Sodium in PDB 8i1c: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 9.1

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 9.1:
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 9.1, PDB code: 8i1c 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)	30.63 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.799, 47.96, 123.627, 90, 90, 90
R / Rfree (%)	15.3 / 18.4

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp at pH 9.1 (pdb code 8i1c). 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 9.1, PDB code: 8i1c:
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 9.1


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 9.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:12.6 occ:1.00 OD1 A:ASP120 2.3 10.7 1.0 O A:HOH346 2.3 17.4 1.0 O A:HOH402 2.3 22.8 1.0 O A:HOH463 2.4 19.7 1.0 OD2 A:ASP119 2.5 10.7 1.0 OD1 A:ASP119 3.1 10.7 1.0 CG A:ASP119 3.1 11.4 1.0 CG A:ASP120 3.4 9.1 1.0 CB A:TRP117 3.6 12.0 1.0 O A:HOH475 3.8 18.7 0.5 OD2 A:ASP120 3.9 12.2 1.0 CZ A:PHE72 4.0 7.7 1.0 CZ2 A:TRP123 4.1 9.1 1.0 O A:HOH475 4.1 24.5 0.5 NE1 A:TRP123 4.1 8.8 1.0 CG A:TRP117 4.1 12.6 1.0 O A:HOH325 4.2 11.3 1.0 CE2 A:TRP123 4.5 8.1 1.0 N A:ASP120 4.5 7.9 1.0 O A:HOH454 4.5 35.5 1.0 CE2 A:PHE72 4.5 8.9 1.0 CB A:ASP119 4.6 8.9 1.0 CD1 A:TRP117 4.7 14.1 1.0 OD1 A:ASN33 4.7 21.1 1.0 CB A:ASP120 4.7 8.7 1.0 CE1 A:PHE72 4.8 8.6 1.0 CA A:TRP117 4.8 9.7 1.0 CA A:ASP120 4.9 8.7 1.0 CD2 A:TRP117 5.0 12.4 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 9.1


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 9.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:19.4 occ:1.00 O A:PHE113 2.1 13.7 1.0 O A:HOH386 2.5 13.0 1.0 O A:MET116 2.8 11.2 1.0 C A:PHE113 3.2 11.4 1.0 C A:MET116 3.8 8.9 1.0 CA A:LYS114 3.9 16.5 1.0 N A:LYS114 4.0 13.8 1.0 C A:LYS114 4.0 14.3 1.0 N A:MET116 4.1 7.8 1.0 O A:TRP117 4.2 9.0 1.0 CA A:PHE113 4.2 9.2 1.0 O A:LYS114 4.2 16.1 1.0 C A:TRP117 4.3 8.5 1.0 OG A:SER121 4.4 16.8 1.0 CA A:MET116 4.4 7.3 1.0 CB A:PHE113 4.4 9.2 1.0 CA A:PRO118 4.4 9.8 1.0 N A:PRO118 4.5 9.2 1.0 N A:ASP115 4.6 11.6 1.0 CB A:MET116 4.6 8.7 1.0 N A:TRP117 4.8 9.2 1.0 O A:HOH470 5.0 21.6 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 9.1


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 9.1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:27.5 occ:1.00 OE2 A:GLU56 2.2 21.4 1.0 O A:HOH469 2.3 40.1 1.0 O A:GLY36 2.3 12.1 1.0 O A:HOH318 2.4 28.7 1.0 O A:HOH468 2.4 37.8 1.0 O A:HOH306 3.0 27.1 1.0 CD A:GLU56 3.2 19.6 1.0 C A:GLY36 3.5 9.4 1.0 OE1 A:GLU56 3.6 17.2 1.0 NZ A:LYS23 3.7 48.0 1.0 O A:HOH478 3.8 40.4 1.0 O A:HOH482 4.0 49.2 1.0 CA A:GLY37 4.0 9.7 1.0 N A:GLY37 4.2 9.6 1.0 OE1 A:GLU52 4.3 22.2 1.0 CG A:GLU56 4.4 18.3 1.0 O A:HOH378 4.5 26.0 1.0 O A:HOH416 4.6 18.1 1.0 N A:GLY36 4.6 10.3 1.0 CA A:GLY36 4.7 10.2 1.0 O A:HOH492 4.7 42.0 1.0 CE A:LYS23 4.9 46.9 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 9.1


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 9.1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:11.8 occ:1.00 OD1 B:ASP120 2.3 11.8 1.0 O B:HOH390 2.3 26.1 1.0 O B:HOH452 2.4 36.2 1.0 O3 B:GOL202 2.4 19.6 1.0 OD2 B:ASP119 2.4 11.5 1.0 O B:HOH332 2.5 23.9 1.0 OD1 B:ASP119 2.9 11.2 1.0 CG B:ASP119 3.0 11.4 1.0 CG B:ASP120 3.4 9.1 1.0 CB B:TRP117 3.6 13.3 1.0 C3 B:GOL202 3.7 17.7 1.0 O2 B:GOL202 3.8 50.7 1.0 OD2 B:ASP120 3.9 12.2 1.0 CZ B:PHE72 4.0 12.4 1.0 NE1 B:TRP123 4.1 9.6 1.0 CZ2 B:TRP123 4.1 9.4 1.0 O B:HOH352 4.1 10.0 1.0 C2 B:GOL202 4.2 36.3 1.0 CG B:TRP117 4.2 15.9 1.0 N B:ASP120 4.4 9.2 1.0 CB B:ASP119 4.4 10.6 1.0 CE2 B:TRP123 4.5 9.6 1.0 CE2 B:PHE72 4.5 12.2 1.0 CB B:ASP120 4.6 7.4 1.0 O B:HOH446 4.7 32.5 1.0 CD1 B:TRP117 4.7 17.4 1.0 OD1 B:ASN33 4.7 16.1 1.0 CA B:ASP120 4.8 7.8 1.0 CA B:TRP117 4.8 12.0 1.0 CE1 B:PHE72 4.9 13.0 1.0 C B:ASP119 5.0 8.4 1.0 O B:TRP117 5.0 10.6 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