Magnesium in PDB 3vm6: Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate, PDB code: 3vm6 was solved by A.Nakamura, M.Fujihashi, R.Aono, T.Sato, 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)	45.97 / 2.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	146.537, 146.537, 99.649, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 26.2

The structure of Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate (pdb code 3vm6). 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 Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate, PDB code: 3vm6:
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 Kodakarensis KOD1 in Complex with Alpha-D-Ribose-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 Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg323 b:33.9 occ:1.00 OD2 C:ASP304 2.6 40.3 1.0 OD2 B:ASP304 2.7 35.7 1.0 OD1 C:ASP304 2.8 40.1 1.0 OD2 A:ASP304 2.9 43.3 1.0 OD1 A:ASP304 3.0 43.9 1.0 CG C:ASP304 3.1 38.0 1.0 CG A:ASP304 3.3 40.9 1.0 OD1 B:ASP304 3.4 34.6 1.0 CG B:ASP304 3.4 34.0 1.0 CB C:ASP304 4.6 34.2 1.0 O C:HOH661 4.8 21.6 1.0 CB A:ASP304 4.8 36.9 1.0 O A:HOH511 4.9 21.6 1.0 CB B:ASP304 4.9 30.5 1.0 CG2 A:ILE303 4.9 31.1 1.0 CG2 C:ILE303 4.9 30.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis KOD1 in Complex with Alpha-D-Ribose-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 Kodakarensis KOD1 in Complex with Alpha-D-Ribose-1,5- Bisphosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg413 b:38.0 occ:0.50 O C:LYS192 2.9 19.1 1.0 O C:HOH685 3.9 27.3 1.0 C C:LYS192 4.1 20.6 1.0 CA C:LYS192 4.9 20.4 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