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

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

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

Protein crystallography data

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2ein 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 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 187.810, 203.581, 177.927, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.8

Other elements in 2ein:

The structure of Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized 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:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State (pdb code 2ein). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State, PDB code: 2ein:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 2ein

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Zinc binding site 1 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized 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 Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn607

b:55.2
occ:0.60
 NE2 B:HIS22 2.0 79.5 1.0
NE2 B:HIS26 2.4 94.2 1.0
CE1 B:HIS22 3.0 85.8 1.0
CD2 B:HIS22 3.2 79.2 1.0
CE1 B:HIS26 3.3 99.9 1.0
CD2 B:HIS26 3.6 89.2 1.0
OE1 I:GLU41 3.9 95.2 1.0
ND1 B:HIS22 4.2 86.8 1.0
CG B:HIS22 4.3 79.7 1.0
CB I:ALA40 4.3 76.0 1.0
ND1 B:HIS26 4.5 99.4 1.0
CG B:HIS26 4.7 89.2 1.0
CD I:LYS44 4.8 96.5 1.0

Zinc binding site 2 out of 14 in 2ein

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Zinc binding site 2 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized 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 Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn262

b:44.3
occ:1.00
 NE2 C:HIS232 1.9 43.7 1.0
O C:HOH2027 2.0 48.0 1.0
NE2 C:HIS148 2.2 37.0 1.0
OE1 C:GLU236 2.2 55.8 1.0
CE1 C:HIS232 2.9 50.5 1.0
CD C:GLU236 2.9 56.7 1.0
CE1 C:HIS148 2.9 36.0 1.0
CD2 C:HIS232 3.0 46.4 1.0
OE2 C:GLU236 3.0 62.8 1.0
CD2 C:HIS148 3.4 41.5 1.0
ND1 C:HIS232 4.0 50.2 1.0
CG C:HIS232 4.1 45.8 1.0
ND1 C:HIS148 4.2 40.6 1.0
CG C:GLU236 4.3 51.7 1.0
CG C:HIS148 4.4 40.4 1.0
CG C:MET152 4.4 44.6 1.0
O C:HOH2230 4.5 26.1 1.0
SD C:MET152 4.6 51.0 1.0
CB C:GLU236 4.8 48.0 1.0

Zinc binding site 3 out of 14 in 2ein

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Zinc binding site 3 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized 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 Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn605

b:56.9
occ:0.50
 NE2 D:HIS29 2.2 53.0 1.0
CD2 D:HIS29 3.2 45.6 1.0
CE1 D:HIS29 3.2 48.3 1.0
ND1 D:HIS29 4.3 44.8 1.0
CG D:HIS29 4.4 40.2 1.0
O D:ARG61 4.6 62.8 1.0
OG D:SER4 4.7 94.9 1.0
CG D:LYS65 4.9 69.6 1.0

Zinc binding site 4 out of 14 in 2ein

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Zinc binding site 4 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized 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 Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn99

b:54.3
occ:1.00
 SG F:CYS60 2.2 40.9 1.0
SG F:CYS82 2.2 55.8 1.0
SG F:CYS85 2.3 53.9 1.0
SG F:CYS62 2.3 44.4 1.0
CB F:CYS82 3.1 59.6 1.0
CB F:CYS60 3.2 40.0 1.0
CB F:CYS62 3.6 43.2 1.0
N F:CYS85 3.6 56.8 1.0
CB F:CYS85 3.7 49.0 1.0
CA F:CYS62 3.8 45.8 1.0
N F:CYS62 3.9 44.5 1.0
CB F:SER84 4.0 58.1 1.0
O F:CYS60 4.1 45.7 1.0
CA F:CYS85 4.2 56.9 1.0
C F:CYS60 4.3 44.0 1.0
CA F:CYS60 4.4 42.1 1.0
CA F:CYS82 4.5 55.3 1.0
OG F:SER84 4.6 70.3 1.0
C F:SER84 4.6 57.5 1.0
CA F:SER84 4.7 55.0 1.0
N F:GLY86 4.8 57.9 1.0
N F:SER84 4.8 52.0 1.0
CG1 F:ILE70 4.8 38.5 1.0
C F:CYS82 4.9 51.9 1.0
CB F:ILE70 5.0 39.6 1.0
C F:CYS85 5.0 58.9 1.0

Zinc binding site 5 out of 14 in 2ein

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Zinc binding site 5 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized 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 Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn604

b:42.4
occ:0.50
 OE1 F:GLU17 2.1 43.6 1.0
ND1 C:HIS231 2.3 62.9 1.0
OD1 F:ASP9 2.7 56.4 1.0
CD F:GLU17 3.0 60.9 1.0
CG C:HIS231 3.1 57.6 1.0
CB C:HIS231 3.1 57.6 1.0
OE2 F:GLU17 3.4 62.6 1.0
CE1 C:HIS231 3.4 59.4 1.0
CG F:ASP9 3.5 64.3 1.0
O06 C:PGV267 3.8 69.3 1.0
OD2 F:ASP9 3.9 67.4 1.0
C06 C:PGV267 4.1 62.2 1.0
CG F:GLU17 4.2 64.1 1.0
CD2 C:HIS231 4.3 56.4 1.0
CB F:ALA13 4.4 35.9 1.0
NE2 C:HIS231 4.5 57.7 1.0
CB F:ASP9 4.5 65.4 1.0
O C:HOH2165 4.6 93.3 1.0
CA C:HIS231 4.6 53.4 1.0
CA F:ALA13 4.8 51.0 1.0
OG1 C:THR228 4.9 54.2 1.0
CG2 C:THR228 4.9 54.0 1.0
CA F:ASP9 5.0 66.2 1.0

