Magnesium in PDB 2yev: Structure of CAA3-Type Cytochrome Oxidase

All present enzymatic activity of Structure of CAA3-Type Cytochrome Oxidase:
1.9.3.1;

The structure of Structure of CAA3-Type Cytochrome Oxidase, PDB code: 2yev was solved by J.A.Lyons, D.Aragao, T.Soulimane, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.18 / 2.36
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.250, 76.030, 300.267, 90.00, 92.21, 90.00
R / Rfree (%)	17.1 / 21.8

The structure of Structure of CAA3-Type Cytochrome Oxidase also contains other interesting chemical elements:

Iron	(Fe)	6 atoms
Copper	(Cu)	6 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the Structure of CAA3-Type Cytochrome Oxidase (pdb code 2yev). 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 CAA3-Type Cytochrome Oxidase, PDB code: 2yev:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1801 b:39.5 occ:1.00 OD2 A:ASP378 2.3 49.9 1.0 O A:HOH2044 2.3 48.8 1.0 O A:HOH2102 2.4 55.7 1.0 O A:HOH2101 2.4 35.6 1.0 NE2 A:HIS377 2.4 42.8 1.0 OE1 B:GLU199 2.5 90.3 1.0 CD B:GLU199 3.1 45.7 1.0 CE1 A:HIS377 3.2 35.3 1.0 OE2 B:GLU199 3.2 48.5 1.0 CG A:ASP378 3.5 72.1 1.0 CD2 A:HIS377 3.5 41.7 1.0 O A:HOH2105 4.0 33.2 1.0 O B:ALA198 4.1 39.1 1.0 O A:HOH2045 4.2 37.5 1.0 O A:HOH2043 4.3 31.5 1.0 OD2 B:ASP174 4.3 45.3 1.0 CG B:GLU199 4.3 36.9 1.0 CB A:ASP378 4.4 32.5 1.0 ND1 A:HIS377 4.4 38.0 1.0 OD1 A:ASP378 4.4 52.1 1.0 CE2 A:TYR142 4.4 38.4 1.0 O A:HOH2104 4.5 42.1 1.0 CB B:GLU199 4.5 31.3 1.0 O A:HOH2046 4.5 34.5 1.0 OD1 B:ASP174 4.6 44.1 1.0 CG A:HIS377 4.6 37.5 1.0 CA B:GLU199 4.8 32.0 1.0 O A:HOH2090 4.8 35.3 1.0 CG B:ASP174 4.8 57.7 1.0 OG1 A:THR303 4.9 39.8 1.0 OH A:TYR142 4.9 32.1 1.0 O A:HOH2071 5.0 58.5 1.0

Magnesium binding site 2 out of 2 in the Structure of CAA3-Type Cytochrome Oxidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of CAA3-Type Cytochrome Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1801 b:50.0 occ:1.00 O D:HOH2076 2.3 45.6 1.0 OD2 D:ASP378 2.4 63.7 1.0 O D:HOH2027 2.4 42.4 1.0 O D:HOH2070 2.4 46.2 1.0 OE1 E:GLU199 2.5 87.2 1.0 NE2 D:HIS377 2.5 52.9 1.0 CD E:GLU199 3.0 57.5 1.0 OE2 E:GLU199 3.1 48.3 1.0 CE1 D:HIS377 3.3 48.7 1.0 CD2 D:HIS377 3.6 48.8 1.0 CG D:ASP378 3.6 77.5 1.0 O E:ALA198 3.9 45.7 1.0 O D:HOH2078 4.0 60.3 1.0 CG E:GLU199 4.2 35.3 1.0 O D:HOH2024 4.2 43.9 1.0 OD2 E:ASP174 4.3 49.6 1.0 CB E:GLU199 4.3 34.9 1.0 O D:HOH2079 4.3 42.6 1.0 O D:HOH2026 4.3 41.1 1.0 OD1 E:ASP174 4.4 51.6 1.0 CE2 D:TYR142 4.4 46.7 1.0 CB D:ASP378 4.4 44.2 1.0 OD1 D:ASP378 4.4 73.2 1.0 ND1 D:HIS377 4.4 51.8 1.0 O D:HOH2025 4.5 44.6 1.0 CA E:GLU199 4.6 39.6 1.0 CG D:HIS377 4.6 53.0 1.0 CG E:ASP174 4.8 68.2 1.0 OG1 D:THR303 4.9 55.2 1.0 O D:HOH2050 4.9 59.6 1.0 C E:ALA198 4.9 54.0 1.0

J.A.Lyons, D.Aragao, O.Slattery, A.V.Pisliakov, T.Soulimane, M.Caffrey. Structural Insights Into Electron Transfer in CAA3-Type Cytochrome Oxidases. Nature V. 487 514 2012.
ISSN: ISSN 0028-0836
PubMed: 22763450
DOI: 10.1038/NATURE11182