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Sodium in PDB 5w97: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature

Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature

All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97 was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, N.A.Zatsepin, T.D.Grant, P.Fromme, R.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.300, 189.000, 209.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.2

Other elements in 5w97:

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature (pdb code 5w97). 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 Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5w97

Go back to Sodium Binding Sites List in 5w97
Sodium binding site 1 out of 2 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:31.4
occ:1.00
O A:HOH826 2.1 20.0 1.0
OE1 A:GLU40 2.2 30.9 1.0
O A:GLY45 2.3 35.0 1.0
O A:GLU40 2.3 30.5 1.0
O A:SER441 2.3 30.8 1.0
CD A:GLU40 3.3 34.3 1.0
C A:GLU40 3.3 26.6 1.0
O A:HOH710 3.4 47.3 1.0
C A:GLY45 3.4 33.2 1.0
C A:SER441 3.5 28.2 1.0
CG A:GLU40 3.6 31.9 1.0
O A:GLN43 3.9 33.6 1.0
CA A:ASP442 3.9 30.1 1.0
CB A:ASP442 4.0 31.0 1.0
CA A:THR46 4.1 40.3 1.0
N A:LEU41 4.1 25.7 1.0
CA A:LEU41 4.2 26.9 1.0
N A:ASP442 4.2 28.6 1.0
OD1 A:ASP442 4.2 34.5 1.0
CG A:ASP442 4.2 33.0 1.0
N A:THR46 4.2 34.6 1.0
CA A:GLU40 4.2 28.2 1.0
OE2 A:GLU40 4.4 31.1 1.0
CD2 A:LEU41 4.4 27.2 1.0
CB A:GLU40 4.5 30.0 1.0
N A:GLY45 4.5 30.3 1.0
CA A:GLY45 4.5 32.5 1.0
CA A:SER441 4.7 28.4 1.0
N A:LEU47 4.7 44.8 1.0
C A:THR46 4.8 43.4 1.0
OD2 A:ASP442 4.9 32.6 1.0

Sodium binding site 2 out of 2 in 5w97

Go back to Sodium Binding Sites List in 5w97
Sodium binding site 2 out of 2 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Na605

b:50.8
occ:1.00
O a:GLU40 2.3 43.9 1.0
O a:GLY45 2.3 61.5 1.0
O a:SER441 2.3 43.3 1.0
OE1 a:GLU40 2.3 54.1 1.0
OD1 a:ASP442 3.1 53.5 1.0
CD a:GLU40 3.4 54.5 1.0
C a:GLU40 3.4 47.0 1.0
C a:SER441 3.4 45.1 1.0
C a:GLY45 3.5 55.8 1.0
CG a:ASP442 3.7 51.6 1.0
CA a:ASP442 3.8 47.2 1.0
CB a:ASP442 3.8 52.9 1.0
O a:GLN43 3.8 58.3 1.0
CG a:GLU40 3.9 51.7 1.0
N a:ASP442 4.1 43.4 1.0
CA a:LEU41 4.1 52.8 1.0
N a:LEU41 4.2 52.5 1.0
CA a:THR46 4.2 59.0 1.0
N a:THR46 4.3 56.0 1.0
CD2 a:LEU41 4.5 50.6 1.0
CA a:GLU40 4.5 50.3 1.0
OE2 a:GLU40 4.5 46.5 1.0
N a:GLY45 4.5 58.4 1.0
CA a:GLY45 4.6 55.8 1.0
CE2 a:TYR443 4.6 48.6 1.0
CA a:SER441 4.7 47.7 1.0
C a:PRO44 4.7 58.3 1.0
CB a:GLU40 4.7 53.7 1.0
OD2 a:ASP442 4.8 50.0 1.0
CG a:LEU41 4.9 53.8 1.0
C a:GLN43 4.9 59.3 1.0
CA a:PRO44 5.0 51.9 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 11:47:27 2020

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