Sodium in PDB 5ghp: Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp:
3.6.1.55; 3.6.1.56;

The structure of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp, PDB code: 5ghp 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)	43.29 / 1.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.233, 47.237, 123.195, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 17.9

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp (pdb code 5ghp). 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 2- Oxo-Datp, PDB code: 5ghp:
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 2- Oxo-Datp


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 2- Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:21.9 occ:0.65 O A:HOH326 2.2 20.1 1.0 OE2 A:GLU56 2.3 22.0 1.0 O A:HOH302 2.3 37.0 1.0 O A:GLY36 2.3 13.2 1.0 O A:HOH483 2.3 42.5 1.0 CD A:GLU56 3.2 16.7 1.0 O A:HOH466 3.5 44.2 0.4 C A:GLY36 3.5 10.4 1.0 OE1 A:GLU56 3.7 17.4 1.0 O A:HOH466 3.8 44.3 0.6 O A:HOH509 3.8 29.7 1.0 CA A:GLY37 4.0 10.3 1.0 O A:HOH488 4.1 36.0 1.0 OE1 A:GLU52 4.1 26.0 1.0 N A:GLY37 4.2 10.1 1.0 O A:HOH413 4.4 18.7 1.0 O A:HOH456 4.4 20.9 1.0 CG A:GLU56 4.4 18.2 1.0 N A:GLY36 4.6 9.2 1.0 CA A:GLY36 4.7 11.3 1.0

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


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 2- Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:30.6 occ:0.70 O B:HOH331 2.3 27.0 1.0 OE2 B:GLU56 2.4 24.9 1.0 O B:GLY36 2.5 15.7 1.0 O B:HOH475 2.7 34.2 1.0 CD B:GLU56 3.4 22.1 1.0 C B:GLY36 3.6 13.3 1.0 O B:HOH474 3.8 33.3 1.0 OE1 B:GLU56 3.9 18.9 1.0 CA B:GLY37 4.0 12.8 1.0 N B:GLY37 4.3 12.2 1.0 OE1 B:GLU52 4.3 30.3 1.0 O B:HOH415 4.4 22.6 1.0 CE B:LYS23 4.5 39.2 1.0 O B:HOH369 4.5 22.9 1.0 NZ B:LYS23 4.5 41.0 1.0 CG B:GLU56 4.6 24.5 1.0 N B:GLY36 4.7 10.9 1.0 CA B:GLY36 4.8 12.1 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