Sodium in PDB 5gho: Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 8- Oxo-Dgtp

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 8- Oxo-Dgtp:
3.6.1.55; 3.6.1.56;

The structure of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 8- Oxo-Dgtp, PDB code: 5gho 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)	43.35 / 1.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.315, 47.350, 123.123, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 17.7

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 8- Oxo-Dgtp (pdb code 5gho). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 8- Oxo-Dgtp, PDB code: 5gho:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 8- Oxo-Dgtp


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/D120A Mutant) in Complex with 8- Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:29.9 occ:1.00 OE2 A:GLU56 2.3 19.6 1.0 O A:HOH326 2.3 20.4 1.0 O A:GLY36 2.3 13.0 1.0 O A:HOH469 2.4 37.4 1.0 CD A:GLU56 3.3 15.3 1.0 C A:GLY36 3.5 10.8 1.0 O A:HOH496 3.6 33.7 1.0 OE1 A:GLU56 3.8 15.6 1.0 O A:HOH499 3.9 41.9 1.0 CA A:GLY37 3.9 10.3 1.0 OE1 A:GLU52 4.0 25.9 1.0 O A:HOH512 4.0 31.9 1.0 N A:GLY37 4.2 10.1 1.0 O A:HOH452 4.3 20.4 1.0 CG A:GLU56 4.4 17.9 1.0 O A:HOH484 4.4 27.5 1.0 O A:HOH431 4.5 21.3 1.0 O A:HOH526 4.5 47.0 1.0 N A:GLY36 4.7 8.9 1.0 CA A:GLY36 4.7 10.7 1.0 CD A:GLU52 4.8 22.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 8- Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 8- Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:30.6 occ:1.00 O B:HOH455 2.3 31.0 1.0 OE2 B:GLU56 2.3 22.2 1.0 O B:GLY36 2.3 15.3 1.0 O B:HOH327 2.6 29.1 1.0 O B:HOH415 2.7 37.3 1.0 CD B:GLU56 3.3 21.3 1.0 C B:GLY36 3.5 13.3 1.0 OE1 B:GLU56 3.8 18.7 1.0 CA B:GLY37 3.9 13.3 1.0 OE1 B:GLU52 4.1 31.1 1.0 N B:GLY37 4.2 12.1 1.0 O B:HOH456 4.2 30.6 1.0 O B:HOH421 4.3 24.2 1.0 O2G B:8DG201 4.3 52.9 1.0 CG B:GLU56 4.4 21.2 1.0 O B:HOH310 4.6 40.3 1.0 N B:GLY36 4.6 10.5 1.0 CD B:GLU52 4.7 29.2 1.0 CA B:GLY36 4.7 11.9 1.0 O B:HOH374 4.7 23.9 1.0 CE B:LYS23 4.9 49.2 1.0 OE2 B:GLU52 5.0 32.9 1.0 CE B:MET101 5.0 24.3 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