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Sodium in PDB 9mbg: 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex

Enzymatic activity of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex

All present enzymatic activity of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex:
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex, PDB code: 9mbg 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) 36.98 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.195, 47.474, 123.407, 90, 90, 90
R / Rfree (%) 13.9 / 18

Sodium Binding Sites:

The binding sites of Sodium atom in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex (pdb code 9mbg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex, PDB code: 9mbg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 9mbg

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Sodium binding site 1 out of 5 in the 8-Oxo-Dgtp 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 8-Oxo-Dgtp 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:13.8
occ:1.00
 O2A A:8DG201 2.3 14.7 1.0
O A:GLY36 2.3 11.2 1.0
OE2 A:GLU56 2.3 15.4 1.0
O A:HOH393 2.4 13.4 1.0
O1B A:8DG201 2.4 15.6 1.0
O A:HOH344 2.7 33.2 1.0
CD A:GLU56 3.3 13.9 1.0
NA A:NA203 3.3 19.7 1.0
HE3 A:LYS23 3.3 17.3 1.0
HZ1 A:LYS23 3.4 16.7 1.0
PA A:8DG201 3.4 13.3 1.0
HZ2 A:LYS23 3.4 16.7 1.0
PB A:8DG201 3.5 15.6 1.0
C A:GLY36 3.5 10.1 1.0
OE1 A:GLU56 3.5 14.0 1.0
O3A A:8DG201 3.5 13.7 1.0
HA3 A:GLY37 3.7 12.1 1.0
NZ A:LYS23 3.7 13.9 1.0
HA2 A:GLY37 3.8 12.1 1.0
H A:GLY36 3.9 11.4 1.0
CE A:LYS23 4.0 14.4 1.0
CA A:GLY37 4.1 10.1 1.0
HG2 A:GLU100 4.1 31.6 1.0
O5' A:8DG201 4.2 12.6 1.0
N A:GLY37 4.2 10.4 1.0
O3B A:8DG201 4.3 18.7 1.0
OE1 A:GLU52 4.3 19.1 1.0
HB3 A:GLU100 4.5 26.5 1.0
O A:HOH377 4.5 11.7 1.0
O2G A:8DG201 4.5 29.2 1.0
O A:HOH304 4.6 24.0 1.0
N A:GLY36 4.6 9.5 1.0
HZ3 A:LYS23 4.6 16.7 1.0
CG A:GLU56 4.6 14.7 1.0
CA A:GLY36 4.6 10.2 1.0
HE2 A:LYS23 4.6 17.3 1.0
C4' A:8DG201 4.7 11.9 1.0
O1A A:8DG201 4.7 14.9 1.0
O2B A:8DG201 4.7 14.3 1.0
HG2 A:GLU56 4.8 17.6 1.0
HD3 A:LYS23 4.8 16.7 1.0
HG3 A:GLU56 4.9 17.6 1.0
C5' A:8DG201 5.0 12.6 1.0
CG A:GLU100 5.0 26.4 1.0

