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

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

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

Protein crystallography data

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State, PDB code: 2eim 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 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 183.909, 206.721, 178.337, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.6

Other elements in 2eim:

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

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 2eim

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Zinc binding site 1 out of 6 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc 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:Zn603

b:40.2
occ:0.90
NE2 L:HIS2 2.0 35.1 1.0
NE2 A:HIS503 2.1 30.7 1.0
O A:HOH2078 2.3 17.5 1.0
O A:HOH2077 2.3 11.5 1.0
CE1 A:HIS503 2.6 34.6 1.0
CE1 L:HIS2 2.8 51.2 1.0
CD2 L:HIS2 3.3 55.8 1.0
CD2 A:HIS503 3.3 40.2 1.0
ND1 A:HIS503 3.9 35.2 1.0
ND1 L:HIS2 4.0 58.8 1.0
CG A:HIS503 4.2 40.9 1.0
CG L:HIS2 4.3 56.8 1.0
O C:HOH2079 4.3 42.0 1.0
CB C:MET10 4.8 35.5 1.0
CE1 A:TYR502 4.9 32.2 1.0
O C:HOH2086 4.9 61.5 1.0

Zinc binding site 2 out of 6 in 2eim

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Zinc binding site 2 out of 6 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc 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:Zn262

b:40.8
occ:1.00
NE2 C:HIS148 1.9 48.2 1.0
NE2 C:HIS232 1.9 32.2 1.0
O C:HOH2027 2.2 35.8 1.0
OE1 C:GLU236 2.2 41.8 1.0
CE1 C:HIS148 2.7 47.8 1.0
CE1 C:HIS232 2.9 29.7 1.0
CD C:GLU236 3.0 44.8 1.0
CD2 C:HIS232 3.0 33.7 1.0
OE2 C:GLU236 3.1 52.1 1.0
CD2 C:HIS148 3.1 46.9 1.0
ND1 C:HIS148 4.0 47.8 1.0
ND1 C:HIS232 4.1 30.1 1.0
CG C:HIS232 4.1 33.4 1.0
CG C:HIS148 4.2 42.6 1.0
CG C:MET152 4.3 46.3 1.0
CG C:GLU236 4.4 37.6 1.0
SD C:MET152 4.4 42.5 1.0
O C:HOH2230 4.6 36.5 1.0
CB C:GLU236 4.9 30.6 1.0

Zinc binding site 3 out of 6 in 2eim

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Zinc binding site 3 out of 6 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc 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
F:Zn99

b:36.5
occ:1.00
SG F:CYS85 2.2 41.5 1.0
SG F:CYS82 2.2 28.2 1.0
SG F:CYS60 2.2 34.5 1.0
SG F:CYS62 2.3 31.1 1.0
CB F:CYS60 3.1 30.2 1.0
CB F:CYS82 3.1 39.3 1.0
CB F:CYS62 3.5 26.9 1.0
CA F:CYS62 3.6 36.0 1.0
CB F:CYS85 3.6 42.0 1.0
N F:CYS62 3.7 34.8 1.0
N F:CYS85 3.7 48.6 1.0
CA F:CYS85 4.2 47.1 1.0
C F:CYS60 4.2 24.6 1.0
CA F:CYS60 4.3 22.2 1.0
CB F:SER84 4.3 45.9 1.0
O F:CYS60 4.3 25.1 1.0
O F:HOH2339 4.4 27.0 1.0
CA F:CYS82 4.6 37.3 1.0
CG1 F:ILE70 4.6 30.2 1.0
N F:ILE61 4.7 27.5 1.0
C F:ILE61 4.7 30.7 1.0
C F:SER84 4.7 51.1 1.0
C F:CYS85 4.9 52.1 1.0
CB F:ILE70 4.9 31.0 1.0
CA F:SER84 4.9 47.0 1.0
OH F:TYR89 4.9 39.5 1.0
C F:CYS62 5.0 40.5 1.0
N F:GLY86 5.0 54.3 1.0
N F:SER84 5.0 43.0 1.0
OG1 F:THR87 5.0 49.7 1.0
OG F:SER84 5.0 48.2 1.0

