Sodium in PDB 9mbe: Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp

All present enzymatic activity of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp:
3.6.1.55; 3.6.1.56;

The structure of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp, PDB code: 9mbe was solved by K.Fujimiya, K.Hirata, A.Ostermann, T.E.Schrader, T.Hiromoto, T.Arimori, Y.Hirano, T.Tamada, T.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.85, 48.16, 124.1, 90, 90, 90
R / Rfree (%)	21.5 / 24

The binding sites of Sodium atom in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp (pdb code 9mbe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp, PDB code: 9mbe:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:18.2 occ:1.00 OE2 A:GLU56 2.2 18.3 1.0 O1A A:8DG201 2.3 15.1 1.0 O A:GLY36 2.3 10.7 1.0 O A:HOH393 2.3 17.5 1.0 O2B A:8DG201 2.4 18.2 1.0 D1 A:HOH393 2.4 20.2 1.0 O A:HOH371 2.7 31.8 1.0 D2 A:HOH393 2.8 20.2 1.0 CD A:GLU56 3.2 16.0 1.0 NA A:NA203 3.3 20.2 1.0 HZ2 A:LYS23 3.3 19.0 0.3 DZ2 A:LYS23 3.3 19.0 0.7 PA A:8DG201 3.4 15.5 1.0 HE3 A:LYS23 3.4 17.3 1.0 PB A:8DG201 3.5 17.2 1.0 O3A A:8DG201 3.5 16.1 1.0 OE1 A:GLU56 3.5 13.7 1.0 C A:GLY36 3.5 9.2 1.0 HA3 A:GLY37 3.7 10.6 1.0 HA2 A:GLY37 3.7 10.6 1.0 HG2 A:GLU100 3.8 40.3 1.0 DZ3 A:LYS23 3.8 19.0 0.7 NZ A:LYS23 3.9 15.8 1.0 HZ3 A:LYS23 3.9 19.0 0.3 D A:GLY36 3.9 9.9 0.8 H A:GLY36 3.9 9.9 0.2 H4' A:8DG201 3.9 11.9 1.0 O5' A:8DG201 4.0 12.4 1.0 CA A:GLY37 4.1 8.8 1.0 CE A:LYS23 4.1 14.4 1.0 OE1 A:GLU52 4.2 18.4 1.0 N A:GLY37 4.3 8.4 1.0 O3B A:8DG201 4.3 21.7 1.0 O A:HOH304 4.4 21.9 1.0 HB3 A:GLU100 4.5 20.8 1.0 O A:HOH377 4.5 12.1 1.0 N A:GLY36 4.6 8.2 1.0 CG A:GLU56 4.6 19.2 1.0 O1G A:8DG201 4.6 29.2 1.0 D2 A:HOH377 4.6 14.5 1.0 HZ1 A:LYS23 4.7 19.0 0.5 DZ1 A:LYS23 4.7 19.0 0.5 CA A:GLY36 4.7 7.9 1.0 O2A A:8DG201 4.7 17.9 1.0 O1B A:8DG201 4.7 14.7 1.0 HG2 A:GLU56 4.7 23.0 1.0 CG A:GLU100 4.7 33.6 1.0 C4' A:8DG201 4.7 9.9 1.0 D2 A:HOH311 4.7 28.4 1.0 HE2 A:LYS23 4.7 17.3 1.0 HD3 A:LYS23 4.8 16.3 1.0 HG3 A:GLU56 4.8 23.0 1.0 D1 A:HOH391 4.9 25.9 1.0 C5' A:8DG201 4.9 11.5 1.0 H3' A:8DG201 5.0 12.1 1.0

Sodium binding site 2 out of 4 in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:20.2 occ:1.00 OE1 A:GLU52 2.3 18.4 1.0 O2B A:8DG201 2.4 18.2 1.0 O A:HOH304 2.4 21.9 1.0 OE2 A:GLU56 2.5 18.3 1.0 O A:HOH315 2.5 31.5 1.0 D1 A:HOH311 2.7 28.4 1.0 D2 A:HOH311 2.8 28.4 1.0 O A:HOH311 2.8 23.6 1.0 CD A:GLU52 3.2 21.5 1.0 NA A:NA202 3.3 18.2 1.0 O A:HOH438 3.3 8.7 0.5 CD A:GLU56 3.4 16.0 1.0 HA3 A:GLY37 3.4 10.6 1.0 HG3 A:GLU56 3.5 23.0 1.0 OE2 A:GLU52 3.5 21.2 1.0 HG2 A:GLU56 3.6 23.0 1.0 PB A:8DG201 3.7 17.2 1.0 CG A:GLU56 3.7 19.2 1.0 HG2 A:GLU100 3.7 40.3 1.0 O A:GLY36 3.8 10.7 1.0 O A:HOH371 4.0 31.8 1.0 O1G A:8DG201 4.1 29.2 1.0 O1B A:8DG201 4.1 14.7 1.0 OE2 A:GLU100 4.1 47.4 1.0 CA A:GLY37 4.3 8.8 1.0 C A:GLY36 4.4 9.2 1.0 HB3 A:GLU52 4.4 14.9 1.0 OE1 A:GLU56 4.5 13.7 1.0 CG A:GLU100 4.6 33.6 1.0 CD A:GLU100 4.6 45.4 1.0 CG A:GLU52 4.6 15.3 1.0 HA2 A:GLY37 4.7 10.6 1.0 OE1 A:GLU55 4.7 28.8 1.0 HA A:GLU52 4.7 15.0 1.0 N A:GLY37 4.7 8.4 1.0 O3B A:8DG201 4.8 21.7 1.0 O3A A:8DG201 4.8 16.1 1.0 D1 A:HOH393 4.8 20.2 1.0 DH11 A:ARG51 4.8 26.2 1.0 O A:HOH438 4.9 19.0 0.5 HB2 A:GLU55 4.9 20.2 1.0 O A:HOH355 4.9 31.9 1.0 CB A:GLU52 5.0 12.4 1.0 HG3 A:GLU52 5.0 18.4 1.0

