Sodium in PDB 8i18: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 7.7

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 7.7, PDB code: 8i18 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)	33.29 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.442, 47.754, 124.159, 90, 90, 90
R / Rfree (%)	14.5 / 16.9

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 7.7 (pdb code 8i18). 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 8-Oxo-Dgtp at pH 7.7, PDB code: 8i18:
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 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:13.3 occ:1.00 O2A A:8DG201 2.3 12.1 1.0 OE2 A:GLU56 2.3 13.0 1.0 O A:GLY36 2.3 9.4 1.0 O1B A:8DG201 2.4 12.6 1.0 O A:HOH373 2.4 11.9 1.0 O A:HOH426 2.8 28.8 1.0 CD A:GLU56 3.2 11.4 1.0 NA A:NA203 3.3 15.2 1.0 HE3 A:LYS23 3.3 14.1 1.0 HZ1 A:LYS23 3.4 14.9 1.0 PA A:8DG201 3.4 10.8 1.0 PB A:8DG201 3.5 12.4 1.0 OE1 A:GLU56 3.5 11.0 1.0 C A:GLY36 3.5 7.6 1.0 O3A A:8DG201 3.5 11.1 1.0 HZ2 A:LYS23 3.6 14.9 1.0 HA3 A:GLY37 3.7 9.8 1.0 HA2 A:GLY37 3.7 9.8 1.0 NZ A:LYS23 3.8 12.4 1.0 H A:GLY36 3.9 9.1 1.0 HG2 A:GLU100 3.9 24.6 1.0 CE A:LYS23 4.0 11.8 1.0 CA A:GLY37 4.1 8.2 1.0 O5' A:8DG201 4.2 10.1 1.0 N A:GLY37 4.3 7.6 1.0 O3B A:8DG201 4.3 13.6 1.0 OE1 A:GLU52 4.3 15.0 1.0 HB3 A:GLU100 4.4 19.2 1.0 O A:HOH368 4.5 10.3 1.0 O A:HOH316 4.5 19.1 1.0 N A:GLY36 4.6 7.5 1.0 CG A:GLU56 4.6 11.8 1.0 HE2 A:LYS23 4.6 14.1 1.0 CA A:GLY36 4.7 8.4 1.0 HZ3 A:LYS23 4.7 14.9 1.0 O1A A:8DG201 4.7 11.7 1.0 O2B A:8DG201 4.7 11.8 1.0 C4' A:8DG201 4.7 9.7 1.0 O2G A:8DG201 4.7 22.6 1.0 HG2 A:GLU56 4.7 14.1 1.0 HD3 A:LYS23 4.8 14.6 1.0 CG A:GLU100 4.8 20.5 1.0 HG3 A:GLU56 4.8 14.1 1.0 C5' A:8DG201 5.0 10.7 1.0 O3' A:8DG201 5.0 9.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:15.2 occ:1.00 OE1 A:GLU52 2.3 15.0 1.0 O A:HOH316 2.3 19.1 1.0 O1B A:8DG201 2.4 12.6 1.0 OE2 A:GLU56 2.4 13.0 1.0 O A:HOH306 2.5 23.7 1.0 O A:HOH311 3.0 19.9 1.0 NA A:NA202 3.3 13.3 1.0 CD A:GLU52 3.3 14.3 1.0 O A:HOH486 3.3 16.4 1.0 CD A:GLU56 3.4 11.4 1.0 HG3 A:GLU56 3.4 14.1 1.0 HA3 A:GLY37 3.5 9.8 1.0 OE2 A:GLU52 3.6 17.7 1.0 HG2 A:GLU100 3.6 24.6 1.0 HG2 A:GLU56 3.7 14.1 1.0 PB A:8DG201 3.7 12.4 1.0 CG A:GLU56 3.7 11.8 1.0 O A:GLY36 3.8 9.4 1.0 O2B A:8DG201 4.1 11.8 1.0 O A:HOH426 4.1 28.8 1.0 O2G A:8DG201 4.2 22.6 1.0 OE1 A:GLU56 4.4 11.0 1.0 OE2 A:GLU100 4.4 24.1 1.0 CA A:GLY37 4.4 8.2 1.0 HB3 A:GLU52 4.4 13.8 1.0 C A:GLY36 4.5 7.6 1.0 CG A:GLU100 4.5 20.5 1.0 CG A:GLU52 4.6 13.5 1.0 CD A:GLU100 4.7 22.2 1.0 HA A:GLU52 4.7 11.8 1.0 OE1 A:GLU55 4.7 26.6 1.0 O3B A:8DG201 4.7 13.6 1.0 HA2 A:GLY37 4.7 9.8 1.0 N A:GLY37 4.8 7.6 1.0 O3A A:8DG201 4.8 11.1 1.0 HH12 A:ARG51 4.8 20.7 1.0 O A:HOH439 4.9 27.4 1.0 HB2 A:GLU55 4.9 18.7 1.0 CB A:GLU52 5.0 11.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:17.7 occ:0.55 NA B:NA202 0.0 17.7 0.6 NA B:NA202 1.8 23.8 0.5 OE2 B:GLU56 2.2 17.0 1.0 O1A B:8DG201 2.2 28.4 1.0 O B:GLY36 2.3 11.5 1.0 O2B B:8DG201 2.4 45.8 1.0 O B:HOH399 2.4 23.1 1.0 HZ2 B:LYS23 3.2 63.6 1.0 CD B:GLU56 3.3 14.6 1.0 PA B:8DG201 3.4 24.6 1.0 HE3 B:LYS23 3.4 62.8 1.0 C B:GLY36 3.5 9.7 1.0 HA3 B:GLY37 3.6 10.8 1.0 PB B:8DG201 3.6 38.1 1.0 HZ1 B:LYS23 3.6 63.6 1.0 HA2 B:GLY37 3.7 10.8 1.0 OE1 B:GLU56 3.7 13.8 1.0 O3A B:8DG201 3.7 31.6 1.0 NZ B:LYS23 3.7 53.0 1.0 O B:HOH320 3.8 52.1 1.0 H B:GLY36 3.9 10.3 1.0 CA B:GLY37 4.0 9.0 1.0 O5' B:8DG201 4.0 19.0 1.0 CE B:LYS23 4.0 52.3 1.0 OE1 B:GLU52 4.1 21.4 1.0 N B:GLY37 4.2 8.7 1.0 HD3 B:LYS23 4.4 61.4 1.0 CG B:GLU56 4.5 14.9 1.0 HZ3 B:LYS23 4.5 63.6 1.0 O1B B:8DG201 4.6 34.5 1.0 HE1 B:MET101 4.6 43.7 0.3 N B:GLY36 4.6 8.6 1.0 HG2 B:GLU56 4.6 17.9 1.0 O B:HOH351 4.6 15.1 1.0 HG2 B:LYS23 4.6 59.4 1.0 CA B:GLY36 4.7 9.0 1.0 O B:HOH304 4.7 47.3 1.0 HG3 B:GLU56 4.7 17.9 1.0 O2A B:8DG201 4.7 28.5 1.0 CD B:LYS23 4.7 51.2 1.0 O3B B:8DG201 4.8 42.7 1.0 C4' B:8DG201 4.8 13.9 1.0 HE2 B:LYS23 4.8 62.8 1.0 HE2 B:MET101 4.8 43.7 0.3 C5' B:8DG201 4.9 16.4 1.0 O1G B:8DG201 4.9 49.9 1.0 CD B:GLU52 5.0 20.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp 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 8-Oxo-Dgtp at pH 7.7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:23.8 occ:0.45 NA B:NA202 0.0 23.8 0.5 NA B:NA202 1.8 17.7 0.6 OE2 B:GLU56 2.2 17.0 1.0 O2B B:8DG201 2.2 45.8 1.0 OE1 B:GLU52 2.5 21.4 1.0 O B:GLY36 2.5 11.5 1.0 HA3 B:GLY37 2.9 10.8 1.0 O B:HOH304 3.2 47.3 1.0 CD B:GLU56 3.2 14.6 1.0 CD B:GLU52 3.4 20.9 1.0 PB B:8DG201 3.5 38.1 1.0 C B:GLY36 3.5 9.7 1.0 O B:HOH323 3.6 29.7 1.0 CA B:GLY37 3.7 9.0 1.0 O1A B:8DG201 3.7 28.4 1.0 HG3 B:GLU56 3.8 17.9 1.0 HA2 B:GLY37 3.8 10.8 1.0 OE2 B:GLU52 3.8 23.9 1.0 O B:HOH320 3.8 52.1 1.0 CG B:GLU56 3.9 14.9 1.0 O1B B:8DG201 3.9 34.5 1.0 OE1 B:GLU56 3.9 13.8 1.0 O B:HOH399 4.0 23.1 1.0 HG2 B:GLU56 4.0 17.9 1.0 N B:GLY37 4.0 8.7 1.0 O3A B:8DG201 4.1 31.6 1.0 H B:GLY36 4.2 10.3 1.0 HB3 B:GLU52 4.3 17.8 1.0 O1G B:8DG201 4.5 49.9 1.0 PA B:8DG201 4.5 24.6 1.0 CG B:GLU52 4.6 18.1 1.0 CA B:GLY36 4.7 9.0 1.0 HG3 B:GLU52 4.7 21.8 1.0 H B:LYS38 4.8 10.7 1.0 O3B B:8DG201 4.8 42.7 1.0 N B:GLY36 4.8 8.6 1.0 H B:GLY37 4.8 10.4 1.0 HE3 B:LYS23 4.8 62.8 1.0 CB B:GLU52 4.9 14.8 1.0 HA2 B:GLY36 4.9 10.8 1.0 C B:GLY37 5.0 9.1 1.0 HZ2 B:LYS23 5.0 63.6 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