Sodium in PDB 8i1d: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 7.7

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 7.7:
3.6.1.55; 3.6.1.56;

The structure of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 7.7, PDB code: 8i1d was solved by T.Nakamura, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.17 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.145, 47.7, 123.984, 90, 90, 90
R / Rfree (%)	13.6 / 16.3

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 7.7 (pdb code 8i1d). 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 at pH 7.7, PDB code: 8i1d:
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 at pH 7.7


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 at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:40.3 occ:0.50 O A:HOH309 0.1 40.3 0.5 OE2 A:GLU52 2.4 25.0 1.0 O2B A:6U4201 2.4 16.4 0.4 O A:HOH371 2.5 25.0 1.0 O2B A:6U4201 2.7 17.2 0.6 O A:HOH362 2.8 47.8 1.0 NA A:NA204 3.2 24.2 0.4 CD A:GLU52 3.3 22.7 1.0 HH12 A:ARG51 3.4 24.4 1.0 OE1 A:GLU52 3.4 21.9 1.0 O1B A:6U4201 3.5 17.8 0.6 PB A:6U4201 3.5 17.5 0.6 H A:LYS38 3.6 12.9 1.0 PB A:6U4201 3.6 21.2 0.4 O A:HOH302 3.7 39.5 1.0 HA3 A:GLY37 3.7 13.2 1.0 O A:HOH427 3.8 32.8 0.7 O2G A:6U4201 3.8 24.1 0.4 HE21 A:GLN40 3.8 28.2 1.0 O1B A:6U4201 3.9 22.7 0.4 HB2 A:LYS38 4.1 13.6 1.0 N A:LYS38 4.2 10.8 1.0 NH1 A:ARG51 4.2 20.3 1.0 O2G A:6U4201 4.3 28.3 0.6 HH22 A:ARG51 4.3 20.9 1.0 O A:LYS38 4.4 13.7 1.0 O3B A:6U4201 4.5 19.5 0.4 OE1 A:GLU55 4.5 31.9 1.0 O3B A:6U4201 4.6 21.6 0.6 NE2 A:GLN40 4.6 23.5 1.0 HH11 A:ARG51 4.6 24.4 1.0 CA A:GLY37 4.6 11.0 1.0 CG A:GLU52 4.7 18.2 1.0 HE22 A:GLN40 4.7 28.2 1.0 O3A A:6U4201 4.8 16.1 0.6 O A:HOH453 4.8 41.9 1.0 C A:GLY37 4.8 11.7 1.0 O3A A:6U4201 4.9 19.5 0.4 HG2 A:GLU52 4.9 21.9 1.0 PG A:6U4201 4.9 18.2 0.4 CB A:LYS38 4.9 11.3 1.0 O1G A:6U4201 4.9 28.2 0.6 HG3 A:GLU52 5.0 21.9 1.0 PG A:6U4201 5.0 25.7 0.6 CA A:LYS38 5.0 11.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 7.7


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 at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:21.0 occ:1.00 O2A A:6U4201 2.1 17.1 0.4 OE2 A:GLU56 2.2 24.1 0.6 O A:HOH354 2.3 20.5 1.0 O A:GLY36 2.4 13.4 1.0 O1B A:6U4201 2.4 17.8 0.6 O2A A:6U4201 2.6 23.5 0.6 CD A:GLU56 3.2 22.4 0.6 NA A:NA204 3.2 24.2 0.4 O1B A:6U4201 3.3 22.7 0.4 PA A:6U4201 3.5 16.2 0.4 OE1 A:GLU56 3.5 21.5 0.6 O3A A:6U4201 3.5 16.1 0.6 PB A:6U4201 3.6 17.5 0.6 PA A:6U4201 3.6 23.0 0.6 C A:GLY36 3.6 11.0 1.0 HA3 A:GLY37 3.6 13.2 1.0 HA2 A:GLY37 3.7 13.2 1.0 O3A A:6U4201 3.9 19.5 0.4 OE1 A:GLU56 4.0 14.6 0.4 CA A:GLY37 4.0 11.0 1.0 H A:GLY36 4.0 12.9 1.0 PB A:6U4201 4.1 21.2 0.4 O5' A:6U4201 4.1 18.3 0.6 O5' A:6U4201 4.2 14.5 0.4 O A:HOH427 4.2 32.8 0.7 OE1 A:GLU52 4.3 21.9 1.0 N A:GLY37 4.3 10.3 1.0 O1G A:6U4201 4.3 28.2 0.6 CD A:GLU56 4.3 14.2 0.4 O3B A:6U4201 4.4 21.6 0.6 O A:HOH372 4.4 18.2 1.0 OE2 A:GLU56 4.4 16.8 0.4 CG A:GLU56 4.5 21.9 0.6 HG2 A:GLU56 4.6 26.2 0.6 O2B A:6U4201 4.6 16.4 0.4 C4' A:6U4201 4.6 14.9 1.0 N A:GLY36 4.7 10.7 1.0 HG3 A:GLU56 4.7 26.2 0.6 O1A A:6U4201 4.7 19.7 0.4 O2B A:6U4201 4.7 17.2 0.6 CA A:GLY36 4.8 11.1 1.0 C5' A:6U4201 4.8 15.0 1.0 O1A A:6U4201 4.9 27.8 0.6

Sodium binding site 3 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 7.7


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 at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:24.2 occ:0.42 O A:HOH427 2.2 32.8 0.7 OE1 A:GLU52 2.3 21.9 1.0 O1B A:6U4201 2.4 17.8 0.6 O A:HOH302 2.4 39.5 1.0 OE2 A:GLU56 2.5 24.1 0.6 NA A:NA203 3.2 21.0 1.0 NA A:NA202 3.2 40.3 0.5 O A:HOH309 3.3 40.3 0.5 CD A:GLU52 3.3 22.7 1.0 HG2 A:GLU56 3.3 26.2 0.6 CD A:GLU56 3.4 22.4 0.6 HG3 A:GLU56 3.4 26.2 0.6 O1B A:6U4201 3.5 22.7 0.4 HA3 A:GLY37 3.6 13.2 1.0 CG A:GLU56 3.6 21.9 0.6 OE2 A:GLU52 3.6 25.0 1.0 PB A:6U4201 3.7 17.5 0.6 O2B A:6U4201 3.8 16.4 0.4 O A:GLY36 3.9 13.4 1.0 O1G A:6U4201 4.0 28.2 0.6 O2B A:6U4201 4.1 17.2 0.6 PB A:6U4201 4.1 21.2 0.4 HB2 A:GLU56 4.4 19.1 0.4 HB3 A:GLU52 4.4 20.6 1.0 CA A:GLY37 4.5 11.0 1.0 OE1 A:GLU56 4.5 21.5 0.6 C A:GLY36 4.6 11.0 1.0 OE1 A:GLU55 4.6 31.9 1.0 O A:HOH362 4.6 47.8 1.0 CG A:GLU52 4.6 18.2 1.0 O3A A:6U4201 4.7 16.1 0.6 O3B A:6U4201 4.7 21.6 0.6 O2A A:6U4201 4.7 17.1 0.4 HA A:GLU52 4.7 18.2 1.0 HA2 A:GLY37 4.7 13.2 1.0 OE1 A:GLU56 4.8 14.6 0.4 HB2 A:GLU55 4.9 27.0 1.0 N A:GLY37 4.9 10.3 1.0 PG A:6U4201 4.9 25.7 0.6 CB A:GLU52 4.9 17.1 1.0 HH12 A:ARG51 5.0 24.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 7.7


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 at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:43.2 occ:1.00 OE2 B:GLU56 2.1 33.4 1.0 O1A B:6U4201 2.3 32.0 0.6 O B:GLY36 2.4 15.6 1.0 O B:HOH328 2.4 28.9 1.0 O2A B:6U4201 2.5 39.2 0.4 O2B B:6U4201 2.6 59.2 0.6 O B:HOH301 2.8 54.1 1.0 CD B:GLU56 3.2 29.7 1.0 O3A B:6U4201 3.3 42.0 0.6 PA B:6U4201 3.4 34.0 0.6 HA3 B:GLY37 3.4 14.3 1.0 PA B:6U4201 3.5 38.0 0.4 PB B:6U4201 3.6 51.6 0.6 C B:GLY36 3.6 12.8 1.0 HA2 B:GLY37 3.6 14.3 1.0 OE1 B:GLU56 3.7 28.9 1.0 OE1 B:GLU52 3.8 24.9 1.0 O1A B:6U4201 3.8 38.8 0.4 CA B:GLY37 3.9 11.9 1.0 O5' B:6U4201 3.9 25.1 0.4 O5' B:6U4201 4.1 25.4 0.6 H B:GLY36 4.1 15.6 1.0 N B:GLY37 4.2 11.6 1.0 CG B:GLU56 4.4 29.2 1.0 HE3 B:LYS23 4.4 49.2 1.0 HZ1 B:LYS23 4.4 49.9 1.0 HG2 B:GLU56 4.4 35.1 1.0 O B:HOH320 4.4 21.9 1.0 O1B B:6U4201 4.5 49.9 0.6 HG3 B:GLU56 4.6 35.1 1.0 O2A B:6U4201 4.7 36.0 0.6 C4' B:6U4201 4.7 16.7 0.6 CD B:GLU52 4.7 21.5 1.0 O B:HOH303 4.7 46.9 1.0 N B:GLY36 4.7 13.0 1.0 O3B B:6U4201 4.7 57.6 0.6 CA B:GLY36 4.8 13.1 1.0 C4' B:6U4201 4.8 18.2 0.4 C5' B:6U4201 4.8 20.1 0.4 O3A B:6U4201 4.9 46.0 0.4 HE2 B:LYS23 4.9 49.2 1.0 C5' B:6U4201 4.9 17.5 0.6 CE B:LYS23 5.0 41.0 1.0

T.Nakamura, Y.Koga-Ogawa, K.Fujimiya, M.Chirifu, M.Goto, S.Ikemizu, Y.Nakabeppu, Y.Yamagata. Protonation States of Asp Residues in the Human Nudix Hydrolase MTH1 Contribute to Its Broad Substrate Recognition. Febs Lett. 2023.
ISSN: ISSN 0014-5793
PubMed: 36914375
DOI: 10.1002/1873-3468.14611