
SG D:CYS252 2.3 29.8 1.0
SG D:CYS256 2.3 31.6 1.0
CU D:CU14 2.6 33.1 1.0
O D:GLU254 2.6 30.7 1.0
CE1 D:HIS260 2.8 31.9 1.0
CG D:HIS260 3.1 31.3 1.0
CB D:CYS252 3.3 28.5 1.0
CB D:CYS256 3.4 31.5 1.0
C D:GLU254 3.5 30.8 1.0
CA D:HIS260 3.6 31.5 1.0
CB D:HIS260 3.7 31.8 1.0
N D:CYS256 3.7 31.2 1.0
O D:HIS260 3.9 31.3 1.0
NE2 D:HIS260 4.0 30.6 1.0
C D:CYS252 4.1 29.1 1.0
CD2 D:HIS260 4.2 30.5 1.0
N D:GLU254 4.2 30.4 1.0
CA D:CYS256 4.2 31.6 1.0
O D:CYS252 4.2 28.5 1.0
CA D:LEU255 4.2 31.1 1.0
C D:HIS260 4.2 31.1 1.0
ND1 D:HIS217 4.2 27.2 1.0
N D:LEU255 4.3 30.4 1.0
C D:LEU255 4.3 30.9 1.0
CA D:CYS252 4.3 29.1 1.0
SD D:MET263 4.5 31.4 1.0
CA D:GLU254 4.5 30.7 1.0
N D:SER253 4.6 29.7 1.0
CG D:MET263 4.7 31.6 1.0
N D:HIS260 4.9 32.0 1.0
CA D:HIS217 4.9 31.5 1.0

Copper binding site 6 out of 6 in 3fyi

Go back to Copper Binding Sites List in 3fyi
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 Bound with Cyanide


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 Bound with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu4

b:33.1
occ:1.00
ND1 D:HIS217 2.1 27.2 1.0
SG D:CYS252 2.3 29.8 1.0
SG D:CYS256 2.4 31.6 1.0
SD D:MET263 2.4 31.4 1.0
CU D:CU13 2.6 33.2 1.0
CE1 D:HIS217 3.0 28.0 1.0
CE D:MET263 3.0 27.5 1.0
CG D:HIS217 3.2 29.4 1.0
CB D:CYS256 3.3 31.5 1.0
CB D:CYS252 3.4 28.5 1.0
CG D:MET263 3.5 31.6 1.0
CB D:HIS217 3.6 31.4 1.0
NE2 D:HIS217 4.1 25.7 1.0
CA D:HIS217 4.2 31.5 1.0
CD2 D:HIS217 4.3 27.9 1.0
O D:GLU254 4.3 30.7 1.0
CD1 D:TRP143 4.4 37.1 1.0
ND1 D:HIS260 4.5 33.0 1.0
CA D:CYS256 4.7 31.6 1.0
O D:TYR141 4.7 35.1 1.0
CA D:HIS260 4.8 31.5 1.0
CB D:MET263 4.8 31.6 1.0
CA D:CYS252 4.8 29.1 1.0
O D:HIS260 5.0 31.3 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 11:09:47 2020

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