Sodium in PDB 5ghm: Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0:
3.6.1.55; 3.6.1.56;

The structure of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0, PDB code: 5ghm was solved by T.Nakamura, S.Waz, K.Hirata, Y.Nakabeppu, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.80 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.790, 47.778, 123.610, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.6

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0 (pdb code 5ghm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0, PDB code: 5ghm:

Sodium binding site 1 out of 1 in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:48.0 occ:1.00 O A:HOH310 2.3 26.8 1.0 O A:HOH337 2.4 33.3 1.0 O1B A:8DG201 2.5 0.8 1.0 OE2 A:GLU56 2.6 29.1 1.0 O A:GLY36 2.8 15.3 1.0 O2A A:8DG201 2.9 0.8 1.0 O3A A:8DG201 3.6 0.2 1.0 PB A:8DG201 3.6 0.7 1.0 CD A:GLU56 3.7 28.3 1.0 O A:HOH448 3.8 66.5 1.0 PA A:8DG201 3.8 0.7 1.0 C A:GLY36 3.9 12.2 1.0 CA A:GLY37 4.1 14.3 1.0 OE1 A:GLU56 4.2 23.2 1.0 O5' A:8DG201 4.5 0.6 1.0 N A:GLY37 4.5 13.1 1.0 OE1 A:GLU52 4.6 28.4 1.0 O3G A:8DG201 4.6 1.0 1.0 O2B A:8DG201 4.6 0.5 1.0 O3B A:8DG201 4.8 0.8 1.0 OE1 A:GLU100 4.8 65.5 1.0 CG A:GLU56 4.8 22.5 1.0 C5' A:8DG201 4.8 91.9 1.0

S.Waz, T.Nakamura, K.Hirata, Y.Koga-Ogawa, M.Chirifu, T.Arimori, T.Tamada, S.Ikemizu, Y.Nakabeppu, Y.Yamagata. Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism For Its Broad Substrate Specificity J. Biol. Chem. V. 292 2785 2017.
ISSN: ESSN 1083-351X
PubMed: 28035004
DOI: 10.1074/JBC.M116.749713