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Copper in PDB 3dtu: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid:
1.9.3.1;

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid, PDB code: 3dtu was solved by L.Qin, D.A.Mills, L.Buhrow, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.243, 132.052, 167.966, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.2

Other elements in 3dtu:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides Complexed with Deoxycholic Acid also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Cadmium (Cd) 5 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 Complexed with Deoxycholic Acid (pdb code 3dtu). 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 Complexed with Deoxycholic Acid, PDB code: 3dtu:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 3dtu

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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 Complexed with Deoxycholic Acid


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1023

b:32.5
occ:1.00
NE2 A:HIS334 2.0 29.8 1.0
O A:OH1501 2.1 35.7 1.0
ND1 A:HIS284 2.1 30.9 1.0
NE2 A:HIS333 2.1 37.2 1.0
CD2 A:HIS334 2.9 30.2 1.0
O A:HOH1511 2.9 25.6 1.0
CE1 A:HIS334 3.0 29.8 1.0
CG A:HIS284 3.1 31.2 1.0
CE1 A:HIS284 3.1 30.5 1.0
CE1 A:HIS333 3.1 35.2 1.0
CD2 A:HIS333 3.1 34.1 1.0
CB A:HIS284 3.3 30.3 1.0
CA A:HIS284 4.0 30.3 1.0
CG A:HIS334 4.0 31.2 1.0
ND1 A:HIS334 4.0 30.9 1.0
ND1 A:HIS333 4.2 34.8 1.0
CD2 A:HIS284 4.2 31.4 1.0
NE2 A:HIS284 4.2 30.9 1.0
CG A:HIS333 4.3 34.0 1.0
NA A:HEA1503 4.5 30.4 1.0
C1A A:HEA1503 4.6 30.5 1.0
C4A A:HEA1503 4.6 29.3 1.0
C2A A:HEA1503 4.8 30.1 1.0
C3A A:HEA1503 4.8 29.6 1.0
N A:HIS284 4.8 30.3 1.0
FE A:HEA1503 4.9 28.4 1.0
O A:HOH1557 4.9 42.0 1.0

Copper binding site 2 out of 6 in 3dtu

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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 Complexed with Deoxycholic Acid


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1022

b:28.3
occ:1.00
ND1 B:HIS260 2.1 28.0 1.0
SG B:CYS256 2.3 29.7 1.0
SG B:CYS252 2.3 29.3 1.0
CU B:CU1004 2.6 29.5 1.0
O B:GLU254 2.6 30.7 1.0
CE1 B:HIS260 3.0 29.4 1.0
CG B:HIS260 3.2 27.6 1.0
CB B:CYS252 3.3 28.1 1.0
CB B:CYS256 3.4 29.7 1.0
C B:GLU254 3.5 30.1 1.0
CB B:HIS260 3.6 27.4 1.0
CA B:HIS260 3.6 27.5 1.0
N B:CYS256 3.7 29.6 1.0
O B:HIS260 3.9 27.9 1.0
N B:GLU254 4.1 29.9 1.0
NE2 B:HIS260 4.1 28.3 1.0
CA B:LEU255 4.2 29.2 1.0
C B:LEU255 4.2 29.4 1.0
C B:CYS252 4.2 28.9 1.0
C B:HIS260 4.2 27.7 1.0
CA B:CYS256 4.2 29.4 1.0
N B:LEU255 4.2 29.7 1.0
CD2 B:HIS260 4.2 28.7 1.0
O B:CYS252 4.3 28.2 1.0
ND1 B:HIS217 4.3 23.3 1.0
CA B:CYS252 4.4 28.5 1.0
SD B:MET263 4.4 28.1 1.0
CA B:GLU254 4.5 30.4 1.0
N B:SER253 4.6 29.4 1.0
CG B:MET263 4.7 27.5 1.0
N B:HIS260 4.8 27.9 1.0
CA B:HIS217 4.9 26.9 1.0

Copper binding site 3 out of 6 in 3dtu

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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 Complexed with Deoxycholic Acid


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1004

b:29.5
occ:1.00
ND1 B:HIS217 2.1 23.3 1.0
SG B:CYS252 2.4 29.3 1.0
SD B:MET263 2.4 28.1 1.0
SG B:CYS256 2.4 29.7 1.0
CU B:CU1022 2.6 28.3 1.0
CE B:MET263 3.0 23.6 1.0
CE1 B:HIS217 3.0 25.1 1.0
CG B:HIS217 3.2 26.2 1.0
CB B:CYS256 3.3 29.7 1.0
CB B:CYS252 3.5 28.1 1.0
CG B:MET263 3.5 27.5 1.0
CB B:HIS217 3.6 26.1 1.0
NE2 B:HIS217 4.2 26.0 1.0
CA B:HIS217 4.2 26.9 1.0
O B:GLU254 4.2 30.7 1.0
CD2 B:HIS217 4.3 24.6 1.0
CD1 B:TRP143 4.5 30.8 1.0
ND1 B:HIS260 4.6 28.0 1.0
O B:TYR141 4.7 31.7 1.0
CA B:CYS256 4.7 29.4 1.0
CA B:HIS260 4.8 27.5 1.0
CA B:CYS252 4.9 28.5 1.0
CB B:MET263 4.9 28.2 1.0

