Atomistry » Cadmium » PDB 3cn6-3haf » 3dtu
Atomistry »
  Cadmium »
    PDB 3cn6-3haf »
      3dtu »

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: Sat Dec 12 08:21:14 2020

Last articles

Zn in 7OQY
Zn in 7PEL
Zn in 7OYG
Zn in 7P3S
Zn in 7PE7
Zn in 7RZC
Zn in 7PE9
Zn in 7PE8
Zn in 7RAG
Zn in 7RN5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy