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Cadmium in PDB 2gsm: Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides

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

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

Protein crystallography data

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides, PDB code: 2gsm was solved by L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.020, 131.639, 176.802, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 23.2

Other elements in 2gsm:

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides 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 (pdb code 2gsm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides, PDB code: 2gsm:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 2gsm

Go back to Cadmium Binding Sites List in 2gsm
Cadmium binding site 1 out of 4 in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3008

b:35.6
occ:1.00
 OE1 B:GLU280 2.1 35.2 1.0
NE2 B:HIS285 2.2 43.4 1.0
ND1 B:HIS283 2.3 40.9 1.0
OE2 B:GLU280 2.3 37.0 1.0
CD B:GLU280 2.5 36.6 1.0
CE1 B:HIS285 3.2 43.0 1.0
CD2 B:HIS285 3.2 43.3 1.0
CE1 B:HIS283 3.2 41.0 1.0
CG B:HIS283 3.2 39.9 1.0
CB B:HIS283 3.5 41.0 1.0
CG B:GLU280 4.1 34.5 1.0
ND1 B:HIS285 4.3 44.1 1.0
NE2 B:HIS283 4.3 38.2 1.0
CG B:HIS285 4.3 45.1 1.0
CD2 B:HIS283 4.4 40.2 1.0
O B:GLU280 4.9 33.9 1.0
O B:HIS283 4.9 42.3 1.0
CA B:HIS283 4.9 41.1 1.0
CB B:GLU280 5.0 34.4 1.0

Cadmium binding site 2 out of 4 in 2gsm

Go back to Cadmium Binding Sites List in 2gsm
Cadmium binding site 2 out of 4 in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd3009

b:40.9
occ:0.50
 OE1 B:GLU101 2.0 45.4 1.0
O B:HOH5113 2.2 35.8 1.0
OE2 B:GLU101 2.3 48.4 1.0
CD B:GLU101 2.5 46.1 1.0
ND1 B:HIS96 2.6 40.9 1.0
O B:HOH5114 2.7 46.4 1.0
CE1 B:HIS96 3.5 41.0 1.0
CG B:HIS96 3.6 41.0 1.0
CB B:HIS96 3.8 41.1 1.0
CA B:HIS96 4.0 41.2 1.0
CG B:GLU101 4.0 45.2 1.0
N B:ASN97 4.4 43.4 1.0
O B:THR95 4.5 40.3 1.0
NE2 B:HIS96 4.7 42.3 1.0
CD2 B:HIS96 4.7 41.1 1.0
C B:HIS96 4.8 42.1 1.0
CB B:GLU101 4.8 45.2 1.0
CG A:PRO315 4.9 36.3 1.0
CE1 A:PHE311 4.9 35.8 1.0

Cadmium binding site 3 out of 4 in 2gsm

Go back to Cadmium Binding Sites List in 2gsm
Cadmium binding site 3 out of 4 in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd4008

b:35.1
occ:1.00
 OE1 D:GLU280 2.0 29.1 1.0
ND1 D:HIS283 2.1 41.8 1.0
OE2 D:GLU280 2.3 36.1 1.0
NE2 D:HIS285 2.3 45.6 1.0
CD D:GLU280 2.4 33.8 1.0
CE1 D:HIS283 3.1 41.8 1.0
CG D:HIS283 3.2 42.0 1.0
CE1 D:HIS285 3.2 45.1 1.0
CD2 D:HIS285 3.3 46.2 1.0
CB D:HIS283 3.6 43.0 1.0
CG D:GLU280 4.0 34.4 1.0
NE2 D:HIS283 4.2 41.3 1.0
CD2 D:HIS283 4.3 42.0 1.0
ND1 D:HIS285 4.4 45.6 1.0
CG D:HIS285 4.4 47.0 1.0
CB D:GLU280 4.9 35.2 1.0
O D:GLU280 4.9 36.1 1.0
CA D:HIS283 4.9 43.4 1.0

Cadmium binding site 4 out of 4 in 2gsm

Go back to Cadmium Binding Sites List in 2gsm
Cadmium binding site 4 out of 4 in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd4009

b:42.5
occ:0.30
 O D:HOH1196 1.8 41.8 1.0
OE2 D:GLU101 1.9 53.7 1.0
O D:HOH1197 2.2 55.3 1.0
OE1 D:GLU101 2.3 52.7 1.0
CD D:GLU101 2.4 53.2 1.0
ND1 D:HIS96 2.7 54.5 1.0
CG D:HIS96 3.6 53.2 1.0
CB D:HIS96 3.6 52.5 1.0
CE1 D:HIS96 3.8 55.0 1.0
CA D:HIS96 3.8 52.4 1.0
CG D:GLU101 3.9 53.0 1.0
N D:ASN97 4.3 53.3 1.0
O D:THR95 4.4 51.1 1.0
C D:HIS96 4.7 52.8 1.0
CB D:GLU101 4.7 52.7 1.0
CD2 D:HIS96 4.8 54.0 1.0
NE2 D:HIS96 4.8 54.3 1.0
N D:HIS96 4.9 51.6 1.0
CE1 C:PHE311 4.9 41.5 1.0

Reference:

L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller. Identification of Conserved Lipid/Detergent-Binding Sites in A High-Resolution Structure of the Membrane Protein Cytochrome C Oxidase. Proc.Natl.Acad.Sci.Usa V. 103 16117 2006.
ISSN: ISSN 0027-8424
PubMed: 17050688
DOI: 10.1073/PNAS.0606149103
Page generated: Sun Jan 24 09:43:34 2021

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