Sodium in PDB 8i1i: Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 2- Oxo-Datp at pH 7.7

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/D120N 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/D120N Mutant) in Complex with 2- Oxo-Datp at pH 7.7, PDB code: 8i1i 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)	33.24 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.403, 47.628, 123.864, 90, 90, 90
R / Rfree (%)	13.6 / 16.3

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 2- Oxo-Datp at pH 7.7 (pdb code 8i1i). 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/D120N Mutant) in Complex with 2- Oxo-Datp at pH 7.7, PDB code: 8i1i:
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/D120N 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/D120N 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:30.7 occ:1.00 O A:HOH384 2.3 24.3 1.0 O A:HOH321 2.4 46.0 1.0 O2B A:6U4201 2.4 14.4 0.5 OE2 A:GLU52 2.4 24.3 1.0 O2B A:6U4201 2.5 20.2 0.5 O A:HOH317 2.6 44.2 1.0 O3G A:6U4201 3.3 35.9 0.5 HH12 A:ARG51 3.4 23.4 1.0 CD A:GLU52 3.4 21.0 1.0 H A:LYS38 3.5 12.8 1.0 PB A:6U4201 3.5 19.6 0.5 HE21 A:GLN40 3.5 26.7 1.0 OE1 A:GLU52 3.6 22.6 1.0 PB A:6U4201 3.6 13.9 0.5 O1B A:6U4201 3.7 21.4 0.5 HA3 A:GLY37 3.9 12.5 1.0 HB2 A:LYS38 3.9 13.0 1.0 O1B A:6U4201 4.0 16.9 0.5 O2G A:6U4201 4.0 15.7 0.5 HH22 A:ARG51 4.1 23.4 1.0 N A:LYS38 4.1 10.7 1.0 NH1 A:ARG51 4.2 19.5 1.0 O A:LYS38 4.2 13.1 1.0 NE2 A:GLN40 4.3 22.3 1.0 O A:HOH479 4.3 48.4 1.0 O3B A:6U4201 4.4 25.9 0.5 HE22 A:GLN40 4.5 26.7 1.0 PG A:6U4201 4.5 34.6 0.5 O3B A:6U4201 4.5 13.8 0.5 OE1 A:GLU55 4.6 29.0 1.0 HH11 A:ARG51 4.6 23.4 1.0 CG A:GLU52 4.8 17.3 1.0 O3A A:6U4201 4.8 15.0 1.0 CA A:GLY37 4.8 10.4 1.0 CB A:LYS38 4.8 10.8 1.0 NH2 A:ARG51 4.8 19.5 1.0 C A:GLY37 4.9 10.6 1.0 CA A:LYS38 4.9 10.7 1.0 PG A:6U4201 4.9 12.8 0.5 HG2 A:GLU52 4.9 20.7 1.0 CZ A:ARG51 5.0 18.6 1.0 HG3 A:GLU52 5.0 20.7 1.0 C A:LYS38 5.0 10.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human MTH1(G2K/D120N 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/D120N 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:19.9 occ:0.70 OE2 A:GLU56 2.2 23.1 0.4 O A:HOH388 2.3 46.5 1.0 O A:HOH319 2.3 24.2 1.0 O A:GLY36 2.4 12.1 1.0 O2A A:6U4201 2.6 21.3 1.0 O1B A:6U4201 2.7 21.4 0.5 CD A:GLU56 3.1 24.9 0.4 OE1 A:GLU56 3.2 25.6 0.4 O1B A:6U4201 3.3 16.9 0.5 C A:GLY36 3.6 10.9 1.0 HA3 A:GLY37 3.6 12.5 1.0 HA2 A:GLY37 3.6 12.5 1.0 PA A:6U4201 3.7 15.4 1.0 O3A A:6U4201 3.8 15.0 1.0 PB A:6U4201 3.8 19.6 0.5 O A:HOH395 3.9 59.2 1.0 OE1 A:GLU56 3.9 14.3 0.6 CA A:GLY37 4.0 10.4 1.0 PB A:6U4201 4.1 13.9 0.5 H A:GLY36 4.1 12.7 1.0 O A:HOH321 4.1 46.0 1.0 O5' A:6U4201 4.2 13.3 1.0 OE1 A:GLU52 4.2 22.6 1.0 N A:GLY37 4.2 9.7 1.0 O A:HOH356 4.4 49.0 1.0 CD A:GLU56 4.4 15.7 0.6 O A:HOH368 4.4 14.7 1.0 CG A:GLU56 4.5 23.5 0.4 OE2 A:GLU56 4.5 19.5 0.6 C4' A:6U4201 4.6 11.9 1.0 O2B A:6U4201 4.7 14.4 0.5 HG2 A:GLU56 4.7 28.2 0.4 HG3 A:GLU56 4.7 28.2 0.4 N A:GLY36 4.7 10.6 1.0 O2B A:6U4201 4.8 20.2 0.5 CA A:GLY36 4.8 10.7 1.0 C5' A:6U4201 4.9 12.5 1.0 O3B A:6U4201 4.9 25.9 0.5

