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Manganese in PDB 9mbh: 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex

Enzymatic activity of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex

All present enzymatic activity of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M 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-3M Complex, PDB code: 9mbh 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) 25.96 / 1.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.488, 47.612, 123.846, 90, 90, 90
R / Rfree (%) 13.9 / 17.1

Other elements in 9mbh:

The structure of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex (pdb code 9mbh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex, PDB code: 9mbh:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 9mbh

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Manganese binding site 1 out of 6 in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn204

b:18.8
occ:0.50
 NA A:NA202 0.1 13.6 0.5
O A:GLY36 2.1 12.2 1.0
OE2 A:GLU56 2.1 19.9 1.0
O2A A:8DG201 2.2 18.2 1.0
O A:HOH421 2.2 15.3 1.0
O1B A:8DG201 2.3 24.5 1.0
O A:HOH312 2.4 41.3 1.0
CD A:GLU56 3.1 17.2 1.0
MN A:MN205 3.2 14.3 0.3
NA A:NA203 3.2 29.3 0.7
C A:GLY36 3.4 10.6 1.0
PA A:8DG201 3.4 17.1 1.0
OE1 A:GLU56 3.5 16.0 1.0
PB A:8DG201 3.5 24.8 1.0
HZ2 A:LYS23 3.5 23.7 1.0
HE3 A:LYS23 3.6 23.3 1.0
O3A A:8DG201 3.6 19.6 1.0
OE2 A:GLU100 3.6 27.5 0.5
HA3 A:GLY37 3.6 13.1 1.0
HA2 A:GLY37 3.7 13.1 1.0
H A:GLY36 3.7 11.1 1.0
HZ1 A:LYS23 3.7 23.7 1.0
NZ A:LYS23 3.9 19.8 1.0
CA A:GLY37 4.0 10.9 1.0
N A:GLY37 4.1 10.4 1.0
OE1 A:GLU52 4.2 19.9 1.0
O5' A:8DG201 4.2 13.6 1.0
CE A:LYS23 4.2 19.4 1.0
O A:HOH379 4.3 11.6 1.0
O1G A:8DG201 4.4 43.6 1.0
N A:GLY36 4.4 9.2 1.0
CG A:GLU56 4.4 15.6 1.0
O3B A:8DG201 4.5 33.0 1.0
CA A:GLY36 4.5 9.4 1.0
HG2 A:GLU56 4.5 18.7 1.0
O A:HOH309 4.5 11.3 0.2
HB3 A:GLU100 4.6 28.1 0.5
HB3 A:GLU100 4.6 27.2 0.5
O1A A:8DG201 4.6 19.9 1.0
C4' A:8DG201 4.6 12.3 1.0
HG2 A:GLU100 4.7 32.1 0.5
O2B A:8DG201 4.7 19.2 1.0
CD A:GLU100 4.7 27.7 0.5
HG3 A:GLU56 4.7 18.7 1.0
HZ3 A:LYS23 4.8 23.7 1.0
HG2 A:GLU100 4.8 30.4 0.5
HD3 A:LYS23 4.8 20.7 1.0
O2G A:8DG201 4.9 42.9 1.0
PG A:8DG201 4.9 42.4 1.0
O3' A:8DG201 4.9 11.4 1.0
HE2 A:LYS23 4.9 23.3 1.0
C5' A:8DG201 4.9 13.2 1.0
H A:GLY37 5.0 12.5 1.0

