Sodium in PDB 8i1h: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.7

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.7:
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 9.7, PDB code: 8i1h 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)	33.20 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.979, 47.995, 123.977, 90, 90, 90
R / Rfree (%)	13.5 / 16.6

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.7 (pdb code 8i1h). 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 Mutant) in Complex with 2-Oxo-Datp at pH 9.7, PDB code: 8i1h:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.7


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 9.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:61.4 occ:1.00 OE2 A:GLU56 2.3 28.2 0.5 O A:GLY36 2.5 16.1 1.0 O A:HOH312 2.7 41.7 1.0 O A:HOH454 2.9 43.2 1.0 CD A:GLU56 3.3 24.0 0.5 HA3 A:GLY37 3.5 14.7 1.0 HA2 A:GLY37 3.5 14.7 1.0 C A:GLY36 3.7 12.9 1.0 OE1 A:GLU56 3.8 24.6 0.5 CA A:GLY37 3.9 12.3 1.0 OE1 A:GLU52 4.2 31.0 1.0 OE1 A:GLU56 4.2 26.6 0.5 O A:HOH407 4.2 28.4 1.0 N A:GLY37 4.2 12.3 1.0 H A:GLY36 4.3 14.6 1.0 CG A:GLU56 4.4 22.8 0.5 HG2 A:GLU56 4.5 27.3 0.5 HG3 A:GLU56 4.5 27.3 0.5 HE1 A:MET101 4.7 36.2 0.5 CD A:GLU56 4.8 27.5 0.5 CA A:GLY36 4.9 13.8 1.0 N A:GLY36 4.9 12.2 1.0 O A:HOH363 5.0 36.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.7


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 9.7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:18.3 occ:1.00 O A:HOH439 2.1 36.0 1.0 O3 A:GOL202 2.3 22.3 1.0 OD1 A:ASP120 2.3 14.6 1.0 OD2 A:ASP119 2.4 13.2 1.0 O A:HOH386 2.4 40.1 1.0 HB2 A:TRP117 2.8 17.9 1.0 CG A:ASP119 3.0 12.1 1.0 OD1 A:ASP119 3.0 12.9 1.0 HZ2 A:TRP123 3.2 15.7 1.0 HB3 A:TRP117 3.3 17.9 1.0 HZ A:PHE72 3.3 16.3 1.0 HE1 A:TRP123 3.4 13.9 1.0 CG A:ASP120 3.4 13.8 1.0 CB A:TRP117 3.5 14.9 1.0 C3 A:GOL202 3.5 26.4 1.0 O2 A:GOL202 3.8 33.5 1.0 C2 A:GOL202 3.9 32.9 1.0 OD2 A:ASP120 3.9 15.2 1.0 CZ A:PHE72 3.9 13.6 1.0 H A:ASP120 4.0 13.2 1.0 CZ2 A:TRP123 4.1 13.1 1.0 CG A:TRP117 4.1 17.4 1.0 NE1 A:TRP123 4.2 11.6 1.0 O A:HOH328 4.2 13.8 1.0 HD21 A:ASN33 4.2 30.2 0.8 HE1 A:PHE72 4.3 15.8 1.0 N A:ASP120 4.4 11.0 1.0 CB A:ASP119 4.4 12.2 1.0 CE1 A:PHE72 4.5 13.2 1.0 CE2 A:TRP123 4.5 11.1 1.0 O A:HOH436 4.5 16.4 0.4 HA A:ASP120 4.6 13.3 1.0 H A:ASP119 4.7 13.9 1.0 CB A:ASP120 4.7 11.4 1.0 CD1 A:TRP117 4.7 19.1 1.0 HD1 A:TRP117 4.7 22.9 1.0 HB2 A:ASP119 4.7 14.7 1.0 CA A:TRP117 4.7 13.4 1.0 H A:TRP117 4.7 14.7 1.0 ND2 A:ASN33 4.7 25.2 0.8 CE2 A:PHE72 4.8 14.7 1.0 HE2 A:PHE72 4.8 17.6 1.0 CA A:ASP120 4.8 11.1 1.0 HD22 A:LEU9 4.8 19.0 1.0 HD21 A:LEU9 4.9 19.0 1.0 O A:TRP117 4.9 12.1 1.0 CD2 A:TRP117 4.9 17.8 1.0 C A:ASP119 5.0 10.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 2-Oxo-Datp at pH 9.7


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 9.7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:17.4 occ:1.00 O B:HOH350 2.2 30.9 0.6 O3 B:GOL201 2.3 32.0 1.0 OD2 B:ASP119 2.3 13.1 1.0 OD1 B:ASP120 2.3 16.7 1.0 O B:HOH350 2.4 18.9 0.4 HB2 B:TRP117 2.8 18.2 1.0 OD1 B:ASP119 2.9 14.1 1.0 CG B:ASP119 2.9 12.0 1.0 HB3 B:TRP117 3.3 18.2 1.0 HZ2 B:TRP123 3.3 15.5 1.0 HZ B:PHE72 3.4 15.3 1.0 HE1 B:TRP123 3.4 13.2 1.0 CG B:ASP120 3.5 13.2 1.0 CB B:TRP117 3.5 15.1 1.0 C3 B:GOL201 3.5 41.7 1.0 O2 B:GOL201 3.7 49.1 1.0 OD2 B:ASP120 4.0 14.9 1.0 H B:ASP120 4.0 13.2 1.0 CZ B:PHE72 4.0 12.8 1.0 NE1 B:TRP123 4.2 11.0 1.0 CG B:TRP117 4.2 19.1 1.0 C2 B:GOL201 4.2 46.5 1.0 CZ2 B:TRP123 4.2 12.9 1.0 O B:HOH329 4.2 14.0 1.0 HD21 B:ASN33 4.3 32.5 0.8 HE1 B:PHE72 4.3 16.8 1.0 N B:ASP120 4.4 11.0 1.0 CB B:ASP119 4.4 12.2 1.0 CE1 B:PHE72 4.5 14.0 1.0 CE2 B:TRP123 4.5 11.2 1.0 H B:ASP119 4.6 14.5 1.0 HA B:ASP120 4.6 12.8 1.0 HD1 B:TRP117 4.6 26.1 1.0 HD12 B:ILE70 4.7 21.7 0.2 HB2 B:ASP119 4.7 14.7 1.0 CD1 B:TRP117 4.7 21.7 1.0 O B:HOH398 4.7 28.5 0.5 CB B:ASP120 4.7 11.1 1.0 HD22 B:LEU9 4.7 17.6 1.0 CA B:TRP117 4.8 14.4 1.0 H B:TRP117 4.8 15.1 1.0 HD11 B:ILE70 4.8 21.7 0.2 ND2 B:ASN33 4.8 27.1 0.8 CA B:ASP120 4.8 10.7 1.0 CE2 B:PHE72 4.9 13.4 1.0 O B:TRP117 4.9 12.8 1.0 HD21 B:LEU9 4.9 17.6 1.0 HB3 B:ASP119 4.9 14.7 1.0 C B:ASP119 4.9 11.1 1.0 HE2 B:PHE72 4.9 16.1 1.0 C B:TRP117 5.0 12.3 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