Sodium binding site 2 out of 5 in 9mbg

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Sodium binding site 2 out of 5 in the 8-Oxo-Dgtp 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 8-Oxo-Dgtp 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:19.7
occ:1.00
 OE1 A:GLU52 2.3 19.1 1.0
O1B A:8DG201 2.4 15.6 1.0
O A:HOH304 2.4 24.0 1.0
O A:HOH306 2.4 30.5 1.0
OE2 A:GLU56 2.4 15.4 1.0
O A:HOH318 3.0 22.6 1.0
NA A:NA202 3.3 13.8 1.0
CD A:GLU52 3.3 17.8 1.0
O A:HOH461 3.3 17.7 0.7
CD A:GLU56 3.4 13.9 1.0
HG3 A:GLU56 3.5 17.6 1.0
HA3 A:GLY37 3.5 12.1 1.0
OE2 A:GLU52 3.6 19.2 1.0
HG2 A:GLU56 3.6 17.6 1.0
PB A:8DG201 3.7 15.6 1.0
CG A:GLU56 3.7 14.7 1.0
O A:GLY36 3.8 11.2 1.0
HG2 A:GLU100 3.8 31.6 1.0
O A:HOH344 3.9 33.2 1.0
O2G A:8DG201 4.0 29.2 1.0
O2B A:8DG201 4.1 14.3 1.0
OE2 A:GLU100 4.2 30.4 1.0
OE1 A:GLU56 4.4 14.0 1.0
HB3 A:GLU52 4.4 17.5 1.0
C A:GLY36 4.4 10.1 1.0
CA A:GLY37 4.4 10.1 1.0
OE1 A:GLU55 4.5 28.3 1.0
O A:HOH461 4.6 19.1 0.3
CG A:GLU100 4.6 26.4 1.0
CG A:GLU52 4.6 16.0 1.0
HA A:GLU52 4.6 16.0 1.0
CD A:GLU100 4.7 29.0 1.0
O3B A:8DG201 4.7 18.7 1.0
HH12 A:ARG51 4.7 23.8 1.0
N A:GLY37 4.8 10.4 1.0
HA2 A:GLY37 4.8 12.1 1.0
O A:HOH314 4.8 37.0 1.0
O3A A:8DG201 4.8 13.7 1.0
HB2 A:GLU55 4.9 21.6 1.0
CB A:GLU52 4.9 14.6 1.0

Sodium binding site 3 out of 5 in 9mbg

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Sodium binding site 3 out of 5 in the 8-Oxo-Dgtp 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 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:29.7
occ:0.50
 NA B:NA202 0.0 29.7 0.5
NA B:NA202 1.6 22.0 0.5
O1A B:8DG201 2.2 34.5 1.0
OE2 B:GLU56 2.2 21.6 1.0
O B:GLY36 2.4 15.1 1.0
O2B B:8DG201 2.5 54.9 1.0
O B:HOH398 2.6 29.0 1.0
CD B:GLU56 3.2 19.9 1.0
HE2 B:LYS23 3.2 70.9 1.0
PA B:8DG201 3.5 33.5 1.0
HA3 B:GLY37 3.6 15.9 1.0
HZ3 B:LYS23 3.6 72.5 1.0
C B:GLY36 3.6 13.2 1.0
OE1 B:GLU56 3.7 17.1 1.0
PB B:8DG201 3.7 50.5 1.0
HA2 B:GLY37 3.8 15.9 1.0
O3A B:8DG201 3.9 42.1 1.0
CE B:LYS23 4.0 59.1 1.0
H B:GLY36 4.0 14.6 1.0
HZ1 B:LYS23 4.0 72.5 1.0
CA B:GLY37 4.1 13.2 1.0
NZ B:LYS23 4.1 60.4 1.0
OE1 B:GLU52 4.1 27.7 1.0
O5' B:8DG201 4.2 25.6 1.0
HD3 B:LYS23 4.2 67.8 1.0
N B:GLY37 4.3 13.4 1.0
CG B:GLU56 4.4 20.9 1.0
HG2 B:GLU56 4.5 25.0 1.0
O1G B:8DG201 4.5 61.2 1.0
NA B:NA203 4.5 68.9 1.0
HE1 B:MET101 4.5 49.1 0.3
HG3 B:GLU56 4.6 25.0 1.0
O1B B:8DG201 4.7 49.2 1.0
CD B:LYS23 4.7 56.5 1.0
N B:GLY36 4.7 12.1 1.0
O2A B:8DG201 4.7 34.9 1.0
CA B:GLY36 4.8 12.6 1.0
O B:HOH366 4.8 17.9 1.0
HE3 B:LYS23 4.8 70.9 1.0
HG2 B:LYS23 4.8 63.4 1.0
HZ2 B:LYS23 4.9 72.5 1.0
O3B B:8DG201 4.9 55.5 1.0
CD B:GLU52 5.0 26.5 1.0
C4' B:8DG201 5.0 17.1 1.0