Manganese binding site 2 out of 6 in 9mbh

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Manganese binding site 2 out of 6 in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn205

b:14.3
occ:0.30
 NA A:NA203 0.2 29.3 0.7
O A:HOH309 2.1 11.3 0.2
O A:HOH315 2.2 29.1 1.0
OE1 A:GLU52 2.2 19.9 1.0
OE2 A:GLU100 2.3 27.5 0.5
OE2 A:GLU56 2.3 19.9 1.0
O1B A:8DG201 2.4 24.5 1.0
O A:HOH309 3.0 26.9 0.8
NA A:NA202 3.2 13.6 0.5
MN A:MN204 3.2 18.8 0.5
CD A:GLU52 3.3 17.7 1.0
CD A:GLU56 3.3 17.2 1.0
HG3 A:GLU56 3.3 18.7 1.0
CD A:GLU100 3.4 27.7 0.5
HG2 A:GLU56 3.5 18.7 1.0
O A:HOH312 3.6 41.3 1.0
CG A:GLU56 3.6 15.6 1.0
PB A:8DG201 3.7 24.8 1.0
OE2 A:GLU52 3.7 19.5 1.0
HG2 A:GLU100 3.7 32.1 0.5
MN A:MN206 3.7 14.6 0.2
HA3 A:GLY37 3.8 13.1 1.0
O2G A:8DG201 3.8 42.9 1.0
OE1 A:GLU100 3.8 29.5 0.5
O A:GLY36 3.9 12.2 1.0
O2B A:8DG201 4.2 19.2 1.0
OE1 A:GLU55 4.2 24.7 1.0
O A:HOH377 4.2 37.6 1.0
HB3 A:GLU52 4.2 19.0 1.0
OE1 A:GLU56 4.4 16.0 1.0
OE2 A:GLU100 4.4 30.6 0.5
HB2 A:GLU55 4.6 21.4 1.0
C A:GLY36 4.6 10.6 1.0
HA A:GLU52 4.6 17.5 1.0
CG A:GLU52 4.6 16.2 1.0
CG A:GLU100 4.6 26.8 0.5
CA A:GLY37 4.6 10.9 1.0
CG A:GLU100 4.6 25.3 0.5
O3B A:8DG201 4.6 33.0 1.0
HG2 A:GLU100 4.7 30.4 0.5
PG A:8DG201 4.7 42.4 1.0
CB A:GLU52 4.8 15.8 1.0
O3A A:8DG201 4.9 19.6 1.0
HA2 A:GLY37 4.9 13.1 1.0
N A:GLY37 4.9 10.4 1.0
O2A A:8DG201 4.9 18.2 1.0
HH12 A:ARG51 5.0 26.2 1.0

Manganese binding site 3 out of 6 in 9mbh

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Manganese binding site 3 out of 6 in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn206

b:14.6
occ:0.20
 O A:HOH309 0.8 26.9 0.8
O A:HOH332 2.1 29.1 1.0
O A:HOH309 2.2 11.3 0.2
O A:HOH377 2.3 37.6 1.0
OE2 A:GLU52 2.3 19.5 1.0
O A:HOH466 2.5 47.0 1.0
O2B A:8DG201 2.7 19.2 1.0
HH12 A:ARG51 3.2 26.2 1.0
CD A:GLU52 3.3 17.7 1.0
NA A:NA203 3.5 29.3 0.7
H A:LYS38 3.5 13.0 0.5
HE21 A:GLN40 3.5 34.0 1.0
H A:LYS38 3.6 13.9 0.5
OE1 A:GLU52 3.6 19.9 1.0
MN A:MN205 3.7 14.3 0.3
PB A:8DG201 3.7 24.8 1.0
HA3 A:GLY37 3.8 13.1 1.0
O1B A:8DG201 3.9 24.5 1.0
HH22 A:ARG51 3.9 24.4 1.0
HB2 A:LYS38 3.9 17.1 0.5
NH1 A:ARG51 4.0 21.8 1.0
HB2 A:LYS38 4.0 12.7 0.5
N A:LYS38 4.1 10.8 0.5
N A:LYS38 4.2 11.6 0.5
O A:LYS38 4.2 13.9 0.5
O A:LYS38 4.2 13.5 0.5
O A:HOH499 4.2 38.5 1.0
NE2 A:GLN40 4.3 28.4 1.0
O A:HOH315 4.4 29.1 1.0
O2G A:8DG201 4.4 42.9 1.0
OE1 A:GLU55 4.4 24.7 1.0
HE22 A:GLN40 4.4 34.0 1.0
HH11 A:ARG51 4.5 26.2 1.0
O3B A:8DG201 4.6 33.0 1.0
NH2 A:ARG51 4.6 20.3 1.0
CG A:GLU52 4.7 16.2 1.0
CA A:GLY37 4.7 10.9 1.0
CB A:LYS38 4.8 14.2 0.5
CZ A:ARG51 4.8 20.3 1.0
HG2 A:GLU52 4.8 19.4 1.0
C A:GLY37 4.8 10.4 1.0
HD2 A:LYS38 4.8 24.1 0.5
CB A:LYS38 4.9 10.5 0.5
CA A:LYS38 4.9 12.8 0.5
CA A:LYS38 4.9 11.2 0.5
HG3 A:GLU52 4.9 19.4 1.0
C A:LYS38 5.0 12.0 0.5
C A:LYS38 5.0 12.5 0.5

