Magnesium in PDB 9jws: Haloquadratum Walsbyi Middle Rhodopsin

The structure of Haloquadratum Walsbyi Middle Rhodopsin, PDB code: 9jws was solved by L.N.Ko, G.Z.Lim, T.Ko, C.S.Yang, G.Y.Li, J.C.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.81 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.46, 62.47, 122.35, 90, 90, 90
R / Rfree (%)	29.6 / 32.4

The binding sites of Magnesium atom in the Haloquadratum Walsbyi Middle Rhodopsin (pdb code 9jws). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Haloquadratum Walsbyi Middle Rhodopsin, PDB code: 9jws:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Haloquadratum Walsbyi Middle Rhodopsin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Haloquadratum Walsbyi Middle Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:28.2 occ:1.00 OD1 A:ASP213 2.3 20.0 1.0 OD2 A:ASP213 2.3 28.1 1.0 CG A:ASP213 2.4 26.2 1.0 CE A:LYS217 2.5 27.5 1.0 OD2 A:ASP84 2.9 34.9 1.0 NZ A:LYS217 3.0 22.6 1.0 NE1 A:TRP85 3.2 21.0 1.0 C14 A:RET301 3.4 24.0 1.0 C15 A:RET301 3.5 29.0 1.0 CD1 A:TRP85 3.6 23.9 1.0 CB A:ASP213 3.6 21.1 1.0 CD A:LYS217 3.9 27.9 1.0 CG A:ASP84 3.9 32.4 1.0 OD1 A:ASP84 4.1 30.8 1.0 C13 A:RET301 4.4 24.5 1.0 CA A:ASP213 4.5 21.7 1.0 CE2 A:TRP85 4.5 23.3 1.0 OH A:TYR185 4.6 24.0 1.0 C12 A:RET301 4.9 27.7 1.0 CG A:TRP85 4.9 24.9 1.0 OG1 A:THR88 4.9 24.5 1.0 CG A:LYS217 4.9 20.4 1.0 OH A:TYR55 5.0 25.7 1.0 CE2 A:TYR55 5.0 20.9 1.0

Magnesium binding site 2 out of 4 in the Haloquadratum Walsbyi Middle Rhodopsin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Haloquadratum Walsbyi Middle Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:23.6 occ:1.00 OH A:TYR185 1.8 24.0 1.0 OG1 A:THR216 2.1 17.0 1.0 CG2 A:THR216 2.2 18.4 1.0 CB A:THR216 2.5 14.7 1.0 CZ A:TYR185 2.7 22.7 1.0 C20 A:RET301 2.8 15.6 1.0 CE1 A:TYR185 2.9 19.8 1.0 C13 A:RET301 3.2 24.5 1.0 O A:LEU212 3.4 17.2 1.0 OD1 A:ASP213 3.5 20.0 1.0 C14 A:RET301 3.7 24.0 1.0 C12 A:RET301 3.8 27.7 1.0 C A:LEU212 3.9 18.6 1.0 CE2 A:TYR185 3.9 18.0 1.0 CA A:THR216 3.9 20.3 1.0 C15 A:RET301 4.0 29.0 1.0 CA A:ASP213 4.1 21.7 1.0 N A:ASP213 4.2 17.3 1.0 N A:THR216 4.3 12.7 1.0 CD1 A:TYR185 4.3 17.8 1.0 CB A:LEU212 4.5 19.4 1.0 CG A:ASP213 4.6 26.2 1.0 CD1 A:TRP182 4.7 19.5 1.0 NE1 A:TRP182 4.7 23.6 1.0 CA A:LEU212 4.8 18.1 1.0 C A:THR216 4.8 22.8 1.0 C11 A:RET301 4.9 27.4 1.0 NZ A:LYS217 4.9 22.6 1.0 CD2 A:TYR185 4.9 19.2 1.0 CB A:ASP213 5.0 21.1 1.0 CE A:LYS217 5.0 27.5 1.0 O A:ASP213 5.0 20.1 1.0 C A:ASP213 5.0 19.2 1.0

Magnesium binding site 3 out of 4 in the Haloquadratum Walsbyi Middle Rhodopsin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Haloquadratum Walsbyi Middle Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:23.9 occ:1.00 OD1 B:ASP213 2.2 11.5 1.0 CG B:ASP213 2.6 18.5 1.0 OD2 B:ASP84 2.7 31.0 1.0 OD2 B:ASP213 2.8 19.7 1.0 NE1 B:TRP85 2.9 16.9 1.0 CE B:LYS217 2.9 25.2 1.0 CD1 B:TRP85 3.1 22.8 1.0 C14 B:RET301 3.2 16.5 1.0 NZ B:LYS217 3.5 28.0 1.0 C15 B:RET301 3.7 22.1 1.0 CB B:ASP213 3.8 18.8 1.0 CG B:ASP84 3.8 25.0 1.0 CE2 B:TRP85 4.2 20.0 1.0 CD B:LYS217 4.2 21.3 1.0 OD1 B:ASP84 4.3 28.4 1.0 C13 B:RET301 4.3 15.2 1.0 CG B:TRP85 4.5 27.4 1.0 OH B:TYR185 4.6 15.3 1.0 CA B:ASP213 4.6 19.1 1.0 C12 B:RET301 4.7 18.1 1.0 MG B:MG303 4.7 28.1 1.0 CE2 B:TYR185 4.8 17.3 1.0 OG1 B:THR88 4.9 24.6 1.0 CZ2 B:TRP85 5.0 17.3 1.0 CD2 B:TRP85 5.0 26.1 1.0

Magnesium binding site 4 out of 4 in the Haloquadratum Walsbyi Middle Rhodopsin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Haloquadratum Walsbyi Middle Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:28.1 occ:1.00 OH B:TYR185 1.4 15.3 1.0 OG1 B:THR216 1.6 21.4 1.0 CB B:THR216 2.6 15.6 1.0 O B:LEU212 2.7 13.3 1.0 CZ B:TYR185 2.7 20.3 1.0 CG2 B:THR216 2.7 23.7 1.0 OD1 B:ASP213 3.1 11.5 1.0 C B:LEU212 3.1 15.8 1.0 CA B:ASP213 3.2 19.1 1.0 N B:ASP213 3.4 20.1 1.0 CE1 B:TYR185 3.4 19.4 1.0 C14 B:RET301 3.5 16.5 1.0 C20 B:RET301 3.5 18.3 1.0 C15 B:RET301 3.6 22.1 1.0 C13 B:RET301 3.7 15.2 1.0 CE2 B:TYR185 3.8 17.3 1.0 CA B:THR216 3.8 21.5 1.0 N B:THR216 3.9 16.1 1.0 CG B:ASP213 4.0 18.5 1.0 C B:ASP213 4.1 19.5 1.0 CB B:ASP213 4.1 18.8 1.0 O B:ASP213 4.1 22.4 1.0 CA B:LEU212 4.2 16.2 1.0 CB B:LEU212 4.2 18.1 1.0 CE B:LYS217 4.2 25.2 1.0 NZ B:LYS217 4.4 28.0 1.0 C B:THR216 4.5 25.0 1.0 C12 B:RET301 4.6 18.1 1.0 N B:LYS217 4.7 29.5 1.0 CD1 B:TYR185 4.7 17.6 1.0 MG B:MG302 4.7 23.9 1.0

L.N.Ko, G.Z.Lim, T.Ko, C.S.Yang. Crystal Structure of Haloquadratum Walsbyi Middle Rhodopsin at 2.5 Angstroms Resolution. To Be Published.