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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

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