Magnesium in PDB 1m56: Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)

All present enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type):
1.9.3.1;

The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56 was solved by M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brezezinski, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	340.360, 340.360, 89.668, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 27.5

The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) (pdb code 1m56). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2006 b:23.8 occ:1.00 OE1 B:GLU254 2.1 23.4 1.0 O B:HOH1007 2.1 22.4 1.0 NE2 A:HIS411 2.2 20.6 1.0 OD2 A:ASP412 2.2 25.9 1.0 O B:HOH1010 2.2 29.2 1.0 O A:HOH2060 2.2 23.3 1.0 CD2 A:HIS411 3.1 19.9 1.0 CE1 A:HIS411 3.2 18.6 1.0 O A:HOH2108 3.2 34.4 1.0 CG A:ASP412 3.3 25.4 1.0 CD B:GLU254 3.3 24.8 1.0 O A:HOH2058 3.5 29.2 1.0 O B:HOH1008 3.7 26.9 1.0 OE2 B:GLU254 4.0 29.1 1.0 O B:SER253 4.1 17.0 1.0 CB A:ASP412 4.1 22.4 1.0 OD1 A:ASP412 4.2 27.0 1.0 CG A:HIS411 4.2 16.8 1.0 ND1 A:HIS411 4.3 18.6 1.0 OD2 B:ASP229 4.3 30.5 1.0 OD1 B:ASP229 4.5 28.8 1.0 CG B:GLU254 4.5 19.4 1.0 CB B:GLU254 4.6 16.3 1.0 OG1 A:THR337 4.8 26.5 1.0 CG B:ASP229 4.8 29.1 1.0 O A:HOH2104 4.9 17.9 1.0

Magnesium binding site 2 out of 2 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg3006 b:23.5 occ:1.00 O H:HOH1050 2.1 21.4 1.0 NE2 G:HIS411 2.1 20.4 1.0 OE1 H:GLU254 2.2 23.7 1.0 O G:HOH3061 2.2 23.1 1.0 O H:HOH1054 2.2 30.1 1.0 OD2 G:ASP412 2.2 25.2 1.0 CD2 G:HIS411 3.1 19.6 1.0 O G:HOH3114 3.1 33.7 1.0 CE1 G:HIS411 3.1 19.0 1.0 CD H:GLU254 3.4 24.7 1.0 CG G:ASP412 3.4 25.9 1.0 O G:HOH3059 3.8 29.7 1.0 O H:HOH1051 3.9 28.3 1.0 OE2 H:GLU254 4.0 28.0 1.0 OD2 H:ASP229 4.1 31.6 1.0 O H:SER253 4.2 18.1 1.0 CG G:HIS411 4.2 16.9 1.0 ND1 G:HIS411 4.2 18.8 1.0 OD1 G:ASP412 4.3 27.6 1.0 CB G:ASP412 4.3 23.1 1.0 OD1 H:ASP229 4.5 28.9 1.0 CG H:GLU254 4.5 19.5 1.0 OG1 G:THR337 4.5 25.9 1.0 CB H:GLU254 4.6 16.4 1.0 CG H:ASP229 4.7 29.2 1.0 CE2 G:TYR175 4.9 16.8 1.0 O G:HOH3110 5.0 18.1 1.0

M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brzezinski, S.Iwata. The X-Ray Crystal Structures of Wild-Type and Eq(I-286) Mutant Cytochrome C Oxidases From Rhodobacter Sphaeroides. J.Mol.Biol. V. 321 329 2002.
ISSN: ISSN 0022-2836
PubMed: 12144789
DOI: 10.1016/S0022-2836(02)00619-8