Zinc binding site 4 out of 6 in 2eim

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc 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:Zn1603

b:43.4
occ:0.80
NE2 Y:HIS2 2.1 68.1 1.0
NE2 N:HIS503 2.1 58.4 1.0
O Y:HOH3078 2.3 26.2 1.0
O Y:HOH3077 2.4 13.9 1.0
CE1 N:HIS503 2.7 63.3 1.0
CE1 Y:HIS2 2.9 80.3 1.0
CD2 Y:HIS2 3.4 80.3 1.0
CD2 N:HIS503 3.4 58.3 1.0
ND1 N:HIS503 4.0 53.4 1.0
ND1 Y:HIS2 4.2 86.1 1.0
CG N:HIS503 4.4 51.5 1.0
CG Y:HIS2 4.4 83.2 1.0
O N:HOH3079 4.5 38.8 1.0
CE1 N:TYR502 4.8 52.2 1.0
CB P:MET10 4.9 54.3 1.0

Zinc binding site 5 out of 6 in 2eim

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc 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:Zn1262

b:46.1
occ:1.00
NE2 P:HIS148 1.9 42.0 1.0
NE2 P:HIS232 2.1 40.9 1.0
OE1 P:GLU236 2.1 47.5 1.0
O P:HOH3027 2.2 27.1 1.0
CD P:GLU236 2.8 53.0 1.0
OE2 P:GLU236 2.9 53.0 1.0
CE1 P:HIS148 2.9 42.7 1.0
CD2 P:HIS232 3.0 26.8 1.0
CD2 P:HIS148 3.0 44.8 1.0
CE1 P:HIS232 3.1 27.7 1.0
SD P:MET152 4.0 44.6 1.0
ND1 P:HIS148 4.1 43.6 1.0
CG P:HIS148 4.1 48.8 1.0
CG P:HIS232 4.2 29.0 1.0
CG P:GLU236 4.2 46.8 1.0
ND1 P:HIS232 4.2 33.6 1.0
CG P:MET152 4.3 45.3 1.0
O P:HOH3230 4.6 34.9 1.0
CB P:GLU236 4.8 42.2 1.0

Zinc binding site 6 out of 6 in 2eim

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc 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
S:Zn99

b:44.8
occ:1.00
SG S:CYS85 2.2 50.9 1.0
SG S:CYS60 2.2 41.8 1.0
SG S:CYS62 2.2 46.4 1.0
SG S:CYS82 2.2 31.3 1.0
CB S:CYS82 2.9 38.1 1.0
CB S:CYS60 3.3 38.3 1.0
CB S:CYS85 3.3 50.3 1.0
N S:CYS85 3.4 44.4 1.0
CB S:CYS62 3.5 45.3 1.0
CA S:CYS62 3.8 46.6 1.0
CA S:CYS85 3.9 48.7 1.0
N S:CYS62 4.0 47.8 1.0
CB S:SER84 4.3 47.9 1.0
CA S:CYS82 4.3 43.9 1.0
O S:HOH3339 4.4 64.5 1.0
OG1 S:THR87 4.4 58.9 1.0
C S:SER84 4.5 44.4 1.0
CA S:CYS60 4.5 37.1 1.0
N S:GLY86 4.6 50.6 1.0
C S:CYS85 4.6 49.0 1.0
C S:CYS60 4.6 38.1 1.0
N S:SER84 4.7 46.4 1.0
CA S:SER84 4.7 44.8 1.0
O S:CYS60 4.7 34.2 1.0
OG S:SER84 4.7 53.4 1.0
CG1 S:ILE70 4.7 35.1 1.0
C S:CYS82 4.7 45.2 1.0
NZ N:LYS514 4.8 69.9 1.0
O S:CYS82 4.9 49.8 1.0
N S:THR87 4.9 53.4 1.0
CB S:ILE70 5.0 37.4 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: Wed Dec 16 03:24:27 2020

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