Magnesium in PDB 1qvj: Structure of NUDT9 Complexed with Ribose-5-Phosphate

All present enzymatic activity of Structure of NUDT9 Complexed with Ribose-5-Phosphate:
3.6.1.13;

The structure of Structure of NUDT9 Complexed with Ribose-5-Phosphate, PDB code: 1qvj was solved by B.W.Shen, A.-L.Perraud, A.S.Scharenberg, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.97 / 1.91
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.900, 87.455, 120.308, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.2

The binding sites of Magnesium atom in the Structure of NUDT9 Complexed with Ribose-5-Phosphate (pdb code 1qvj). 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 NUDT9 Complexed with Ribose-5-Phosphate, PDB code: 1qvj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of NUDT9 Complexed with Ribose-5-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of NUDT9 Complexed with Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg560 b:55.7 occ:1.00 O A:HOH443 2.7 50.4 1.0 O3X A:RP5554 2.8 38.3 1.0 O A:GLY214 2.9 27.9 1.0 O A:HOH549 2.9 53.1 1.0 MG A:MG561 3.5 69.5 1.0 O A:HOH428 3.6 30.6 1.0 CA A:GLY215 3.9 23.7 1.0 C A:GLY214 4.0 26.7 1.0 P' A:RP5554 4.0 34.9 1.0 O A:HOH492 4.1 39.8 1.0 O2X A:RP5554 4.1 35.3 1.0 O A:HOH458 4.2 34.8 1.0 NH1 A:ARG204 4.4 37.8 1.0 N A:GLY215 4.4 25.9 1.0 OE1 A:GLU230 4.6 39.1 1.0 O1X A:RP5554 4.6 33.6 1.0

Magnesium binding site 2 out of 2 in the Structure of NUDT9 Complexed with Ribose-5-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of NUDT9 Complexed with Ribose-5-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg561 b:69.5 occ:1.00 O A:HOH514 2.8 53.0 1.0 O A:HOH445 2.9 51.5 1.0 O A:HOH443 2.9 50.4 1.0 OE2 A:GLU230 3.0 41.7 1.0 OE1 A:GLU230 3.2 39.1 1.0 CD A:GLU230 3.4 37.4 1.0 MG A:MG560 3.5 55.7 1.0 CA A:GLY215 4.0 23.7 1.0 O A:HOH531 4.2 42.7 1.0 O A:GLY214 4.4 27.9 1.0 N A:MSE216 4.5 25.2 1.0 CG A:GLU230 4.7 35.7 1.0 O3X A:RP5554 4.7 38.3 1.0 C A:GLY215 4.8 25.0 1.0 OD2 A:ASP305 4.8 44.2 1.0 O A:HOH492 4.8 39.8 1.0 NH1 A:ARG229 4.9 37.5 1.0

B.W.Shen, A.-L.Perraud, A.S.Scharenberg, B.L.Stoddard. The Crystal Structure and Mutational Analysis of Human NUDT9 J.Mol.Biol. V. 332 385 2003.
ISSN: ISSN 0022-2836
PubMed: 12948489
DOI: 10.1016/S0022-2836(03)00954-9