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

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

The structure of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp, PDB code: 5ghj 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)	37.18 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.530, 47.289, 123.672, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 17.6

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp (pdb code 5ghj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp, PDB code: 5ghj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Human MTH1(G2K 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 Mutant) in Complex with 2-Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:24.6 occ:1.00 O A:HOH383 2.2 20.2 1.0 O A:HOH366 2.4 27.1 1.0 O2B A:6U4201 2.4 15.6 1.0 OE2 A:GLU52 2.4 19.5 1.0 O A:HOH309 2.5 31.2 1.0 O A:HOH322 2.5 26.8 1.0 CD A:GLU52 3.4 18.2 1.0 PB A:6U4201 3.6 15.0 1.0 OE1 A:GLU52 3.6 20.0 1.0 O1B A:6U4201 3.8 17.7 1.0 O A:HOH481 3.9 41.0 1.0 O2G A:6U4201 4.0 21.4 1.0 N A:LYS38 4.1 11.0 1.0 O A:HOH504 4.1 33.9 1.0 O A:LYS38 4.1 14.0 1.0 NH1 A:ARG51 4.1 20.4 1.0 NE2 A:GLN40 4.3 22.3 1.0 O A:HOH341 4.5 45.2 1.0 O3B A:6U4201 4.5 17.3 1.0 OE1 A:GLU55 4.5 29.5 1.0 CA A:GLY37 4.7 11.5 1.0 CB A:LYS38 4.7 12.0 1.0 O A:HOH316 4.7 31.9 1.0 C A:GLY37 4.8 11.1 1.0 CG A:GLU52 4.8 17.0 1.0 O3A A:6U4201 4.8 14.7 1.0 CA A:LYS38 4.8 11.2 1.0 NH2 A:ARG51 4.8 18.7 1.0 C A:LYS38 4.9 11.5 1.0 PG A:6U4201 4.9 16.9 1.0 CZ A:ARG51 5.0 19.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human MTH1(G2K 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 Mutant) in Complex with 2-Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:17.0 occ:0.55 NA A:NA203 0.0 17.0 0.6 O A:HOH382 2.3 32.0 1.0 NA A:NA203 2.4 15.2 0.5 OE2 A:GLU56 2.4 25.9 0.2 O A:GLY36 2.6 12.5 1.0 OE1 A:GLU56 2.9 26.0 0.3 O2A A:6U4201 2.9 20.9 1.0 O1B A:6U4201 3.2 17.7 1.0 CD A:GLU56 3.2 26.1 0.2 OE1 A:GLU56 3.3 26.5 0.2 CD A:GLU56 3.4 26.0 0.3 O A:HOH378 3.4 41.8 1.0 OE1 A:GLU56 3.7 25.4 0.4 O A:HOH416 3.7 39.0 1.0 C A:GLY36 3.8 11.4 1.0 OE2 A:GLU56 3.8 26.0 0.3 PA A:6U4201 3.9 15.6 1.0 O3A A:6U4201 3.9 14.7 1.0 O A:HOH322 4.1 26.8 1.0 PB A:6U4201 4.1 15.0 1.0 O5' A:6U4201 4.2 13.8 1.0 CD A:GLU56 4.2 24.2 0.4 CA A:GLY37 4.2 11.5 1.0 O A:HOH318 4.3 18.9 1.0 OE2 A:GLU56 4.4 23.0 0.4 CG A:GLU56 4.4 24.6 0.3 N A:GLY37 4.5 11.4 1.0 OE1 A:GLU52 4.5 20.0 1.0 CG A:GLU56 4.5 24.8 0.2 C4' A:6U4201 4.6 11.9 1.0 O A:HOH367 4.7 29.9 1.0 N A:GLY36 4.8 11.3 1.0 C5' A:6U4201 4.8 12.6 1.0 O A:HOH335 4.9 42.3 1.0 CA A:GLY36 4.9 11.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Human MTH1(G2K 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 Mutant) in Complex with 2-Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:15.2 occ:0.45 NA A:NA203 0.0 15.2 0.5 O1B A:6U4201 2.2 17.7 1.0 O2A A:6U4201 2.3 20.9 1.0 O A:HOH367 2.4 29.9 1.0 NA A:NA203 2.4 17.0 0.6 O A:HOH378 2.5 41.8 1.0 O A:HOH316 3.3 31.9 1.0 PB A:6U4201 3.4 15.0 1.0 PA A:6U4201 3.5 15.6 1.0 O3A A:6U4201 3.6 14.7 1.0 O A:HOH416 3.8 39.0 1.0 OE2 A:GLU56 4.0 25.9 0.2 O3B A:6U4201 4.0 17.3 1.0 O A:HOH382 4.2 32.0 1.0 O A:HOH322 4.3 26.8 1.0 OE1 A:GLU56 4.3 26.0 0.3 O1G A:6U4201 4.4 20.6 1.0 OE1 A:GLU100 4.5 50.2 1.0 O1A A:6U4201 4.5 20.4 1.0 OE2 A:GLU56 4.5 26.0 0.3 O5' A:6U4201 4.6 13.8 1.0 PG A:6U4201 4.7 16.9 1.0 O2B A:6U4201 4.7 15.6 1.0 OE1 A:GLU56 4.7 26.5 0.2 O2G A:6U4201 4.8 21.4 1.0 CD A:GLU56 4.8 26.0 0.3 O A:GLY36 4.8 12.5 1.0 CD A:GLU56 4.8 26.1 0.2 O A:HOH370 4.8 28.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human MTH1(G2K 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 4 of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:30.1 occ:1.00 OE2 B:GLU56 2.3 34.8 1.0 O B:GLY36 2.4 14.3 1.0 O B:HOH342 2.4 25.2 1.0 O1A B:6U4201 2.5 29.7 1.0 O2B B:6U4201 2.7 47.5 1.0 CD B:GLU56 3.3 32.3 1.0 O3A B:6U4201 3.4 36.8 1.0 PA B:6U4201 3.5 30.0 1.0 C B:GLY36 3.6 13.0 1.0 PB B:6U4201 3.6 43.1 1.0 OE1 B:GLU56 3.8 30.2 1.0 CA B:GLY37 3.9 12.0 1.0 OE1 B:GLU52 4.0 25.6 1.0 O5' B:6U4201 4.0 22.2 1.0 N B:GLY37 4.2 11.6 1.0 O B:HOH330 4.4 20.3 1.0 CG B:GLU56 4.5 30.1 1.0 O1B B:6U4201 4.6 38.3 1.0 CE B:LYS23 4.7 40.2 1.0 C4' B:6U4201 4.7 14.1 1.0 O B:HOH305 4.7 34.2 1.0 N B:GLY36 4.7 12.1 1.0 CA B:GLY36 4.8 11.8 1.0 NZ B:LYS23 4.8 40.2 1.0 O2A B:6U4201 4.8 28.8 1.0 O3B B:6U4201 4.8 50.4 1.0 CD B:GLU52 4.9 23.4 1.0 C5' B:6U4201 4.9 15.9 1.0 O3G B:6U4201 5.0 58.8 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