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

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

All present enzymatic activity of 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es/Ep-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/Ep-3M Complex, PDB code: 9mbi 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) 32.13 / 1.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.497, 47.637, 123.839, 90, 90, 90
R / Rfree (%) 14 / 16.4

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/Ep-3M Complex (pdb code 9mbi). 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/Ep-3M Complex, PDB code: 9mbi:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 9mbi

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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/Ep-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/Ep-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:12.0
occ:0.60
 O2A A:8DG204 2.1 21.1 0.5
O1B A:8DG204 2.1 19.9 0.5
O A:HOH409 2.1 16.6 0.5
OE2 A:GLU56 2.1 17.1 1.0
O A:GLY36 2.2 12.2 1.0
O A:HOH421 2.2 14.1 1.0
OP2 A:8OG205 2.3 14.7 0.5
O A:HOH306 2.3 33.5 1.0
MN A:MN202 3.1 13.5 0.3
CD A:GLU56 3.1 14.0 1.0
PB A:8DG204 3.4 20.1 0.5
PA A:8DG204 3.4 20.6 0.5
C A:GLY36 3.4 10.0 1.0
P A:8OG205 3.4 11.7 0.5
OP3 A:8OG205 3.5 16.0 0.5
OE1 A:GLU56 3.5 12.4 1.0
HE3 A:LYS23 3.6 17.2 1.0
HZ2 A:LYS23 3.6 17.5 1.0
OE1 A:GLU100 3.6 20.8 0.3
O3A A:8DG204 3.6 21.0 0.5
HA3 A:GLY37 3.6 12.6 1.0
HA2 A:GLY37 3.7 12.6 1.0
H A:GLY36 3.7 10.0 1.0
HZ1 A:LYS23 3.8 17.5 1.0
CA A:GLY37 4.0 10.5 1.0
NZ A:LYS23 4.0 14.6 1.0
OE1 A:GLU52 4.1 21.0 1.0
N A:GLY37 4.1 9.8 1.0
O5' A:8OG205 4.2 11.5 0.5
O3B A:8DG204 4.3 24.6 0.5
CE A:LYS23 4.3 14.3 1.0
O5' A:8DG204 4.3 18.2 0.5
O A:HOH373 4.4 10.8 1.0
N A:GLY36 4.4 8.3 1.0
CG A:GLU56 4.5 13.1 1.0
HB3 A:GLU100 4.5 20.6 0.3
HB3 A:GLU100 4.5 25.6 0.7
O1G A:8DG204 4.5 29.2 0.5
CA A:GLY36 4.5 9.0 1.0
O2B A:8DG204 4.5 20.9 0.5
O A:HOH302 4.5 14.7 0.3
O1A A:8DG204 4.5 22.3 0.5
HG2 A:GLU56 4.6 15.8 1.0
OP1 A:8OG205 4.6 14.9 0.5
HG2 A:GLU100 4.6 31.6 0.7
O A:HOH301 4.7 18.7 0.5
C4' A:8DG204 4.7 13.7 0.5
C4' A:8OG205 4.7 9.8 0.5
HG3 A:GLU56 4.7 15.8 1.0
CD A:GLU100 4.8 20.4 0.3
HD3 A:LYS23 4.8 16.2 1.0
HZ3 A:LYS23 4.9 17.5 1.0
O A:HOH307 4.9 39.6 1.0
O3' A:8DG204 5.0 11.8 0.5
O3' A:8OG205 5.0 10.1 0.5
HE2 A:LYS23 5.0 17.2 1.0
C5' A:8OG205 5.0 10.4 0.5
H A:GLY37 5.0 11.8 1.0

