Sodium in PDB 9mbk: 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex

All present enzymatic activity of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex:
3.6.1.55; 3.6.1.56;

The structure of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex, PDB code: 9mbk was solved by K.Hirata, T.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.17 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.541, 47.292, 123.469, 90, 90, 90
R / Rfree (%)	13 / 15.7

The binding sites of Sodium atom in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex (pdb code 9mbk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex, PDB code: 9mbk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:18.2 occ:1.00 O2B A:6U4201 2.2 12.8 1.0 O A:HOH304 2.3 12.8 1.0 O A:HOH387 2.3 20.2 1.0 O1A A:6U4201 2.3 12.4 1.0 O A:HOH307 2.4 25.4 1.0 O A:HOH385 2.5 17.4 1.0 PB A:6U4201 3.4 11.3 1.0 O A:HOH373 3.5 30.6 0.5 O A:HOH322 3.5 23.1 1.0 PA A:6U4201 3.5 10.9 1.0 O3A A:6U4201 3.6 11.2 1.0 O A:HOH373 3.8 20.6 0.5 O A:HOH456 3.8 31.8 1.0 OE2 A:GLU100 3.9 39.9 1.0 OE1 A:GLU56 4.0 22.7 0.4 O3B A:6U4201 4.1 12.1 1.0 O A:HOH321 4.2 17.9 1.0 OE1 A:GLU56 4.3 13.9 0.6 O2G A:6U4201 4.4 21.0 1.0 OE2 A:GLU56 4.5 14.2 0.6 O5' A:6U4201 4.5 10.5 1.0 O2A A:6U4201 4.6 12.9 1.0 CD A:GLU56 4.7 14.4 0.6 O1B A:6U4201 4.7 12.2 1.0 O A:GLY36 4.7 10.1 1.0 CD A:GLU100 4.7 38.9 1.0 HE2 A:LYS23 4.7 58.7 1.0 PG A:6U4201 4.7 11.5 1.0 O1G A:6U4201 4.8 18.0 1.0 O A:HOH384 4.9 19.4 1.0 HA3 A:GLY37 4.9 11.0 1.0 HA2 A:GLY37 4.9 11.0 1.0 OE1 A:GLU100 5.0 40.0 1.0 O A:HOH320 5.0 35.8 1.0

Sodium binding site 2 out of 4 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:15.6 occ:1.00 O A:HOH371 2.3 15.3 1.0 O A:HOH327 2.4 26.9 1.0 O1B A:6U4201 2.4 12.2 1.0 O A:HOH346 2.4 18.9 1.0 OE2 A:GLU52 2.4 14.9 1.0 O A:HOH321 2.5 17.9 1.0 HH12 A:ARG51 3.4 23.1 1.0 H A:LYS38 3.4 11.6 1.0 CD A:GLU52 3.4 14.8 1.0 PB A:6U4201 3.5 11.3 1.0 HE21 A:GLN40 3.6 23.1 1.0 OE1 A:GLU52 3.6 14.1 1.0 O2B A:6U4201 3.8 12.8 1.0 O A:HOH495 3.9 38.1 1.0 HB2 A:LYS38 3.9 11.3 1.0 HA3 A:GLY37 3.9 11.0 1.0 N A:LYS38 4.0 9.6 1.0 O1G A:6U4201 4.1 18.0 1.0 HH22 A:ARG51 4.1 22.5 1.0 O A:LYS38 4.1 11.3 1.0 NH1 A:ARG51 4.2 19.2 1.0 O A:HOH525 4.2 31.7 1.0 NE2 A:GLN40 4.3 19.3 1.0 O3B A:6U4201 4.4 12.1 1.0 HE22 A:GLN40 4.4 23.1 1.0 O A:HOH374 4.5 22.0 1.0 OE1 A:GLU55 4.5 24.9 1.0 O A:HOH322 4.6 23.1 1.0 O A:HOH523 4.6 53.7 1.0 HH11 A:ARG51 4.6 23.1 1.0 CB A:LYS38 4.7 9.4 1.0 CA A:GLY37 4.7 9.2 1.0 O3A A:6U4201 4.7 11.2 1.0 CA A:LYS38 4.8 9.6 1.0 C A:GLY37 4.8 9.2 1.0 CG A:GLU52 4.8 14.0 1.0 NH2 A:ARG51 4.8 18.8 1.0 C A:LYS38 4.9 9.6 1.0 PG A:6U4201 4.9 11.5 1.0 HD2 A:LYS38 4.9 12.2 1.0 HG2 A:GLU52 5.0 16.8 1.0 CZ A:ARG51 5.0 18.9 1.0

