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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy