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Cadmium 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
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Copper (Cu) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 5 binding sites of Cadmium 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 Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in 3dtu

Go back to Cadmium Binding Sites List in 3dtu
Cadmium binding site 1 out of 5 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 Cadmium with other atoms in the Cd 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
B:Cd1008

b:35.2
occ:1.00
 OE1 B:GLU280 2.0 34.0 1.0
ND1 B:HIS283 2.2 42.5 1.0
NE2 B:HIS285 2.3 48.1 1.0
OE2 B:GLU280 2.4 36.7 1.0
CD B:GLU280 2.6 34.9 1.0
CG B:HIS283 3.2 43.8 1.0
CE1 B:HIS283 3.2 44.2 1.0
CE1 B:HIS285 3.2 49.1 1.0
CD2 B:HIS285 3.3 48.6 1.0
CB B:HIS283 3.4 43.8 1.0
CG B:GLU280 4.1 35.0 1.0
NE2 B:HIS283 4.3 44.5 1.0
CD2 B:HIS283 4.3 44.0 1.0
ND1 B:HIS285 4.3 49.1 1.0
CG B:HIS285 4.4 51.1 1.0
O B:HOH1167 4.4 40.7 1.0
O2 B:HTO1 4.8 54.1 1.0
CA B:HIS283 4.8 44.3 1.0
O B:HOH1163 4.9 58.9 1.0
O B:GLU280 4.9 36.5 1.0
O B:HIS283 4.9 45.8 1.0

Cadmium binding site 2 out of 5 in 3dtu

Go back to Cadmium Binding Sites List in 3dtu
Cadmium binding site 2 out of 5 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 Cadmium with other atoms in the Cd 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:Cd1009

b:45.1
occ:0.30
 OE1 B:GLU101 2.0 59.5 1.0
O B:HOH1157 2.2 52.7 1.0
OE2 B:GLU101 2.4 61.6 1.0
CD B:GLU101 2.5 60.3 1.0
ND1 B:HIS96 2.6 63.4 1.0
O B:HOH1158 2.7 65.0 1.0
CG B:HIS96 3.6 62.0 1.0
CE1 B:HIS96 3.6 64.6 1.0
CB B:HIS96 3.7 60.7 1.0
CG B:GLU101 4.0 60.0 1.0
CA B:HIS96 4.1 60.3 1.0
O B:THR95 4.5 57.8 1.0
N B:ASN97 4.5 61.4 1.0
NE2 B:HIS96 4.7 64.3 1.0
CG A:PRO315 4.7 43.6 1.0
CD2 B:HIS96 4.7 63.4 1.0
CB B:GLU101 4.7 59.8 1.0
CA A:GLY312 4.9 42.9 1.0
C B:HIS96 4.9 60.9 1.0

Cadmium binding site 3 out of 5 in 3dtu

Go back to Cadmium Binding Sites List in 3dtu
Cadmium binding site 3 out of 5 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 Cadmium with other atoms in the Cd 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:Cd1010

b:53.8
occ:0.50
 NE2 B:HIS286 2.5 61.5 1.0
O B:HOH1162 2.6 42.9 1.0
ND1 B:HIS284 2.7 54.5 1.0
O B:HOH1176 2.7 63.7 1.0
CE1 B:HIS286 3.4 61.7 1.0
CD2 B:HIS286 3.4 61.1 1.0
CG B:HIS284 3.6 52.6 1.0
CE1 B:HIS284 3.6 55.7 1.0
CB B:HIS284 3.7 50.0 1.0
CA B:HIS284 4.3 49.8 1.0
ND1 B:HIS286 4.5 61.5 1.0
CG B:HIS286 4.5 60.4 1.0
NE2 B:HIS284 4.7 55.5 1.0
CD2 B:HIS284 4.7 53.7 1.0
N B:HIS285 4.8 51.7 1.0
O B:HOH1177 4.8 56.5 1.0

Cadmium binding site 4 out of 5 in 3dtu

Go back to Cadmium Binding Sites List in 3dtu
Cadmium binding site 4 out of 5 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 Cadmium with other atoms in the Cd 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
D:Cd8

b:36.6
occ:1.00
 OE1 D:GLU280 2.2 34.7 1.0
NE2 D:HIS285 2.3 47.3 1.0
ND1 D:HIS283 2.3 41.9 1.0
OE2 D:GLU280 2.3 36.6 1.0
CD D:GLU280 2.6 34.7 1.0
CE1 D:HIS285 3.2 47.0 1.0
CE1 D:HIS283 3.3 41.5 1.0
CG D:HIS283 3.3 42.4 1.0
CD2 D:HIS285 3.3 47.2 1.0
CB D:HIS283 3.5 42.9 1.0
CG D:GLU280 4.1 35.5 1.0
ND1 D:HIS285 4.4 46.6 1.0
NE2 D:HIS283 4.4 42.2 1.0
CD2 D:HIS283 4.4 43.3 1.0
CG D:HIS285 4.4 48.0 1.0
O D:HIS283 4.9 44.6 1.0
CA D:HIS283 4.9 43.3 1.0
O D:GLU280 4.9 37.1 1.0

Cadmium binding site 5 out of 5 in 3dtu

Go back to Cadmium Binding Sites List in 3dtu
Cadmium binding site 5 out of 5 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 Cadmium with other atoms in the Cd 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:Cd9

b:46.1
occ:1.00
 O4 C:DXC576 2.3 51.4 1.0
O C:HOH719 2.4 28.9 1.0
OE1 D:GLU101 2.5 42.5 1.0
O3 C:DXC576 2.5 51.9 1.0
ND1 D:HIS96 2.5 43.1 1.0
OE2 D:GLU101 2.5 40.4 1.0
C23 C:DXC576 2.7 52.3 1.0
CD D:GLU101 2.8 42.0 1.0
CE1 D:HIS96 3.3 44.5 1.0
CG D:HIS96 3.5 41.9 1.0
CB D:HIS96 3.8 39.6 1.0
CA D:HIS96 4.0 39.6 1.0
C22 C:DXC576 4.2 52.5 1.0
O6 C:DMU568 4.3 69.6 1.0
CG D:GLU101 4.3 40.2 1.0
O C:HOH718 4.4 46.5 1.0
NE2 D:HIS96 4.4 45.7 1.0
N D:ASN97 4.4 40.5 1.0
CD2 D:HIS96 4.5 44.6 1.0
O D:HOH421 4.6 55.1 1.0
O D:THR95 4.6 37.7 1.0
C D:HIS96 4.8 39.8 1.0
CA C:GLY312 4.8 30.0 1.0
CG C:PRO315 4.9 29.2 1.0
CB D:GLU101 5.0 41.6 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: Thu Jul 10 12:31:16 2025

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