Zinc binding site 6 out of 14 in 2ein

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Zinc binding site 6 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized 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 Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn608

b:72.9
occ:0.50
 OE1 H:GLU78 2.1 67.7 1.0
OE2 H:GLU78 2.1 63.5 1.0
NE2 G:HIS51 2.2 75.4 1.0
CD H:GLU78 2.3 70.5 1.0
CE1 G:HIS51 3.1 78.2 1.0
CD2 G:HIS51 3.3 70.0 1.0
CG H:GLU78 3.7 71.6 1.0
ND1 G:HIS51 4.3 74.5 1.0
CG G:HIS51 4.4 71.3 1.0
O H:HOH2180 4.5 69.5 1.0
CB H:GLU78 4.6 72.7 1.0
O G:PRO49 4.9 83.5 1.0
OG1 H:THR80 5.0 59.7 1.0

Zinc binding site 7 out of 14 in 2ein

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Zinc binding site 7 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zinc 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
L:Zn603

b:50.0
occ:0.70
 NE2 L:HIS2 2.1 69.0 1.0
NE2 A:HIS503 2.1 65.4 1.0
OE1 L:GLU5 2.2 68.8 1.0
OE2 L:GLU5 2.2 72.5 1.0
CD L:GLU5 2.3 65.8 1.0
CE1 L:HIS2 2.9 76.8 1.0
CE1 A:HIS503 2.9 75.6 1.0
CD2 L:HIS2 3.3 79.7 1.0
CD2 A:HIS503 3.3 58.5 1.0
CG L:GLU5 3.6 59.2 1.0
ND1 L:HIS2 4.2 85.6 1.0
ND1 A:HIS503 4.2 80.5 1.0
CG L:HIS2 4.4 82.1 1.0
CG A:HIS503 4.4 67.9 1.0
CB A:PRO501 4.5 61.1 1.0
CB L:GLU5 4.6 54.4 1.0
CB A:TYR502 4.7 64.8 1.0
O L:TYR3 4.9 68.5 1.0
N A:TYR502 4.9 58.0 1.0

Zinc binding site 8 out of 14 in 2ein

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Zinc binding site 8 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zinc 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
N:Zn1603

b:41.3
occ:0.50
 ND1 N:HIS503 2.1 64.7 1.0
O Y:HOH3093 2.1 36.9 1.0
NE2 Y:HIS2 2.4 76.2 1.0
ZN N:ZN1609 2.9 42.2 0.5
CG N:HIS503 3.0 61.4 1.0
CE1 N:HIS503 3.1 67.2 1.0
CB N:HIS503 3.3 57.4 1.0
CE1 Y:HIS2 3.4 78.2 1.0
CD2 Y:HIS2 3.4 83.2 1.0
OE2 N:GLU506 3.6 57.3 1.0
OE1 N:GLU506 3.8 57.4 1.0
CD N:GLU506 4.0 65.0 1.0
CD2 N:HIS503 4.2 59.1 1.0
NE2 N:HIS503 4.2 63.4 1.0
ND1 Y:HIS2 4.6 83.4 1.0
CA N:HIS503 4.6 55.4 1.0
CG Y:HIS2 4.6 88.7 1.0
OE1 Y:GLU5 4.6 74.5 1.0
N N:HIS503 4.7 57.5 1.0

Zinc binding site 9 out of 14 in 2ein

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Zinc binding site 9 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Zinc 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
N:Zn1609

b:42.2
occ:0.50
 OE2 N:GLU506 2.0 57.3 1.0
ND1 P:HIS3 2.3 50.7 0.4
OE1 N:GLU506 2.4 57.4 1.0
CD N:GLU506 2.5 65.0 1.0
CE1 P:HIS3 2.8 48.1 0.4
ZN N:ZN1603 2.9 41.3 0.5
CG P:HIS3 3.7 55.2 0.4
O Y:HOH3093 3.9 36.9 1.0
CG N:GLU506 4.0 61.7 1.0
ND1 N:HIS503 4.1 64.7 1.0
NE2 P:HIS3 4.1 53.5 0.4
CB P:HIS3 4.4 59.8 0.4
CD2 P:HIS3 4.5 55.1 0.4
CB N:HIS503 4.5 57.4 1.0
CG N:HIS503 4.6 61.4 1.0
CB N:GLU506 4.8 62.1 1.0
O N:HOH3084 4.9 66.5 1.0

Zinc binding site 10 out of 14 in 2ein

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Zinc binding site 10 out of 14 in the Zinc Ion Binding Structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Zinc 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
O:Zn1607

b:65.5
occ:0.70
 NE2 O:HIS22 2.1 74.8 1.0
NE2 O:HIS26 2.3 92.3 1.0
CE1 O:HIS22 3.1 82.0 1.0
CD2 O:HIS22 3.2 74.4 1.0
CE1 O:HIS26 3.2 0.0 1.0
CD2 O:HIS26 3.5 87.0 1.0
OE1 V:GLU41 3.9 98.5 1.0
CB V:ALA40 4.2 87.9 1.0
ND1 O:HIS22 4.3 83.0 1.0
CG O:HIS22 4.4 74.2 1.0
ND1 O:HIS26 4.4 97.7 1.0
CG O:HIS26 4.6 88.5 1.0
CD V:LYS44 4.7 0.0 1.0
O V:ALA40 4.9 87.9 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 Oct 16 23:11:15 2024

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