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Sodium in PDB 5wau: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K

Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K

All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K, PDB code: 5wau was solved by R.Fromme, I.Ishigami, S.Y.Yeh, N.Zatsepin, T.Grant, P.Fromme, D.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 177.923, 182.555, 208.450, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.4

Other elements in 5wau:

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K (pdb code 5wau). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K, PDB code: 5wau:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5wau

Go back to Sodium Binding Sites List in 5wau
Sodium binding site 1 out of 2 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:28.5
occ:1.00
O A:HOH835 2.1 23.4 1.0
OE1 A:GLU40 2.2 30.2 1.0
O A:GLY45 2.3 32.0 1.0
O A:SER441 2.3 28.3 1.0
O A:GLU40 2.3 28.6 1.0
CD A:GLU40 3.2 31.6 1.0
O A:HOH723 3.3 45.5 1.0
C A:GLU40 3.3 27.5 1.0
C A:GLY45 3.5 31.6 1.0
C A:SER441 3.5 27.8 1.0
CG A:GLU40 3.6 28.8 1.0
O A:HOH868 3.9 33.5 1.0
O A:GLN43 4.0 30.8 1.0
CA A:ASP442 4.0 28.9 1.0
CB A:ASP442 4.0 28.9 1.0
CA A:THR46 4.0 35.1 1.0
CG A:ASP442 4.1 30.5 1.0
OD1 A:ASP442 4.2 29.7 1.0
N A:LEU41 4.2 25.8 1.0
N A:ASP442 4.2 29.1 1.0
N A:THR46 4.2 32.3 1.0
CA A:GLU40 4.2 27.7 1.0
CA A:LEU41 4.3 25.2 1.0
OE2 A:GLU40 4.4 32.5 1.0
CB A:GLU40 4.5 27.8 1.0
N A:LEU47 4.5 33.7 1.0
CD2 A:LEU41 4.6 28.5 1.0
N A:GLY45 4.6 29.3 1.0
CA A:GLY45 4.6 29.5 1.0
CA A:SER441 4.6 28.8 1.0
C A:THR46 4.7 35.1 1.0
OD2 A:ASP442 4.8 30.0 1.0
CB A:SER441 5.0 31.2 1.0

Sodium binding site 2 out of 2 in 5wau

Go back to Sodium Binding Sites List in 5wau
Sodium binding site 2 out of 2 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Na605

b:48.2
occ:1.00
OE1 a:GLU40 2.3 45.2 1.0
O a:GLU40 2.3 41.1 1.0
O a:GLY45 2.3 55.5 1.0
O a:SER441 2.3 47.4 1.0
O a:HOH831 2.3 42.5 1.0
CD a:GLU40 3.2 45.7 1.0
C a:GLU40 3.4 37.5 1.0
C a:SER441 3.4 42.6 1.0
C a:GLY45 3.5 51.0 1.0
CG a:GLU40 3.6 42.5 1.0
CA a:ASP442 3.9 43.0 1.0
O a:GLN43 4.0 46.2 1.0
CA a:THR46 4.0 52.4 1.0
CB a:ASP442 4.0 43.8 1.0
N a:ASP442 4.1 41.9 1.0
OD1 a:ASP442 4.1 42.2 1.0
N a:THR46 4.2 51.0 1.0
CG a:ASP442 4.2 42.6 1.0
N a:LEU41 4.2 38.4 1.0
OE2 a:GLU40 4.3 45.6 1.0
CA a:GLU40 4.3 39.0 1.0
CA a:LEU41 4.3 40.0 1.0
CB a:GLU40 4.5 40.5 1.0
N a:LEU47 4.6 53.6 1.0
CA a:GLY45 4.6 50.1 1.0
N a:GLY45 4.6 49.4 1.0
CA a:SER441 4.6 44.8 1.0
C a:THR46 4.6 55.0 1.0
CD2 a:LEU41 4.7 40.5 1.0
CB a:SER441 5.0 44.5 1.0

Reference:

I.Ishigami, N.A.Zatsepin, M.Hikita, C.E.Conrad, G.Nelson, J.D.Coe, S.Basu, T.D.Grant, M.H.Seaberg, R.G.Sierra, M.S.Hunter, P.Fromme, R.Fromme, S.R.Yeh, D.L.Rousseau. Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature. Proc. Natl. Acad. Sci. V. 114 8011 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28698372
DOI: 10.1073/PNAS.1705628114
Page generated: Tue Dec 15 11:47:30 2020

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