Manganese binding site 4 out of 6 in 9mbh

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Manganese binding site 4 out of 6 in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:13.9
occ:0.40
 O B:HOH409 2.1 20.5 1.0
OE2 B:GLU56 2.2 18.9 1.0
O B:GLY36 2.2 13.7 1.0
O1A B:8DG201 2.2 21.0 1.0
O2B B:8DG201 2.3 41.8 1.0
OE1 B:GLU100 2.7 45.6 1.0
NA B:NA205 2.9 52.3 0.8
CD B:GLU56 3.1 15.8 1.0
MN B:MN203 3.2 14.1 0.2
HE3 B:LYS23 3.4 44.2 1.0
C B:GLY36 3.4 11.6 1.0
PA B:8DG201 3.4 19.4 1.0
OE1 B:GLU56 3.5 14.9 1.0
CD B:GLU100 3.5 45.8 1.0
PB B:8DG201 3.6 38.8 1.0
HZ2 B:LYS23 3.7 45.0 1.0
H B:GLY36 3.7 12.3 1.0
HA3 B:GLY37 3.7 13.8 1.0
OE2 B:GLU100 3.7 46.2 1.0
HZ1 B:LYS23 3.7 45.0 1.0
O3A B:8DG201 3.7 28.9 1.0
HA2 B:GLY37 3.8 13.8 1.0
NZ B:LYS23 4.0 37.5 1.0
CA B:GLY37 4.0 11.5 1.0
CE B:LYS23 4.1 36.9 1.0
O5' B:8DG201 4.1 16.5 1.0
N B:GLY37 4.2 11.2 1.0
OE1 B:GLU52 4.2 20.3 1.0
O B:HOH356 4.3 15.6 1.0
N B:GLY36 4.3 10.2 1.0
CA B:GLY36 4.5 11.1 1.0
CG B:GLU56 4.5 15.5 1.0
HB3 B:GLU100 4.6 51.3 1.0
HG2 B:GLU56 4.6 18.6 1.0
O2G B:8DG201 4.6 55.9 1.0
O3B B:8DG201 4.7 47.1 1.0
O1B B:8DG201 4.7 38.3 1.0
C4' B:8DG201 4.7 15.2 1.0
O2A B:8DG201 4.7 20.6 1.0
HE2 B:LYS23 4.8 44.2 1.0
HG3 B:GLU56 4.8 18.6 1.0
HD3 B:LYS23 4.8 42.0 1.0
HZ3 B:LYS23 4.9 45.0 1.0
O1G B:8DG201 4.9 55.7 1.0
CG B:GLU100 4.9 44.6 1.0
C5' B:8DG201 4.9 15.1 1.0

