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

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

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

Protein crystallography data

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik 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 (°) 183.321, 206.525, 178.159, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.8

Other elements in 2eik:

The structure of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State (pdb code 2eik). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eik:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 2eik

Go back to Cadmium Binding Sites List in 2eik
Cadmium binding site 1 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd603

b:41.6
occ:1.00
 NE2 L:HIS2 2.2 60.9 1.0
NE2 A:HIS503 2.2 27.6 1.0
O A:HOH2078 2.4 24.8 1.0
O A:HOH2077 2.4 20.3 1.0
CE1 A:HIS503 2.9 26.1 1.0
CE1 L:HIS2 2.9 66.3 1.0
CD2 A:HIS503 3.3 27.1 1.0
CD2 L:HIS2 3.3 67.8 1.0
ND1 A:HIS503 4.1 28.4 1.0
ND1 L:HIS2 4.1 69.1 1.0
O L:HOH2089 4.2 35.4 1.0
CG A:HIS503 4.3 28.8 1.0
CG L:HIS2 4.4 68.4 1.0
CE1 A:TYR502 4.7 19.8 1.0
O A:HOH2079 4.8 27.8 1.0
CD1 A:TYR502 4.9 21.2 1.0
O A:HOH2084 5.0 32.4 1.0
CB C:MET10 5.0 23.2 1.0

Cadmium binding site 2 out of 6 in 2eik

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Cadmium binding site 2 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd262

b:31.9
occ:1.00
 NE2 C:HIS232 2.2 22.9 1.0
NE2 C:HIS148 2.3 33.4 1.0
O C:HOH2027 2.3 41.6 1.0
O C:HOH2409 2.3 44.2 1.0
OE1 C:GLU236 2.4 47.4 1.0
SD C:MET152 2.6 39.5 1.0
CE1 C:HIS148 3.0 33.0 1.0
CE1 C:HIS232 3.1 26.7 1.0
CD C:GLU236 3.2 51.2 1.0
CD2 C:HIS232 3.3 23.1 1.0
CD2 C:HIS148 3.4 30.4 1.0
CG C:MET152 3.6 33.9 1.0
CG C:GLU236 3.8 42.8 1.0
OE2 C:GLU236 3.9 57.7 1.0
CE C:MET152 4.0 36.5 1.0
ND1 C:HIS148 4.2 33.1 1.0
ND1 C:HIS232 4.3 23.6 1.0
CG C:HIS232 4.4 22.0 1.0
CG C:HIS148 4.4 29.6 1.0
O C:HOH2230 4.9 23.1 1.0

Cadmium binding site 3 out of 6 in 2eik

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Cadmium binding site 3 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced 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 Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd606

b:42.6
occ:0.50
 ND1 E:HIS78 2.3 38.6 1.0
O E:HOH4904 2.4 30.9 0.5
OE1 E:GLU80 2.5 40.8 1.0
OE2 E:GLU80 2.5 42.5 1.0
CD E:GLU80 2.6 37.0 1.0
CE1 E:HIS78 3.1 36.6 1.0
CG E:HIS78 3.4 36.2 1.0
CB E:HIS78 3.8 30.4 1.0
CA E:HIS78 3.9 30.3 1.0
CG E:GLU80 3.9 42.7 1.0
O I:HOH4355 4.0 44.5 1.0
NE2 E:HIS78 4.3 37.8 1.0
CD2 E:HIS78 4.5 35.9 1.0
C E:HIS78 4.8 30.3 1.0
N E:HIS78 4.9 29.9 1.0
N E:LYS79 5.0 33.9 1.0

Cadmium binding site 4 out of 6 in 2eik

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Cadmium binding site 4 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cd1603

b:45.4
occ:1.00
 NE2 N:HIS503 2.3 50.4 1.0
NE2 Y:HIS2 2.3 76.3 1.0
O N:HOH3078 2.4 33.1 1.0
O N:HOH3077 2.4 29.2 1.0
CE1 Y:HIS2 3.0 84.2 1.0
CE1 N:HIS503 3.1 46.4 1.0
CD2 N:HIS503 3.4 45.2 1.0
CD2 Y:HIS2 3.4 82.0 1.0
ND1 Y:HIS2 4.2 85.0 1.0
ND1 N:HIS503 4.3 44.8 1.0
O Y:HOH3089 4.4 34.8 1.0
CG Y:HIS2 4.4 82.2 1.0
CG N:HIS503 4.4 41.6 1.0
CE1 N:TYR502 4.7 27.6 1.0
CD1 N:TYR502 5.0 30.2 1.0
O N:HOH3084 5.0 41.0 1.0
O N:HOH3079 5.0 35.5 1.0

Cadmium binding site 5 out of 6 in 2eik

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Cadmium binding site 5 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd1262

b:33.4
occ:1.00
 NE2 P:HIS148 2.3 35.7 1.0
NE2 P:HIS232 2.3 24.2 1.0
OE1 P:GLU236 2.3 47.5 1.0
O P:HOH3027 2.3 52.3 1.0
O P:HOH3409 2.3 44.6 1.0
SD P:MET152 2.5 40.7 1.0
CE1 P:HIS148 3.0 33.2 1.0
CD P:GLU236 3.1 49.8 1.0
CE1 P:HIS232 3.1 19.9 1.0
CD2 P:HIS232 3.4 23.0 1.0
CD2 P:HIS148 3.4 33.0 1.0
CG P:MET152 3.6 31.9 1.0
OE2 P:GLU236 3.8 52.6 1.0
CE P:MET152 3.8 34.9 1.0
CG P:GLU236 3.9 43.7 1.0
ND1 P:HIS148 4.2 36.5 1.0
ND1 P:HIS232 4.3 22.4 1.0
CG P:HIS148 4.4 34.4 1.0
CG P:HIS232 4.5 22.4 1.0
O P:HOH3230 4.8 25.6 1.0

Cadmium binding site 6 out of 6 in 2eik

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Cadmium binding site 6 out of 6 in the Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Cadmium Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cd1609

b:51.7
occ:0.30
 ND1 P:HIS3 2.2 44.5 0.3
OE2 N:GLU506 2.3 54.4 1.0
CE1 P:HIS3 3.0 47.1 0.3
CG P:HIS3 3.3 44.1 0.3
CD N:GLU506 3.5 57.6 1.0
CB P:HIS3 3.8 40.7 0.3
OE1 N:GLU506 4.0 62.4 1.0
NE2 P:HIS3 4.2 48.2 0.3
O N:HOH3084 4.3 41.0 1.0
CD2 P:HIS3 4.4 47.0 0.3
CG N:GLU506 4.7 49.6 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: Sat Dec 12 08:16:55 2020

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