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Magnesium 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:

Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5wau

Go back to Magnesium Binding Sites List in 5wau
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg604

b:27.4
occ:1.00
 NE2 A:HIS368 2.0 24.5 1.0
O B:HOH429 2.1 25.1 1.0
OD2 A:ASP369 2.1 24.4 1.0
OE1 B:GLU198 2.2 32.7 1.0
O B:HOH440 2.2 24.6 1.0
O B:HOH510 2.2 23.7 1.0
CE1 A:HIS368 3.0 22.9 1.0
CD2 A:HIS368 3.0 23.8 1.0
CG A:ASP369 3.3 26.1 1.0
CD B:GLU198 3.4 33.4 1.0
O B:SER197 3.9 25.7 1.0
O A:HOH815 3.9 30.2 1.0
CB A:ASP369 4.0 24.9 1.0
ND1 A:HIS368 4.1 21.9 1.0
OE2 B:GLU198 4.1 33.6 1.0
CG A:HIS368 4.2 23.1 1.0
O A:HOH713 4.3 26.6 1.0
OD2 B:ASP173 4.3 28.9 1.0
O A:HOH751 4.3 24.5 1.0
OD1 A:ASP369 4.3 27.3 1.0
OD1 B:ASP173 4.4 29.0 1.0
OG1 A:THR294 4.4 27.8 1.0
CG B:GLU198 4.5 30.0 1.0
O B:HOH452 4.5 33.1 1.0
O A:HOH808 4.5 24.9 1.0
O A:HOH864 4.6 22.3 1.0
CB B:GLU198 4.6 29.3 1.0
O B:HOH411 4.7 40.9 1.0
CG B:ASP173 4.8 29.4 1.0
CA B:GLU198 5.0 27.3 1.0

Magnesium binding site 2 out of 2 in 5wau

Go back to Magnesium Binding Sites List in 5wau
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg604

b:47.5
occ:1.00
 O b:HOH416 2.0 32.7 1.0
NE2 a:HIS368 2.0 39.6 1.0
O b:HOH426 2.0 38.7 1.0
OD2 a:ASP369 2.2 49.0 1.0
OE2 b:GLU198 2.2 47.4 1.0
CE1 a:HIS368 2.9 36.8 1.0
CD2 a:HIS368 3.1 37.5 1.0
CD b:GLU198 3.4 46.1 1.0
CG a:ASP369 3.4 45.8 1.0
O a:HOH797 3.7 36.9 1.0
OE1 b:GLU198 4.0 49.3 1.0
ND1 a:HIS368 4.0 38.2 1.0
O b:SER197 4.0 41.3 1.0
O a:HOH813 4.1 33.9 1.0
CG a:HIS368 4.1 38.0 1.0
CB a:ASP369 4.2 40.6 1.0
OD2 b:ASP173 4.2 38.5 1.0
OD1 a:ASP369 4.3 43.2 1.0
O a:HOH710 4.4 34.7 1.0
OG1 a:THR294 4.4 34.2 1.0
O a:HOH785 4.5 33.5 1.0
O a:HOH844 4.5 33.3 1.0
OD1 b:ASP173 4.5 40.7 1.0
CG b:GLU198 4.6 44.1 1.0
O a:HOH723 4.6 50.5 1.0
CB b:GLU198 4.8 42.4 1.0
CG b:ASP173 4.8 41.8 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: Mon Sep 30 06:31:19 2024

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