Magnesium in PDB 2gsm: Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides

All present enzymatic activity of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides:
1.9.3.1;

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides, PDB code: 2gsm was solved by L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	125.020, 131.639, 176.802, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 23.2

The structure of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides (pdb code 2gsm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides, PDB code: 2gsm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3006 b:10.7 occ:1.00 O B:HOH5055 1.8 29.3 1.0 O B:HOH5048 1.9 29.3 1.0 OE1 B:GLU254 1.9 27.6 1.0 O B:HOH5042 2.2 19.7 1.0 NE2 A:HIS411 2.2 22.8 1.0 OD2 A:ASP412 2.3 24.8 1.0 CD B:GLU254 3.1 27.6 1.0 CE1 A:HIS411 3.1 22.6 1.0 CD2 A:HIS411 3.2 21.8 1.0 CG A:ASP412 3.4 27.2 1.0 OE2 B:GLU254 3.7 28.9 1.0 O A:HOH6551 3.8 23.8 1.0 O B:SER253 3.9 23.2 1.0 CB A:ASP412 4.2 24.7 1.0 OD1 B:ASP229 4.2 27.5 1.0 ND1 A:HIS411 4.2 21.7 1.0 CG B:GLU254 4.3 24.3 1.0 OD2 B:ASP229 4.3 26.7 1.0 O A:HOH6529 4.3 25.4 1.0 CG A:HIS411 4.3 24.1 1.0 OD1 A:ASP412 4.4 25.6 1.0 O A:HOH6541 4.4 28.1 1.0 O B:HOH5072 4.5 29.6 1.0 CB B:GLU254 4.5 23.7 1.0 O A:HOH6514 4.6 22.6 1.0 OG1 A:THR337 4.6 26.4 1.0 O A:HOH6535 4.6 23.8 1.0 CG B:ASP229 4.7 25.6 1.0 CA B:GLU254 4.8 23.3 1.0 CE2 A:TYR175 4.9 21.1 1.0

Magnesium binding site 2 out of 2 in the Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Core (Subunits I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg4006 b:12.8 occ:1.00 O D:HOH1082 1.8 32.4 1.0 O D:HOH1094 1.8 28.3 1.0 OE1 D:GLU254 1.9 32.9 1.0 OD2 C:ASP412 2.1 26.2 1.0 NE2 C:HIS411 2.2 28.7 1.0 O D:HOH1071 2.2 26.6 1.0 CE1 C:HIS411 3.1 27.6 1.0 CD D:GLU254 3.1 33.9 1.0 CD2 C:HIS411 3.2 26.9 1.0 CG C:ASP412 3.4 28.3 1.0 OE2 D:GLU254 3.7 34.8 1.0 O D:SER253 4.0 28.4 1.0 O C:HOH1093 4.0 32.8 1.0 CB C:ASP412 4.2 27.0 1.0 ND1 C:HIS411 4.2 26.5 1.0 OD1 D:ASP229 4.2 33.0 1.0 CG D:GLU254 4.3 31.0 1.0 OD1 C:ASP412 4.3 30.0 1.0 CG C:HIS411 4.3 25.9 1.0 O C:HOH1041 4.3 32.5 1.0 OD2 D:ASP229 4.3 32.3 1.0 O C:HOH1014 4.4 26.0 1.0 O C:HOH1069 4.4 31.5 1.0 CB D:GLU254 4.5 27.9 1.0 O D:HOH1127 4.5 33.2 1.0 OG1 C:THR337 4.7 31.5 1.0 O C:HOH1051 4.7 25.9 1.0 CG D:ASP229 4.7 31.5 1.0 CA D:GLU254 4.8 28.3 1.0 CE2 C:TYR175 4.9 32.3 1.0

L.Qin, C.Hiser, A.Mulichak, R.M.Garavito, S.Ferguson-Miller. Identification of Conserved Lipid/Detergent-Binding Sites in A High-Resolution Structure of the Membrane Protein Cytochrome C Oxidase. Proc.Natl.Acad.Sci.Usa V. 103 16117 2006.
ISSN: ISSN 0027-8424
PubMed: 17050688
DOI: 10.1073/PNAS.0606149103