Atomistry » Sodium » PDB 3ajn-3b1q » 3asn
Atomistry »
  Sodium »
    PDB 3ajn-3b1q »
      3asn »

Sodium in PDB 3asn: Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength, PDB code: 3asn was solved by M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, 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) 15.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 181.826, 204.098, 177.829, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18.7

Other elements in 3asn:

The structure of Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength (pdb code 3asn). 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 Fully Oxidized State Measured at 1.7470 Angstrom Wavelength, PDB code: 3asn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3asn

Go back to Sodium Binding Sites List in 3asn
Sodium binding site 1 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength


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 Fully Oxidized State Measured at 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na519

b:18.8
occ:1.00
O A:HOH2258 2.2 18.1 1.0
OE1 A:GLU40 2.3 19.4 1.0
O A:SER441 2.3 17.5 1.0
O A:GLY45 2.3 19.8 1.0
O A:GLU40 2.3 17.8 1.0
CD A:GLU40 3.2 19.7 1.0
C A:GLU40 3.4 16.3 1.0
C A:SER441 3.5 16.0 1.0
C A:GLY45 3.5 19.2 1.0
CG A:GLU40 3.5 15.3 1.0
O A:HOH2563 3.8 33.1 1.0
OD2 A:ASP442 3.9 16.6 1.0
CA A:ASP442 4.0 15.2 1.0
CB A:ASP442 4.0 16.1 1.0
CG A:ASP442 4.1 16.3 1.0
O A:GLN43 4.1 20.0 1.0
N A:ASP442 4.2 15.1 1.0
CA A:THR46 4.2 20.2 1.0
N A:LEU41 4.2 16.0 1.0
CA A:GLU40 4.2 15.9 1.0
N A:THR46 4.3 19.6 1.0
N A:GLY45 4.3 18.4 1.0
CA A:LEU41 4.3 15.9 1.0
OE2 A:GLU40 4.4 20.9 1.0
CB A:GLU40 4.5 15.5 1.0
N A:LEU47 4.5 22.8 1.0
CA A:GLY45 4.5 18.5 1.0
CA A:SER441 4.6 15.4 1.0
CD2 A:LEU41 4.6 16.7 1.0
C A:THR46 4.8 21.9 1.0
CB A:SER441 4.9 14.3 1.0
OD1 A:ASP442 4.9 20.3 1.0
C A:PRO44 5.0 18.2 1.0

Sodium binding site 2 out of 2 in 3asn

Go back to Sodium Binding Sites List in 3asn
Sodium binding site 2 out of 2 in the Bovine Heart Cytochrome C Oxidase in the Fully Oxidized State Measured at 1.7470 Angstrom Wavelength


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 Fully Oxidized State Measured at 1.7470 Angstrom Wavelength within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na519

b:21.2
occ:1.00
O N:HOH3258 2.1 22.4 1.0
OE1 N:GLU40 2.3 18.3 1.0
O N:GLU40 2.3 20.5 1.0
O N:GLY45 2.3 22.7 1.0
O N:SER441 2.3 20.6 1.0
CD N:GLU40 3.2 20.6 1.0
C N:GLU40 3.3 19.5 1.0
C N:GLY45 3.4 22.3 1.0
C N:SER441 3.5 20.0 1.0
CG N:GLU40 3.5 19.0 1.0
O N:HOH3563 3.6 28.8 1.0
OD2 N:ASP442 4.0 20.0 1.0
O N:GLN43 4.0 20.1 1.0
O N:HOH3466 4.0 0.0 1.0
CA N:ASP442 4.0 20.0 1.0
CA N:THR46 4.0 24.4 1.0
CB N:ASP442 4.1 20.4 1.0
CG N:ASP442 4.1 20.3 1.0
N N:THR46 4.2 23.5 1.0
N N:ASP442 4.2 19.9 1.0
CA N:GLU40 4.2 19.5 1.0
N N:LEU41 4.2 19.0 1.0
CA N:LEU41 4.3 18.2 1.0
N N:LEU47 4.3 26.1 1.0
OE2 N:GLU40 4.4 21.5 1.0
N N:GLY45 4.4 20.4 1.0
CB N:GLU40 4.4 19.4 1.0
CA N:GLY45 4.5 21.0 1.0
CD2 N:LEU41 4.6 14.8 1.0
CA N:SER441 4.6 20.1 1.0
C N:THR46 4.6 25.6 1.0
CB N:SER441 4.8 20.0 1.0
OD1 N:ASP442 4.9 21.9 1.0
C N:PRO44 5.0 20.6 1.0

Reference:

M.Suga, N.Yano, K.Muramoto, K.Shinzawa-Itoh, T.Maeda, E.Yamashita, T.Tsukihara, S.Yoshikawa. Distinguishing Between Cl- and O2(2-) As the Bridging Element Between FE3+ and CU2+ in Resting-Oxidized Cytochrome C Oxidase Acta Crystallogr.,Sect.D V. 67 742 2011.
ISSN: ISSN 0907-4449
PubMed: 21795816
DOI: 10.1107/S0907444911022803
Page generated: Mon Oct 7 05:52:15 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy