Sodium in PDB 5ghn: Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 2- Oxo-Datp

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 2- Oxo-Datp:
3.6.1.55; 3.6.1.56;

The structure of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 2- Oxo-Datp, PDB code: 5ghn 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)	31.00 / 1.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.228, 47.271, 123.193, 90.00, 90.00, 90.00
R / Rfree (%)	14.9 / 18.9

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 2- Oxo-Datp (pdb code 5ghn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 2- Oxo-Datp, PDB code: 5ghn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Human MTH1(G2K/D120N 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/D120N Mutant) in Complex with 2- Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:25.0 occ:1.00 O A:HOH320 2.4 16.3 1.0 O A:GLY36 2.4 11.3 1.0 OE2 A:GLU56 2.4 18.7 0.5 O A:HOH353 2.4 26.1 0.5 O2A A:6U4201 2.5 23.9 1.0 O1B A:6U4201 3.0 25.6 1.0 CD A:GLU56 3.3 16.9 0.5 OE1 A:GLU56 3.5 27.9 0.6 C A:GLY36 3.6 9.8 1.0 O A:HOH301 3.6 44.9 1.0 O A:HOH317 3.7 42.2 1.0 PA A:6U4201 3.7 18.1 1.0 O A:HOH498 3.7 51.9 1.0 O3A A:6U4201 3.8 18.9 1.0 OE1 A:GLU56 3.8 13.8 0.5 CA A:GLY37 4.0 9.3 1.0 O A:HOH353 4.0 23.4 0.5 PB A:6U4201 4.0 19.2 1.0 OE1 A:GLU52 4.2 25.2 1.0 O5' A:6U4201 4.2 14.5 1.0 O A:HOH385 4.2 26.8 0.6 N A:GLY37 4.2 9.4 1.0 CD A:GLU56 4.2 25.0 0.6 O A:HOH404 4.3 13.8 1.0 CG A:GLU56 4.4 17.9 0.5 OE2 A:GLU56 4.5 26.5 0.6 C4' A:6U4201 4.5 9.8 1.0 N A:GLY36 4.7 8.4 1.0 CA A:GLY36 4.7 9.9 1.0 O2B A:6U4201 4.9 19.4 1.0 C5' A:6U4201 4.9 14.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Human MTH1(G2K/D120N 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/D120N Mutant) in Complex with 2- Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:30.3 occ:1.00 O A:HOH353 2.4 23.4 0.5 OE2 A:GLU52 2.4 22.5 1.0 O A:HOH365 2.4 20.2 1.0 O A:HOH303 2.5 37.7 1.0 O2B A:6U4201 2.5 19.4 1.0 O A:HOH372 2.6 37.1 1.0 CD A:GLU52 3.4 20.8 1.0 PB A:6U4201 3.5 19.2 1.0 OE1 A:GLU52 3.7 25.2 1.0 O1B A:6U4201 3.7 25.6 1.0 O A:HOH353 3.7 26.1 0.5 O2G A:6U4201 3.8 27.7 1.0 NH1 A:ARG51 4.1 20.6 1.0 O A:HOH502 4.1 39.7 1.0 N A:LYS38 4.2 9.7 1.0 NE2 A:GLN40 4.2 25.0 1.0 O A:LYS38 4.2 13.4 1.0 O3B A:6U4201 4.5 33.2 1.0 OE1 A:GLU55 4.6 32.6 1.0 NH2 A:ARG51 4.7 18.9 1.0 CA A:GLY37 4.7 9.3 1.0 CG A:GLU52 4.7 17.4 1.0 O3A A:6U4201 4.7 18.9 1.0 O A:HOH301 4.8 44.9 1.0 PG A:6U4201 4.8 21.8 1.0 C A:GLY37 4.8 9.2 1.0 CZ A:ARG51 4.9 19.7 1.0 CB A:LYS38 4.9 10.3 1.0 CA A:LYS38 5.0 9.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Human MTH1(G2K/D120N 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 3 of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 2- Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:34.6 occ:1.00 OE2 B:GLU56 2.3 37.5 1.0 O B:GLY36 2.5 13.2 1.0 O2B B:6U4201 2.5 41.2 1.0 O1A B:6U4201 2.9 46.7 1.0 O B:HOH326 3.1 22.9 1.0 OE1 B:GLU52 3.2 29.1 1.0 CD B:GLU56 3.4 36.3 1.0 C B:GLY36 3.5 11.8 1.0 PB B:6U4201 3.6 46.0 1.0 O3A B:6U4201 3.7 40.1 1.0 CA B:GLY37 3.7 11.1 1.0 PA B:6U4201 3.9 44.0 1.0 OE1 B:GLU56 4.0 33.1 1.0 CD B:GLU52 4.0 27.5 1.0 N B:GLY37 4.1 10.6 1.0 O B:HOH377 4.3 41.4 1.0 O1B B:6U4201 4.4 49.3 1.0 OE2 B:GLU52 4.4 32.4 1.0 CG B:GLU56 4.5 36.2 1.0 O5' B:6U4201 4.6 25.4 1.0 CA B:GLY36 4.8 11.6 1.0 N B:GLY36 4.8 10.3 1.0 O3B B:6U4201 4.9 48.4 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