Atomistry » Sodium » PDB 3a07-3ahi » 3ag3
Atomistry »
  Sodium »
    PDB 3a07-3ahi »
      3ag3 »

Sodium in PDB 3ag3: Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 3ag3 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, 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 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.289, 208.358, 177.916, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.3

Other elements in 3ag3:

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K 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 the Nitric Oxide-Bound Fully Reduced State at 100 K (pdb code 3ag3). 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 the Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 3ag3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3ag3

Go back to Sodium Binding Sites List in 3ag3
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K


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 the Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na519

b:28.0
occ:1.00
O A:HOH2258 2.2 26.7 1.0
OE1 A:GLU40 2.3 30.8 1.0
O A:GLY45 2.3 28.5 1.0
O A:SER441 2.3 25.9 1.0
O A:GLU40 2.4 27.9 1.0
CD A:GLU40 3.2 27.1 1.0
O A:HOH2563 3.4 32.8 1.0
C A:GLU40 3.4 26.9 1.0
CG A:GLU40 3.5 24.1 1.0
C A:GLY45 3.5 29.3 1.0
C A:SER441 3.5 27.4 1.0
O A:HOH2691 3.7 33.5 1.0
CB A:ASP442 3.9 24.8 1.0
CA A:ASP442 3.9 26.3 1.0
O A:GLN43 4.0 28.1 1.0
CA A:THR46 4.0 32.4 1.0
CG A:ASP442 4.1 27.2 1.0
N A:ASP442 4.2 27.5 1.0
OD2 A:ASP442 4.2 25.8 1.0
N A:THR46 4.2 30.0 1.0
CA A:GLU40 4.3 23.9 1.0
N A:LEU41 4.3 22.7 1.0
CA A:LEU41 4.3 23.9 1.0
OE2 A:GLU40 4.4 31.9 1.0
N A:LEU47 4.5 31.8 1.0
N A:GLY45 4.5 25.7 1.0
CB A:GLU40 4.5 23.5 1.0
C A:THR46 4.6 33.6 1.0
CA A:GLY45 4.6 28.4 1.0
CA A:SER441 4.7 25.8 1.0
CD2 A:LEU41 4.7 25.8 1.0
OD1 A:ASP442 4.8 25.9 1.0
O A:HOH2693 4.9 33.2 1.0

Sodium binding site 2 out of 2 in 3ag3

Go back to Sodium Binding Sites List in 3ag3
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K


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 the Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na519

b:31.2
occ:1.00
O N:HOH3258 2.2 31.0 1.0
OE1 N:GLU40 2.3 31.4 1.0
O N:GLY45 2.3 34.9 1.0
O N:SER441 2.3 30.8 1.0
O N:GLU40 2.3 30.3 1.0
CD N:GLU40 3.2 33.5 1.0
O N:HOH3563 3.4 38.6 1.0
C N:GLU40 3.4 28.4 1.0
CG N:GLU40 3.5 28.5 1.0
C N:GLY45 3.5 34.7 1.0
C N:SER441 3.5 28.4 1.0
O N:HOH3691 3.7 38.5 1.0
CB N:ASP442 3.9 29.8 1.0
CA N:ASP442 3.9 28.7 1.0
O N:GLN43 3.9 32.6 1.0
CA N:THR46 4.0 39.0 1.0
CG N:ASP442 4.1 30.1 1.0
OD2 N:ASP442 4.2 29.6 1.0
N N:ASP442 4.2 26.9 1.0
N N:THR46 4.2 35.4 1.0
CA N:GLU40 4.2 27.4 1.0
N N:LEU41 4.3 27.3 1.0
CA N:LEU41 4.3 25.1 1.0
OE2 N:GLU40 4.4 37.7 1.0
CB N:GLU40 4.4 29.2 1.0
N N:GLY45 4.5 31.9 1.0
N N:LEU47 4.5 38.1 1.0
CD2 N:LEU41 4.6 27.5 1.0
CA N:GLY45 4.6 31.4 1.0
C N:THR46 4.6 39.6 1.0
CA N:SER441 4.7 29.9 1.0
OD1 N:ASP442 4.8 29.8 1.0
CB N:SER441 5.0 30.8 1.0

Reference:

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Tue Dec 15 06:02:05 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy