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Cadmium in PDB 2eil: Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

Enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State

All present enzymatic activity of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State:
1.9.3.1;

Protein crystallography data

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil was solved by K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.379, 205.898, 178.182, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.1

Other elements in 2eil:

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 2eil). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2eil:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 2eil

Go back to Cadmium Binding Sites List in 2eil
Cadmium binding site 1 out of 3 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:34.2
occ:0.50
 O A:HOH2095 2.3 67.0 1.0
NE2 L:HIS2 2.3 72.2 1.0
O L:HOH2093 2.3 38.2 1.0
ND1 A:HIS503 2.4 38.7 1.0
CE1 L:HIS2 3.3 77.9 1.0
CG A:HIS503 3.4 35.5 1.0
CE1 A:HIS503 3.4 39.1 1.0
CD2 L:HIS2 3.4 80.2 1.0
CB A:HIS503 3.6 31.7 1.0
OE1 L:GLU5 4.0 45.5 1.0
OE1 A:GLU506 4.2 63.7 1.0
N A:HIS503 4.4 29.1 1.0
ND1 L:HIS2 4.5 78.4 1.0
CD2 A:HIS503 4.6 38.1 1.0
CG L:HIS2 4.6 79.7 1.0
NE2 A:HIS503 4.6 37.2 1.0
CA A:HIS503 4.6 31.5 1.0
CD A:GLU506 4.7 57.8 1.0
OE2 A:GLU506 4.8 63.9 1.0

Cadmium binding site 2 out of 3 in 2eil

Go back to Cadmium Binding Sites List in 2eil
Cadmium binding site 2 out of 3 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd262

b:32.2
occ:1.00
 NE2 C:HIS232 2.2 22.3 1.0
NE2 C:HIS148 2.3 36.7 1.0
O C:HOH2409 2.3 38.2 1.0
O C:HOH2027 2.3 51.5 1.0
OE1 C:GLU236 2.4 44.3 1.0
SD C:MET152 2.6 38.8 1.0
CE1 C:HIS148 3.0 33.9 1.0
CE1 C:HIS232 3.1 25.7 1.0
CD C:GLU236 3.1 49.6 1.0
CD2 C:HIS232 3.2 25.7 1.0
CD2 C:HIS148 3.4 35.0 1.0
CG C:MET152 3.6 33.4 1.0
CG C:GLU236 3.8 41.8 1.0
OE2 C:GLU236 3.9 55.8 1.0
CE C:MET152 4.0 36.6 1.0
ND1 C:HIS148 4.2 35.5 1.0
ND1 C:HIS232 4.3 23.6 1.0
CG C:HIS232 4.4 23.1 1.0
CG C:HIS148 4.4 33.0 1.0
O C:HOH2230 4.9 27.6 1.0
CB C:MET152 5.0 28.9 1.0

Cadmium binding site 3 out of 3 in 2eil

Go back to Cadmium Binding Sites List in 2eil
Cadmium binding site 3 out of 3 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd1262

b:33.5
occ:1.00
 OE1 P:GLU236 2.3 51.5 1.0
NE2 P:HIS232 2.3 24.2 1.0
NE2 P:HIS148 2.3 37.9 1.0
O P:HOH3027 2.3 48.9 1.0
O P:HOH3409 2.3 41.0 1.0
SD P:MET152 2.6 37.6 1.0
CE1 P:HIS148 3.0 35.6 1.0
CD P:GLU236 3.1 52.4 1.0
CE1 P:HIS232 3.2 23.3 1.0
CD2 P:HIS232 3.3 23.6 1.0
CD2 P:HIS148 3.4 34.8 1.0
CG P:MET152 3.6 31.2 1.0
OE2 P:GLU236 3.8 56.6 1.0
CE P:MET152 3.8 37.0 1.0
CG P:GLU236 3.8 47.8 1.0
ND1 P:HIS148 4.3 37.1 1.0
ND1 P:HIS232 4.4 25.5 1.0
CG P:HIS232 4.4 23.5 1.0
CG P:HIS148 4.5 37.0 1.0
O P:HOH3230 5.0 31.1 1.0

Reference:

K.Muramoto, K.Hirata, K.Shinzawa-Itoh, S.Yoko-O, E.Yamashita, H.Aoyama, T.Tsukihara, S.Yoshikawa. A Histidine Residue Acting As A Controlling Site For Dioxygen Reduction and Proton Pumping By Cytochrome C Oxidase Proc.Natl.Acad.Sci.Usa V. 104 7881 2007.
ISSN: ISSN 0027-8424
PubMed: 17470809
DOI: 10.1073/PNAS.0610031104
Page generated: Thu Jul 10 11:45:57 2025

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