Magnesium in PDB 3a11: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1, PDB code: 3a11 was solved by A.Nakamura, M.Fujihashi, Y.Nishiba, S.Yoshida, A.Yano, H.Atomi, T.Imanaka, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.66 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	117.291, 130.808, 132.815, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 26.6

The binding sites of Magnesium atom in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1 (pdb code 3a11). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1, PDB code: 3a11:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg411 b:51.3 occ:1.00 OD1 B:ASP304 2.5 55.5 1.0 O B:HOH678 2.9 49.5 1.0 OD1 D:ASP304 3.4 33.6 1.0 CG B:ASP304 3.4 46.4 1.0 OD2 B:ASP304 3.5 47.9 1.0 OD2 F:ASP304 3.6 46.0 1.0 OD1 F:ASP304 3.8 43.3 1.0 NH1 D:ARG307 3.9 73.7 1.0 CG F:ASP304 4.1 34.5 1.0 CG D:ASP304 4.3 31.7 1.0 OD2 D:ASP304 4.4 37.1 1.0 CG2 F:ILE303 4.4 37.0 1.0 O B:HOH684 4.5 45.5 1.0 O F:TYR300 4.6 32.0 1.0 CB B:ASP304 4.8 30.5 1.0 CZ D:ARG307 4.9 67.9 1.0 NH2 D:ARG307 5.0 70.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg411 b:56.8 occ:1.00 OD1 E:ASP304 2.6 56.9 1.0 O E:HOH643 3.2 38.1 1.0 OD2 E:ASP304 3.2 57.3 1.0 CG E:ASP304 3.2 54.6 1.0 OD1 A:ASP304 3.6 45.2 1.0 OD2 A:ASP304 3.9 41.3 1.0 OD1 C:ASP304 4.1 52.5 1.0 O A:TYR300 4.1 34.9 1.0 CG A:ASP304 4.2 35.6 1.0 OD2 C:ASP304 4.3 62.3 1.0 CG C:ASP304 4.6 57.0 1.0 CB E:ASP304 4.7 41.8 1.0 CG2 A:ILE303 5.0 18.4 1.0

A.Nakamura, M.Fujihashi, R.Aono, T.Sato, Y.Nishiba, S.Yoshida, A.Yano, H.Atomi, T.Imanaka, K.Miki. Dynamic, Ligand-Dependent Conformational Change Triggers Reaction of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 J.Biol.Chem. V. 287 20784 2012.
ISSN: ISSN 0021-9258
PubMed: 22511789
DOI: 10.1074/JBC.M112.349423