Copper binding site 4 out of 6 in 3dtu

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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 Complexed with Deoxycholic Acid


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu569

b:26.5
occ:1.00
NE2 C:HIS334 2.0 24.1 1.0
ND1 C:HIS284 2.0 23.1 1.0
O C:OH572 2.0 28.7 1.0
NE2 C:HIS333 2.1 26.6 1.0
CE1 C:HIS334 2.9 20.1 1.0
CE1 C:HIS333 3.0 26.3 1.0
CE1 C:HIS284 3.0 23.7 1.0
CD2 C:HIS334 3.0 22.3 1.0
CG C:HIS284 3.0 24.2 1.0
O C:HOH589 3.1 26.3 1.0
CD2 C:HIS333 3.2 25.0 1.0
CB C:HIS284 3.3 23.3 1.0
CA C:HIS284 4.0 24.1 1.0
ND1 C:HIS334 4.0 21.5 1.0
CG C:HIS334 4.1 22.3 1.0
ND1 C:HIS333 4.1 24.4 1.0
NE2 C:HIS284 4.1 24.3 1.0
CD2 C:HIS284 4.2 24.6 1.0
CG C:HIS333 4.3 26.0 1.0
NA C:HEA575 4.5 25.0 1.0
C1A C:HEA575 4.6 25.0 1.0
C4A C:HEA575 4.6 25.2 1.0
N C:HIS284 4.8 23.3 1.0
C2A C:HEA575 4.8 24.9 1.0
O C:HOH636 4.8 45.9 1.0
C3A C:HEA575 4.8 24.4 1.0
FE C:HEA575 4.9 24.5 1.0

Copper binding site 5 out of 6 in 3dtu

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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 Complexed with Deoxycholic Acid


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu3

b:28.9
occ:1.00
ND1 D:HIS260 2.1 29.8 1.0
SG D:CYS252 2.3 25.9 1.0
SG D:CYS256 2.3 28.0 1.0
O D:GLU254 2.6 28.0 1.0
CU D:CU4 2.6 28.3 1.0
CE1 D:HIS260 2.9 29.9 1.0
CG D:HIS260 3.1 28.3 1.0
CB D:CYS252 3.3 25.2 1.0
CB D:CYS256 3.4 29.1 1.0
C D:GLU254 3.5 28.5 1.0
CB D:HIS260 3.6 27.4 1.0
CA D:HIS260 3.6 27.7 1.0
N D:CYS256 3.7 28.8 1.0
O D:HIS260 4.0 27.3 1.0
NE2 D:HIS260 4.0 29.6 1.0
N D:GLU254 4.1 28.0 1.0
CA D:LEU255 4.2 28.5 1.0
CD2 D:HIS260 4.2 30.0 1.0
C D:CYS252 4.2 26.3 1.0
O D:CYS252 4.2 26.1 1.0
CA D:CYS256 4.2 28.9 1.0
C D:LEU255 4.2 28.4 1.0
C D:HIS260 4.2 27.1 1.0
ND1 D:HIS217 4.2 21.3 1.0
N D:LEU255 4.3 28.3 1.0
CA D:CYS252 4.4 25.9 1.0
SD D:MET263 4.4 29.2 1.0
CA D:GLU254 4.5 28.3 1.0
N D:SER253 4.6 26.5 1.0
CG D:MET263 4.8 28.9 1.0
N D:HIS260 4.8 27.7 1.0

Copper binding site 6 out of 6 in 3dtu

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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 Complexed with Deoxycholic Acid


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 Complexed with Deoxycholic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu4

b:28.3
occ:1.00
ND1 D:HIS217 2.0 21.3 1.0
SG D:CYS252 2.3 25.9 1.0
SG D:CYS256 2.4 28.0 1.0
SD D:MET263 2.4 29.2 1.0
CU D:CU3 2.6 28.9 1.0
CE1 D:HIS217 2.8 22.3 1.0
CE D:MET263 3.0 23.3 1.0
CG D:HIS217 3.2 24.4 1.0
CB D:CYS256 3.4 29.1 1.0
CB D:CYS252 3.4 25.2 1.0
CG D:MET263 3.6 28.9 1.0
CB D:HIS217 3.7 25.7 1.0
NE2 D:HIS217 4.0 23.1 1.0
CD2 D:HIS217 4.2 23.2 1.0
CA D:HIS217 4.2 25.8 1.0
O D:GLU254 4.3 28.0 1.0
CD1 D:TRP143 4.5 32.3 1.0
ND1 D:HIS260 4.5 29.8 1.0
O D:TYR141 4.7 30.9 1.0
CA D:CYS256 4.8 28.9 1.0
CA D:HIS260 4.8 27.7 1.0
CA D:CYS252 4.8 25.9 1.0
CB D:MET263 5.0 28.6 1.0

Reference:

L.Qin, D.A.Mills, L.Buhrow, C.Hiser, S.Ferguson-Miller. A Conserved Steroid Binding Site in Cytochrome C Oxidase. Biochemistry V. 47 9931 2008.
ISSN: ISSN 0006-2960
PubMed: 18759498
DOI: 10.1021/BI8013483
Page generated: Wed Oct 28 14:23:40 2020
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