Sodium binding site 4 out of 5 in 9mbg

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Sodium binding site 4 out of 5 in the 8-Oxo-Dgtp 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 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:22.0
occ:0.50
 NA B:NA202 0.0 22.0 0.5
NA B:NA202 1.6 29.7 0.5
OE2 B:GLU56 2.3 21.6 1.0
O B:GLY36 2.4 15.1 1.0
O2B B:8DG201 2.5 54.9 1.0
OE1 B:GLU52 2.6 27.7 1.0
HA3 B:GLY37 2.9 15.9 1.0
NA B:NA203 3.2 68.9 1.0
CD B:GLU56 3.2 19.9 1.0
C B:GLY36 3.4 13.2 1.0
O1A B:8DG201 3.4 34.5 1.0
CD B:GLU52 3.5 26.5 1.0
O B:HOH368 3.6 48.9 1.0
CA B:GLY37 3.6 13.2 1.0
PB B:8DG201 3.7 50.5 1.0
HA2 B:GLY37 3.8 15.9 1.0
HG3 B:GLU56 3.8 25.0 1.0
OE2 B:GLU52 3.9 29.0 1.0
CG B:GLU56 3.9 20.9 1.0
N B:GLY37 3.9 13.4 1.0
OE1 B:GLU56 3.9 17.1 1.0
HG2 B:GLU56 4.0 25.0 1.0
O B:HOH398 4.0 29.0 1.0
H B:GLY36 4.1 14.6 1.0
O1B B:8DG201 4.1 49.2 1.0
O3A B:8DG201 4.3 42.1 1.0
HB3 B:GLU52 4.3 26.2 1.0
O B:HOH446 4.4 48.3 1.0
O1G B:8DG201 4.4 61.2 1.0
PA B:8DG201 4.4 33.5 1.0
CA B:GLY36 4.6 12.6 1.0
CG B:GLU52 4.6 24.3 1.0
HG3 B:GLU52 4.7 29.1 1.0
N B:GLY36 4.7 12.1 1.0
H B:GLY37 4.8 16.0 1.0
H B:LYS38 4.8 16.8 1.0
HA2 B:GLY36 4.8 15.2 1.0
HE2 B:LYS23 4.8 70.9 1.0
HZ3 B:LYS23 4.9 72.5 1.0
C B:GLY37 4.9 13.3 1.0
CB B:GLU52 5.0 21.9 1.0
O3B B:8DG201 5.0 55.5 1.0

Sodium binding site 5 out of 5 in 9mbg

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Sodium binding site 5 out of 5 in the 8-Oxo-Dgtp 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 5 of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:68.9
occ:1.00
 O B:HOH446 2.3 48.3 1.0
OE2 B:GLU52 2.3 29.0 1.0
O1B B:8DG201 2.7 49.2 1.0
O B:HOH355 2.8 32.0 1.0
CD B:GLU52 3.1 26.5 1.0
OE1 B:GLU52 3.1 27.7 1.0
HA3 B:GLY37 3.1 15.9 1.0
O2B B:8DG201 3.1 54.9 1.0
NA B:NA202 3.2 22.0 0.5
PB B:8DG201 3.4 50.5 1.0
O B:HOH368 3.4 48.9 1.0
HH12 B:ARG51 3.5 32.0 1.0
H B:LYS38 3.5 16.8 1.0
CA B:GLY37 4.1 13.2 1.0
N B:LYS38 4.1 14.0 1.0
O1G B:8DG201 4.2 61.2 1.0
NH1 B:ARG51 4.3 26.7 1.0
O3B B:8DG201 4.4 55.5 1.0
CG B:GLU52 4.5 24.3 1.0
HA2 B:GLY37 4.5 15.9 1.0
C B:GLY37 4.5 13.3 1.0
NA B:NA202 4.5 29.7 0.5
HB2 B:LYS38 4.5 23.2 1.0
O B:LYS38 4.6 18.8 1.0
O3A B:8DG201 4.6 42.1 1.0
HH11 B:ARG51 4.6 32.0 1.0
HH22 B:ARG51 4.7 28.8 1.0
HG3 B:GLU52 4.7 29.1 1.0
O B:GLY36 4.8 15.1 1.0
HG2 B:GLU52 4.8 29.1 1.0
OE1 B:GLU55 4.9 40.5 1.0
N B:GLY37 5.0 13.4 1.0
PG B:8DG201 5.0 61.1 1.0

Reference:

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
Page generated: Mon Aug 18 17:23:44 2025

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