Sodium binding site 3 out of 4 in the Crystal Structure of Human MTH1(G2K/D120N 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/D120N 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:29.4 occ:0.57 NA B:NA202 0.0 29.4 0.6 NA B:NA202 1.5 39.0 0.4 OE2 B:GLU56 2.2 28.7 0.6 O1A B:6U4201 2.3 33.2 1.0 O B:HOH349 2.4 25.7 1.0 O B:GLY36 2.4 14.1 1.0 O2B B:6U4201 2.5 54.7 1.0 O B:HOH420 2.5 55.1 1.0 CD B:GLU56 3.3 27.2 0.6 HA3 B:GLY37 3.5 13.5 1.0 PA B:6U4201 3.5 33.7 1.0 PB B:6U4201 3.6 52.6 1.0 O3A B:6U4201 3.6 42.5 1.0 C B:GLY36 3.6 12.8 1.0 HA2 B:GLY37 3.7 13.5 1.0 OE1 B:GLU56 3.7 27.5 0.6 OE1 B:GLU52 3.9 28.3 1.0 CA B:GLY37 4.0 11.2 1.0 HZ1 B:LYS23 4.0 62.1 1.0 OE1 B:GLU56 4.1 23.3 0.4 O5' B:6U4201 4.1 23.9 1.0 H B:GLY36 4.2 14.8 1.0 N B:GLY37 4.3 11.0 1.0 HE3 B:LYS23 4.4 60.8 1.0 CD B:GLU56 4.4 23.2 0.4 O B:HOH347 4.4 16.8 1.0 HG2 B:GLU56 4.5 30.5 0.6 OE2 B:GLU56 4.5 23.0 0.4 CG B:GLU56 4.5 25.4 0.6 C4' B:6U4201 4.6 13.6 1.0 O3B B:6U4201 4.6 61.3 1.0 O1B B:6U4201 4.7 51.7 1.0 NZ B:LYS23 4.7 51.7 1.0 N B:GLY36 4.8 12.3 1.0 HG3 B:GLU56 4.8 30.5 0.6 HZ2 B:LYS23 4.8 62.1 1.0 CA B:GLY36 4.8 12.8 1.0 O2A B:6U4201 4.8 38.1 1.0 CD B:GLU52 4.9 27.0 1.0 C5' B:6U4201 4.9 16.8 1.0 O B:HOH303 5.0 50.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human MTH1(G2K/D120N 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/D120N 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:39.0 occ:0.43 NA B:NA202 0.0 39.0 0.4 NA B:NA202 1.5 29.4 0.6 OE2 B:GLU56 1.7 28.7 0.6 O2B B:6U4201 2.2 54.7 1.0 O B:GLY36 2.6 14.1 1.0 OE1 B:GLU52 2.6 28.3 1.0 CD B:GLU56 2.8 27.2 0.6 HA3 B:GLY37 3.0 13.5 1.0 O B:HOH420 3.1 55.1 1.0 O B:HOH349 3.4 25.7 1.0 PB B:6U4201 3.5 52.6 1.0 C B:GLY36 3.5 12.8 1.0 O1A B:6U4201 3.6 33.2 1.0 CD B:GLU52 3.6 27.0 1.0 OE1 B:GLU56 3.6 27.5 0.6 CA B:GLY37 3.7 11.2 1.0 CG B:GLU56 3.8 25.4 0.6 HG2 B:GLU56 3.8 30.5 0.6 HG3 B:GLU56 3.8 30.5 0.6 HA2 B:GLY37 3.8 13.5 1.0 O B:HOH303 3.9 50.3 1.0 O B:HOH318 4.0 52.9 1.0 O3A B:6U4201 4.0 42.5 1.0 OE1 B:GLU56 4.0 23.3 0.4 OE2 B:GLU52 4.0 30.5 1.0 N B:GLY37 4.1 11.0 1.0 H B:GLY36 4.2 14.8 1.0 O1B B:6U4201 4.2 51.7 1.0 HB3 B:GLU52 4.3 23.1 1.0 PA B:6U4201 4.4 33.7 1.0 HB2 B:GLU56 4.5 27.6 0.4 CD B:GLU56 4.5 23.2 0.4 CA B:GLY36 4.7 12.8 1.0 CG B:GLU52 4.7 22.1 1.0 O3B B:6U4201 4.7 61.3 1.0 N B:GLY36 4.8 12.3 1.0 HG3 B:GLU52 4.9 26.6 1.0 H B:GLY37 4.9 13.2 1.0 H B:LYS38 4.9 13.5 1.0 HG3 B:GLU56 4.9 27.7 0.4 HA2 B:GLY36 5.0 15.3 1.0 CB B:GLU52 5.0 19.3 1.0 OE2 B:GLU56 5.0 23.0 0.4

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