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Sodium in PDB 6nmp: Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature

Enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature, PDB code: 6nmp was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.700, 189.800, 211.300, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.4

Other elements in 6nmp:

The structure of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature 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 Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature (pdb code 6nmp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature, PDB code: 6nmp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6nmp

Go back to Sodium Binding Sites List in 6nmp
Sodium binding site 1 out of 2 in the Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:39.6
occ:1.00
O A:GLY45 2.2 42.9 1.0
O A:SER441 2.2 38.1 1.0
O A:HOH736 2.2 44.2 1.0
OE1 A:GLU40 2.2 40.7 1.0
O A:GLU40 2.3 47.4 1.0
CD A:GLU40 3.3 41.6 1.0
C A:GLU40 3.4 41.4 1.0
C A:GLY45 3.4 44.2 1.0
C A:SER441 3.4 38.6 1.0
CG A:GLU40 3.7 40.9 1.0
CA A:ASP442 3.9 37.1 1.0
CB A:ASP442 4.0 37.8 1.0
O A:GLN43 4.0 52.1 1.0
N A:ASP442 4.1 37.8 1.0
CA A:THR46 4.2 49.5 1.0
N A:THR46 4.2 46.2 1.0
CG A:ASP442 4.3 39.6 1.0
N A:LEU41 4.3 38.7 1.0
CD2 A:LEU41 4.3 43.1 1.0
N A:GLY45 4.3 42.0 1.0
CA A:LEU41 4.3 39.6 1.0
OD1 A:ASP442 4.3 38.4 1.0
CA A:GLU40 4.3 40.9 1.0
OE2 A:GLU40 4.4 43.4 1.0
CA A:GLY45 4.5 43.7 1.0
CA A:SER441 4.6 39.3 1.0
CB A:GLU40 4.6 41.1 1.0
N A:LEU47 4.8 53.7 1.0
C A:THR46 4.9 52.5 1.0
C A:PRO44 4.9 42.8 1.0
OD2 A:ASP442 5.0 42.0 1.0

Sodium binding site 2 out of 2 in 6nmp

Go back to Sodium Binding Sites List in 6nmp
Sodium binding site 2 out of 2 in the Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sfx Structure of Oxidized Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na603

b:64.6
occ:1.00
O N:GLU40 2.2 60.0 1.0
O N:HOH755 2.2 60.6 1.0
OE1 N:GLU40 2.3 56.4 1.0
O N:SER441 2.3 50.2 1.0
O N:GLY45 2.3 71.3 1.0
CD N:GLU40 3.4 58.7 1.0
C N:GLU40 3.4 59.5 1.0
C N:SER441 3.4 51.5 1.0
C N:GLY45 3.5 74.4 1.0
CG N:GLU40 3.9 60.5 1.0
CA N:ASP442 4.0 57.8 1.0
O N:GLN43 4.0 67.3 1.0
N N:ASP442 4.1 53.5 1.0
CG N:ASP442 4.1 65.6 1.0
CA N:LEU41 4.2 63.6 1.0
CA N:THR46 4.2 74.6 1.0
N N:LEU41 4.2 60.1 1.0
N N:THR46 4.3 76.2 1.0
OD2 N:ASP442 4.3 63.1 1.0
CB N:ASP442 4.3 63.0 1.0
CA N:GLU40 4.4 61.3 1.0
OD1 N:ASP442 4.5 64.5 1.0
OE2 N:GLU40 4.5 58.7 1.0
N N:GLY45 4.5 70.8 1.0
CA N:GLY45 4.6 74.7 1.0
CA N:SER441 4.6 51.9 1.0
CB N:GLU40 4.8 60.0 1.0
N N:LEU47 4.8 76.8 1.0
C N:THR46 4.8 74.5 1.0
CD2 N:LEU41 4.9 69.0 1.0
C N:PRO44 4.9 65.4 1.0
CG N:LEU41 5.0 69.1 1.0
CE2 N:TYR443 5.0 57.7 1.0

Reference:

I.Ishigami, A.Lewis-Ballester, A.Echelmeier, G.Brehm, N.A.Zatsepin, T.D.Grant, J.D.Coe, S.Lisova, G.Nelson, S.Zhang, Z.F.Dobson, S.Boutet, R.G.Sierra, A.Batyuk, P.Fromme, R.Fromme, J.C.H.Spence, A.Ros, S.R.Yeh, D.L.Rousseau. Snapshot of An Oxygen Intermediate in the Catalytic Reaction of Cytochromecoxidase. Proc. Natl. Acad. Sci. V. 116 3572 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30808749
DOI: 10.1073/PNAS.1814526116
Page generated: Tue Dec 15 12:39:37 2020

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