Manganese binding site 5 out of 6 in 9mbh

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Manganese binding site 5 out of 6 in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn203

b:14.1
occ:0.20
 NA B:NA205 0.3 52.3 0.8
O B:HOH322 2.1 43.4 1.0
OE1 B:GLU52 2.2 20.3 1.0
OE2 B:GLU100 2.3 46.2 1.0
OE2 B:GLU56 2.3 18.9 1.0
O2B B:8DG201 2.6 41.8 1.0
NA B:NA206 3.0 52.6 0.9
MN B:MN202 3.2 13.9 0.4
CD B:GLU56 3.3 15.8 1.0
CD B:GLU52 3.3 20.5 1.0
CD B:GLU100 3.3 45.8 1.0
HG3 B:GLU56 3.4 18.6 1.0
HG2 B:GLU56 3.4 18.6 1.0
O1G B:8DG201 3.6 55.7 1.0
OE1 B:GLU100 3.6 45.6 1.0
CG B:GLU56 3.6 15.5 1.0
MN B:MN204 3.6 17.5 0.1
OE2 B:GLU52 3.6 23.3 1.0
O B:GLY36 3.7 13.7 1.0
HA3 B:GLY37 3.7 13.8 1.0
PB B:8DG201 3.7 38.8 1.0
O1B B:8DG201 4.0 38.3 1.0
O B:HOH337 4.1 51.2 1.0
HB3 B:GLU52 4.3 20.8 1.0
OE1 B:GLU55 4.3 34.1 1.0
OE1 B:GLU56 4.4 14.9 1.0
C B:GLY36 4.5 11.6 1.0
CA B:GLY37 4.6 11.5 1.0
CG B:GLU52 4.6 19.4 1.0
CG B:GLU100 4.6 44.6 1.0
HA B:GLU52 4.7 18.3 1.0
PG B:8DG201 4.7 53.6 1.0
HG3 B:GLU100 4.7 53.6 1.0
O3B B:8DG201 4.8 47.1 1.0
HB2 B:GLU55 4.8 27.0 1.0
O1A B:8DG201 4.9 21.0 1.0
CB B:GLU52 4.9 17.3 1.0
O2G B:8DG201 4.9 55.9 1.0
HA2 B:GLY37 4.9 13.8 1.0
N B:GLY37 4.9 11.2 1.0
O3A B:8DG201 4.9 28.9 1.0
H B:GLY36 4.9 12.3 1.0
O B:HOH409 4.9 20.5 1.0

Manganese binding site 6 out of 6 in 9mbh

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Manganese binding site 6 out of 6 in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn204

b:17.5
occ:0.10
 NA B:NA206 0.8 52.6 0.9
O B:HOH337 2.2 51.2 1.0
O B:HOH374 2.2 25.3 1.0
OE2 B:GLU52 2.4 23.3 1.0
O1B B:8DG201 2.7 38.3 1.0
HH12 B:ARG51 3.1 26.0 1.0
CD B:GLU52 3.4 20.5 1.0
NA B:NA205 3.5 52.3 0.8
MN B:MN203 3.6 14.1 0.2
OE1 B:GLU52 3.7 20.3 1.0
H B:LYS38 3.7 13.9 1.0
O1G B:8DG201 3.7 55.7 1.0
PB B:8DG201 3.8 38.8 1.0
HA3 B:GLY37 3.9 13.8 1.0
NH1 B:ARG51 3.9 21.7 1.0
HH22 B:ARG51 4.1 23.7 1.0
O2B B:8DG201 4.1 41.8 1.0
O B:HOH322 4.1 43.4 1.0
HB2 B:LYS38 4.2 18.0 1.0
N B:LYS38 4.3 11.6 1.0
HH11 B:ARG51 4.3 26.0 1.0
OE1 B:GLU55 4.3 34.1 1.0
O B:LYS38 4.4 15.1 1.0
HE21 B:GLN40 4.5 38.8 1.0
O3B B:8DG201 4.6 47.1 1.0
NH2 B:ARG51 4.7 19.8 1.0
CA B:GLY37 4.7 11.5 1.0
CG B:GLU52 4.8 19.4 1.0
CZ B:ARG51 4.8 19.8 1.0
PG B:8DG201 4.8 53.6 1.0
HG2 B:GLU52 4.9 23.2 1.0
C B:GLY37 4.9 11.4 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: Sun Aug 17 02:40:29 2025

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