Sodium binding site 3 out of 4 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:38.9 occ:1.00 OE2 B:GLU56 2.3 26.8 1.0 O B:HOH1155 2.3 24.8 1.0 O1A B:6U41001 2.4 24.3 1.0 O B:GLY36 2.5 12.4 1.0 O B:HOH1103 2.5 51.0 1.0 O1B B:6U41001 2.7 35.1 1.0 O B:HOH1102 3.1 37.2 1.0 CD B:GLU56 3.4 25.3 1.0 PA B:6U41001 3.5 23.6 1.0 HZ2 B:LYS23 3.6 47.0 1.0 C B:GLY36 3.6 10.2 1.0 O3A B:6U41001 3.7 26.2 1.0 HA3 B:GLY37 3.7 12.6 1.0 HA2 B:GLY37 3.7 12.6 1.0 PB B:6U41001 3.8 31.2 1.0 OE1 B:GLU56 3.8 23.6 1.0 HG3 B:GLU100 3.9 40.3 0.5 HZ1 B:LYS23 3.9 47.0 1.0 O5' B:6U41001 4.0 17.2 1.0 H B:GLY36 4.1 11.2 1.0 CA B:GLY37 4.1 10.4 1.0 NZ B:LYS23 4.2 39.1 1.0 OE1 B:GLU52 4.2 23.2 1.0 N B:GLY37 4.3 10.0 1.0 O B:HOH1142 4.4 16.6 1.0 C4' B:6U41001 4.6 12.6 1.0 CG B:GLU56 4.6 24.3 1.0 HG2 B:GLU56 4.6 29.2 1.0 HZ3 B:LYS23 4.7 47.0 1.0 O2B B:6U41001 4.7 29.1 1.0 N B:GLY36 4.7 9.3 1.0 C5' B:6U41001 4.8 13.9 1.0 CA B:GLY36 4.8 9.7 1.0 CG B:GLU100 4.8 33.6 0.5 HG3 B:GLU56 4.8 29.2 1.0 O2A B:6U41001 4.9 25.0 1.0

Sodium binding site 4 out of 4 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1003 b:41.2 occ:1.00 O B:HOH1250 2.3 42.9 1.0 OE2 B:GLU52 2.4 23.5 1.0 O2B B:6U41001 2.4 29.1 1.0 O B:HOH1180 2.6 22.5 1.0 O B:HOH1102 2.8 37.2 1.0 CD B:GLU52 3.3 21.3 1.0 HH12 B:ARG51 3.3 28.6 1.0 PB B:6U41001 3.3 31.2 1.0 O1B B:6U41001 3.4 35.1 1.0 O B:HOH1246 3.5 55.8 1.0 HA3 B:GLY37 3.5 12.6 1.0 OE1 B:GLU52 3.5 23.2 1.0 H B:LYS38 3.6 12.0 1.0 O B:HOH1111 3.7 47.2 1.0 NH1 B:ARG51 4.2 23.8 1.0 N B:LYS38 4.2 10.0 1.0 O3G B:6U41001 4.2 50.3 1.0 HB2 B:LYS38 4.3 16.0 1.0 HE21 B:GLN40 4.3 32.9 1.0 O3B B:6U41001 4.3 40.9 1.0 HH22 B:ARG51 4.4 23.7 1.0 CA B:GLY37 4.4 10.4 1.0 O B:LYS38 4.5 14.2 1.0 HH11 B:ARG51 4.6 28.6 1.0 O3A B:6U41001 4.6 26.2 1.0 CG B:GLU52 4.7 18.9 1.0 C B:GLY37 4.7 10.2 1.0 OE1 B:GLU55 4.8 34.5 1.0 HA2 B:GLY37 4.8 12.6 1.0 PG B:6U41001 4.8 49.0 1.0 HG2 B:GLU52 4.9 22.7 1.0 HG3 B:GLU52 5.0 22.7 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