Magnesium in PDB 3a9c: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1 in Complex with Ribulose-1,5- Bisphosphate

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1 in Complex with Ribulose-1,5- Bisphosphate, PDB code: 3a9c 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)	43.64 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	117.313, 130.615, 132.672, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.5

The binding sites of Magnesium atom in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakaraensis KOD1 in Complex with Ribulose-1,5- Bisphosphate (pdb code 3a9c). 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 in Complex with Ribulose-1,5- Bisphosphate, PDB code: 3a9c:
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 in Complex with Ribulose-1,5- Bisphosphate


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 in Complex with Ribulose-1,5- Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg411 b:49.5 occ:1.00 OD1 E:ASP304 2.6 46.8 1.0 OD2 A:ASP304 3.4 36.0 1.0 O E:HOH643 3.4 40.0 1.0 OD1 A:ASP304 3.5 38.0 1.0 CG E:ASP304 3.7 41.7 1.0 CG A:ASP304 3.8 34.1 1.0 OD1 C:ASP304 4.0 43.3 1.0 OD2 E:ASP304 4.2 42.8 1.0 OD2 C:ASP304 4.6 42.3 1.0 CG C:ASP304 4.7 42.5 1.0 O A:TYR300 4.8 27.8 1.0 CB E:ASP304 4.9 38.3 1.0 CG2 A:ILE303 4.9 21.0 1.0 NH1 E:ARG307 5.0 64.8 1.0

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


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 in Complex with Ribulose-1,5- Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg411 b:47.8 occ:1.00 OD1 B:ASP304 2.7 42.4 1.0 OD1 D:ASP304 3.2 35.6 1.0 O B:HOH678 3.3 30.4 1.0 CG B:ASP304 3.4 37.8 1.0 OD2 B:ASP304 3.5 40.1 1.0 OD2 F:ASP304 3.9 37.5 1.0 OD2 D:ASP304 4.0 35.1 1.0 CG D:ASP304 4.0 33.9 1.0 OD1 F:ASP304 4.2 40.2 1.0 NH1 D:ARG307 4.3 55.8 1.0 CG F:ASP304 4.5 35.9 1.0 O B:HOH697 4.6 51.4 1.0 O F:TYR300 4.8 29.5 1.0 CB B:ASP304 4.9 32.5 1.0 CG2 F:ILE303 4.9 30.0 1.0 CG2 B:ILE303 5.0 28.7 1.0 NH2 D:ARG307 5.0 54.6 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