Magnesium in PDB 5weh: Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State

All present enzymatic activity of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State:
1.9.3.1;

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh was solved by J.Liu, F.Ferguson-Miller, Q.Ling, C.Hiser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.45 / 3.45
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	339.221, 339.221, 89.199, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 26.2

The structure of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Calcium	(Ca)	2 atoms
Copper	(Cu)	6 atoms

The binding sites of Magnesium atom in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State (pdb code 5weh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State, PDB code: 5weh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:95.3 occ:1.00 OE1 B:GLU254 2.0 0.8 1.0 NE2 A:HIS411 2.3 0.2 1.0 OD2 A:ASP412 2.4 0.4 1.0 CD B:GLU254 3.1 0.8 1.0 CE1 A:HIS411 3.3 0.6 1.0 CD2 A:HIS411 3.3 0.6 1.0 OE2 B:GLU254 3.5 0.2 1.0 OD2 B:ASP229 3.6 1.0 1.0 CG A:ASP412 3.6 0.8 1.0 OG1 A:THR337 4.0 0.9 1.0 OD1 A:ASP412 4.2 0.3 1.0 O B:SER253 4.3 0.9 1.0 CG B:GLU254 4.4 96.1 1.0 CG B:ASP229 4.4 0.1 1.0 ND1 A:HIS411 4.4 0.7 1.0 OD1 B:ASP229 4.4 0.1 1.0 CG A:HIS411 4.5 0.4 1.0 CB A:ASP412 4.7 0.8 1.0 CE2 A:TYR175 4.9 85.6 1.0 CB B:GLU254 4.9 94.2 1.0 O A:HIS334 5.0 94.0 1.0

Magnesium binding site 2 out of 2 in the Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cytochrome C Oxidase From Rhodobacter Sphaeroides in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg605 b:86.3 occ:1.00 OE1 H:GLU254 2.1 0.0 1.0 OD2 G:ASP412 2.3 0.1 1.0 NE2 G:HIS411 2.3 0.5 1.0 CD H:GLU254 3.2 0.1 1.0 CD2 G:HIS411 3.2 0.8 1.0 OD2 H:ASP229 3.4 0.3 1.0 CE1 G:HIS411 3.4 0.4 1.0 CG G:ASP412 3.5 0.2 1.0 OE2 H:GLU254 3.7 0.7 1.0 OG1 G:THR337 4.0 0.8 1.0 OD1 H:ASP229 4.1 0.8 1.0 CG H:ASP229 4.1 0.3 1.0 OD1 G:ASP412 4.2 0.4 1.0 O H:SER253 4.2 0.5 1.0 CG G:HIS411 4.4 0.6 1.0 CG H:GLU254 4.4 0.6 1.0 ND1 G:HIS411 4.5 0.5 1.0 NZ H:LYS227 4.5 0.1 1.0 CB G:ASP412 4.6 0.6 1.0 CB H:GLU254 4.9 0.8 1.0

J.Liu, C.Hiser, S.Ferguson-Miller. Role of Conformational Change and K-Path Ligands in Controlling Cytochrome C Oxidase Activity. Biochem. Soc. Trans. V. 45 1087 2017.
ISSN: ISSN 1470-8752
PubMed: 28842531
DOI: 10.1042/BST20160138