Sodium binding site 3 out of 4 in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:26.2 occ:0.62 NA B:NA202 0.0 26.2 0.6 NA B:NA202 1.9 27.3 0.4 O1A B:8DG201 2.0 42.0 1.0 O B:HOH352 2.3 23.9 1.0 OE2 B:GLU56 2.4 29.6 1.0 O B:GLY36 2.4 12.2 1.0 O2B B:8DG201 2.5 91.6 1.0 PA B:8DG201 3.3 54.1 1.0 CD B:GLU56 3.4 27.7 1.0 C B:GLY36 3.6 10.6 1.0 HA3 B:GLY37 3.7 11.2 1.0 HA2 B:GLY37 3.7 11.2 1.0 OE1 B:GLU56 3.7 17.5 1.0 PB B:8DG201 3.7 89.0 1.0 H4' B:8DG201 3.8 40.0 1.0 O3A B:8DG201 3.8 79.1 1.0 D B:GLY36 3.9 14.8 0.7 H B:GLY36 3.9 14.8 0.3 O5' B:8DG201 4.0 41.1 1.0 CA B:GLY37 4.0 9.3 1.0 N B:GLY37 4.3 9.5 1.0 OE1 B:GLU52 4.4 22.6 1.0 O2A B:8DG201 4.5 58.6 1.0 N B:GLY36 4.6 12.4 1.0 O B:HOH358 4.6 20.1 1.0 CG B:GLU56 4.6 27.8 1.0 O1B B:8DG201 4.7 59.3 1.0 C4' B:8DG201 4.7 33.4 1.0 CA B:GLY36 4.7 11.1 1.0 HG2 B:GLU56 4.7 33.4 1.0 C5' B:8DG201 4.8 38.0 1.0 O B:HOH316 4.8 38.4 1.0 HG3 B:GLU56 4.8 33.4 1.0 H5'1 B:8DG201 4.8 45.6 1.0 O3B B:8DG201 4.9 98.0 1.0 O2G B:8DG201 4.9 101.8 1.0 O1G B:8DG201 5.0 105.2 1.0

Sodium binding site 4 out of 4 in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:27.3 occ:0.38 NA B:NA202 0.0 27.3 0.4 NA B:NA202 1.9 26.2 0.6 OE2 B:GLU56 2.2 29.6 1.0 O2B B:8DG201 2.4 91.6 1.0 O B:GLY36 2.6 12.2 1.0 OE1 B:GLU52 2.7 22.6 1.0 HA3 B:GLY37 3.0 11.2 1.0 CD B:GLU56 3.1 27.7 1.0 O B:HOH316 3.2 38.4 1.0 C B:GLY36 3.6 10.6 1.0 O1A B:8DG201 3.6 42.0 1.0 CD B:GLU52 3.6 22.1 1.0 PB B:8DG201 3.7 89.0 1.0 HG3 B:GLU56 3.7 33.4 1.0 HG2 B:GLU56 3.8 33.4 1.0 O B:HOH361 3.8 36.3 1.0 CG B:GLU56 3.8 27.8 1.0 CA B:GLY37 3.8 9.3 1.0 O B:HOH352 3.8 23.9 1.0 OE1 B:GLU56 3.9 17.5 1.0 HA2 B:GLY37 3.9 11.2 1.0 OE2 B:GLU52 4.0 22.4 1.0 N B:GLY37 4.1 9.5 1.0 O1B B:8DG201 4.1 59.3 1.0 D B:GLY36 4.1 14.8 0.7 H B:GLY36 4.1 14.8 0.3 O3A B:8DG201 4.4 79.1 1.0 HB3 B:GLU52 4.5 19.4 1.0 PA B:8DG201 4.6 54.1 1.0 CA B:GLY36 4.7 11.1 1.0 O1G B:8DG201 4.7 105.2 1.0 N B:GLY36 4.8 12.4 1.0 CG B:GLU52 4.8 22.2 1.0 D B:LYS38 4.9 12.9 0.8 H B:LYS38 4.9 12.9 0.2 H B:GLY37 4.9 11.3 0.2 D B:GLY37 4.9 11.3 0.8 O3B B:8DG201 5.0 98.0 1.0 HG3 B:GLU52 5.0 26.7 1.0

K.Hirata, K.Fujimiya, A.Ostermann, T.E.Schrader, T.Hiromoto, M.Goto, T.Arimori, Y.Hirano, K.Kusaka, T.Tamada, T.Nakamura. Neutron and Time-Resolved X-Ray Crystallography Reveal the Substrate Recognition and Catalytic Mechanism of Human Nudix Hydrolase MTH1. Proc.Natl.Acad.Sci.Usa V. 122 85122 2025.
ISSN: ESSN 1091-6490
PubMed: 40674425
DOI: 10.1073/PNAS.2510085122