Magnesium 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:

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 Serial Femtosecond X-Ray Crystallography at Room Temperature (pdb code 5w97). 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 Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5w97

Go back to Magnesium Binding Sites List in 5w97
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg604

b:26.4
occ:1.00
NE2 A:HIS368 2.0 27.7 1.0
O B:HOH419 2.1 17.8 1.0
OE1 B:GLU198 2.1 22.6 1.0
OD2 A:ASP369 2.2 25.0 1.0
O B:HOH421 2.2 20.9 1.0
O B:HOH486 2.2 22.2 1.0
CE1 A:HIS368 3.0 27.1 1.0
CD2 A:HIS368 3.0 27.2 1.0
CG A:ASP369 3.4 22.8 1.0
CD B:GLU198 3.4 27.9 1.0
O A:HOH850 4.0 21.8 1.0
O B:SER197 4.0 27.5 1.0
ND1 A:HIS368 4.1 25.8 1.0
OD2 B:ASP173 4.1 30.8 1.0
CB A:ASP369 4.1 22.3 1.0
CG A:HIS368 4.1 25.1 1.0
OE2 B:GLU198 4.2 26.1 1.0
OD1 A:ASP369 4.2 22.5 1.0
O B:HOH433 4.2 18.8 1.0
O A:HOH771 4.3 20.1 1.0
O A:HOH718 4.3 14.9 1.0
CG B:GLU198 4.4 28.0 1.0
OG1 A:THR294 4.4 25.2 1.0
OD1 B:ASP173 4.5 29.2 1.0
CB B:GLU198 4.5 26.8 1.0
O A:HOH764 4.5 26.6 1.0
O A:HOH750 4.5 20.6 1.0
CG B:ASP173 4.7 29.7 1.0

Magnesium binding site 2 out of 2 in 5w97

Go back to Magnesium Binding Sites List in 5w97
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg604

b:42.0
occ:1.00
O b:HOH429 2.0 25.9 1.0
NE2 a:HIS368 2.0 46.3 1.0
OE2 b:GLU198 2.2 34.7 1.0
O b:HOH435 2.2 32.4 1.0
OD2 a:ASP369 2.2 39.4 1.0
CE1 a:HIS368 2.9 41.5 1.0
CD2 a:HIS368 3.1 39.9 1.0
CD b:GLU198 3.4 35.7 1.0
CG a:ASP369 3.5 39.5 1.0
OD2 b:ASP173 3.8 46.1 1.0
O b:SER197 4.1 48.0 1.0
ND1 a:HIS368 4.1 39.3 1.0
O a:HOH764 4.1 46.2 1.0
OE1 b:GLU198 4.2 33.4 1.0
CG a:HIS368 4.2 38.6 1.0
O a:HOH797 4.2 33.2 1.0
OG1 a:THR294 4.2 34.1 1.0
OD1 b:ASP173 4.3 37.4 1.0
CB a:ASP369 4.3 39.9 1.0
O b:HOH406 4.4 30.6 1.0
O a:HOH814 4.4 37.7 1.0
OD1 a:ASP369 4.4 40.8 1.0
O a:HOH712 4.4 38.5 1.0
CG b:ASP173 4.4 41.6 1.0
CG b:GLU198 4.4 35.9 1.0
O a:HOH770 4.5 33.3 1.0
CB b:GLU198 4.6 41.6 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 Dec 14 21:20:42 2020

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