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Sodium in PDB 1ocz: Bovine Heart Cytochrome C Oxidase in Azide-Bound State

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in Azide-Bound State

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in Azide-Bound State:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in Azide-Bound State, PDB code: 1ocz was solved by T.Tsukihara, M.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.200, 210.600, 178.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 25.5

Other elements in 1ocz:

The structure of Bovine Heart Cytochrome C Oxidase in Azide-Bound State also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State (pdb code 1ocz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State, PDB code: 1ocz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1ocz

Go back to Sodium Binding Sites List in 1ocz
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bovine Heart Cytochrome C Oxidase in Azide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na519

b:20.6
occ:1.00
O A:GLY45 2.3 33.2 1.0
O A:SER441 2.4 23.1 1.0
O A:GLU40 2.5 33.0 1.0
OE2 A:GLU40 2.6 35.7 1.0
C A:SER441 3.5 20.4 1.0
C A:GLY45 3.5 28.7 1.0
C A:GLU40 3.6 17.9 1.0
O A:GLN43 3.6 41.8 1.0
CA A:ASP442 3.7 11.6 1.0
CD A:GLU40 3.7 40.9 1.0
CB A:ASP442 3.9 13.6 1.0
CG A:ASP442 4.0 21.9 1.0
OD1 A:ASP442 4.0 16.3 1.0
CA A:LEU41 4.0 7.0 1.0
N A:GLY45 4.0 21.9 1.0
N A:ASP442 4.0 10.5 1.0
N A:LEU41 4.2 9.8 1.0
CG A:GLU40 4.3 32.3 1.0
CA A:GLY45 4.4 25.9 1.0
CE1 A:TYR443 4.4 18.7 1.0
N A:THR46 4.5 24.8 1.0
CA A:THR46 4.5 35.2 1.0
CD2 A:LEU41 4.5 26.2 1.0
OD2 A:ASP442 4.6 25.2 1.0
CA A:GLU40 4.7 18.7 1.0
C A:PRO44 4.8 20.4 1.0
CA A:SER441 4.8 21.5 1.0
CD1 A:TYR443 4.8 14.1 1.0
C A:GLN43 4.8 40.6 1.0
OE1 A:GLU40 4.8 39.9 1.0
C A:LEU41 4.9 15.4 1.0
CG A:LEU41 4.9 19.2 1.0
CB A:LEU41 4.9 7.0 1.0
C A:ASP442 5.0 17.1 1.0

Sodium binding site 2 out of 2 in 1ocz

Go back to Sodium Binding Sites List in 1ocz
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in Azide-Bound State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bovine Heart Cytochrome C Oxidase in Azide-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na519

b:31.8
occ:1.00
O N:GLY45 2.4 49.5 1.0
O N:GLU40 2.4 37.2 1.0
O N:SER441 2.4 24.2 1.0
OE2 N:GLU40 2.5 38.4 1.0
C N:GLU40 3.5 38.9 1.0
C N:SER441 3.5 28.6 1.0
C N:GLY45 3.5 48.4 1.0
O N:GLN43 3.7 54.4 1.0
CD N:GLU40 3.7 45.4 1.0
CA N:ASP442 3.7 34.5 1.0
CB N:ASP442 3.9 39.6 1.0
CG N:ASP442 3.9 47.5 1.0
OD1 N:ASP442 3.9 43.2 1.0
CA N:LEU41 4.0 37.4 1.0
N N:GLY45 4.0 35.9 1.0
N N:ASP442 4.1 24.0 1.0
N N:LEU41 4.2 40.0 1.0
CG N:GLU40 4.2 43.0 1.0
CE1 N:TYR443 4.3 23.7 1.0
CA N:GLY45 4.4 41.5 1.0
N N:THR46 4.5 49.1 1.0
CD2 N:LEU41 4.5 31.6 1.0
OD2 N:ASP442 4.5 61.1 1.0
CA N:THR46 4.5 51.8 1.0
CA N:GLU40 4.7 35.0 1.0
C N:PRO44 4.7 36.0 1.0
CA N:SER441 4.8 33.8 1.0
CD1 N:TYR443 4.8 16.7 1.0
OE1 N:GLU40 4.8 44.6 1.0
C N:GLN43 4.8 49.0 1.0
C N:LEU41 4.8 39.1 1.0
CG N:LEU41 4.9 37.1 1.0
CB N:LEU41 4.9 35.9 1.0
CA N:PRO44 5.0 38.0 1.0

Reference:

S.Yoshikawa, K.Shinzawa-Itoh, R.Nakashima, R.Yaono, E.Yamashita, N.Inoue, M.Yao, M.J.Fei, C.P.Libeu, T.Mizushima, H.Yamaguchi, T.Tomizaki, T.Tsukihara. Redox-Coupled Crystal Structural Changes in Bovine Heart Cytochrome C Oxidase. Science V. 280 1723 1998.
ISSN: ISSN 0036-8075
PubMed: 9624044
DOI: 10.1126/SCIENCE.280.5370.1723
Page generated: Thu Oct 29 03:55:05 2020

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