Manganese binding site 2 out of 6 in 9mbi

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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/Ep-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/Ep-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:13.5
occ:0.30
 O A:HOH409 1.8 16.6 0.5
O A:HOH307 2.0 39.6 1.0
OE1 A:GLU52 2.2 21.0 1.0
O A:HOH302 2.2 14.7 0.3
OE1 A:GLU100 2.3 20.8 0.3
OE2 A:GLU56 2.3 17.1 1.0
O1B A:8DG204 2.4 19.9 0.5
MN A:MN201 3.1 12.0 0.6
CD A:GLU52 3.3 18.8 1.0
CD A:GLU56 3.4 14.0 1.0
CD A:GLU100 3.4 20.4 0.3
HG3 A:GLU56 3.5 15.8 1.0
O1G A:8DG204 3.5 29.2 0.5
O A:HOH306 3.5 33.5 1.0
HG2 A:GLU56 3.6 15.8 1.0
PB A:8DG204 3.6 20.1 0.5
OE2 A:GLU52 3.6 20.4 1.0
MN A:MN203 3.6 15.2 0.3
HG2 A:GLU100 3.7 31.6 0.7
CG A:GLU56 3.7 13.1 1.0
HA3 A:GLY37 3.7 12.6 1.0
OE2 A:GLU100 3.8 21.1 0.3
O A:GLY36 3.8 12.2 1.0
O2B A:8DG204 3.9 20.9 0.5
O A:HOH359 4.1 32.7 1.0
OE1 A:GLU55 4.2 23.3 1.0
HB3 A:GLU52 4.2 16.9 1.0
O A:HOH301 4.3 18.7 0.5
OE1 A:GLU56 4.5 12.4 1.0
C A:GLY36 4.5 10.0 1.0
O3B A:8DG204 4.5 24.6 0.5
CG A:GLU52 4.6 15.9 1.0
OE2 A:GLU100 4.6 30.3 0.7
HA A:GLU52 4.6 15.6 1.0
CA A:GLY37 4.6 10.5 1.0
CG A:GLU100 4.6 26.3 0.7
HB2 A:GLU55 4.6 20.3 1.0
PG A:8DG204 4.6 28.8 0.5
CG A:GLU100 4.7 19.2 0.3
O2A A:8DG204 4.7 21.1 0.5
OP3 A:8OG205 4.7 16.0 0.5
HG2 A:GLU100 4.8 23.1 0.3
CB A:GLU52 4.8 14.0 1.0
O3A A:8DG204 4.8 21.0 0.5
HA2 A:GLY37 4.9 12.6 1.0
N A:GLY37 4.9 9.8 1.0
HH12 A:ARG51 4.9 24.1 1.0
HG3 A:GLU52 5.0 19.1 1.0
O A:HOH421 5.0 14.1 1.0
HB3 A:GLU100 5.0 25.6 0.7
HB3 A:GLU100 5.0 20.6 0.3

Manganese binding site 3 out of 6 in 9mbi

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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/Ep-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/Ep-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:15.2
occ:0.30
 O A:HOH302 2.1 14.7 0.3
O A:HOH320 2.2 26.9 1.0
O A:HOH359 2.2 32.7 1.0
OE2 A:GLU52 2.3 20.4 1.0
O A:HOH470 2.3 56.6 1.0
O2B A:8DG204 2.7 20.9 0.5
O A:HOH301 3.0 18.7 0.5
HH12 A:ARG51 3.1 24.1 1.0
CD A:GLU52 3.3 18.8 1.0
OE1 A:GLU52 3.6 21.0 1.0
H A:LYS38 3.6 11.9 0.4
HE21 A:GLN40 3.6 32.8 1.0
MN A:MN202 3.6 13.5 0.3
H A:LYS38 3.7 12.6 0.6
O A:HOH409 3.8 16.6 0.5
HA3 A:GLY37 3.8 12.6 1.0
PB A:8DG204 3.8 20.1 0.5
HH22 A:ARG51 3.9 22.4 1.0
NH1 A:ARG51 3.9 20.1 1.0
HB2 A:LYS38 4.0 14.8 0.6
O1B A:8DG204 4.1 19.9 0.5
HB2 A:LYS38 4.2 11.7 0.4
N A:LYS38 4.2 9.9 0.4
O A:HOH307 4.2 39.6 1.0
O A:LYS38 4.2 12.0 0.4
N A:LYS38 4.2 10.5 0.6
O A:HOH500 4.2 38.2 1.0
O A:LYS38 4.3 12.6 0.6
OE1 A:GLU55 4.3 23.3 1.0
NE2 A:GLN40 4.3 27.3 1.0
O1G A:8DG204 4.4 29.2 0.5
HH11 A:ARG51 4.4 24.1 1.0
O2G A:8DG204 4.4 29.8 0.5
HE22 A:GLN40 4.5 32.8 1.0
NH2 A:ARG51 4.5 18.6 1.0
CG A:GLU52 4.6 15.9 1.0
CA A:GLY37 4.7 10.5 1.0
CZ A:ARG51 4.7 18.7 1.0
HG2 A:GLU52 4.7 19.1 1.0
O3B A:8DG204 4.8 24.6 0.5
PG A:8DG204 4.8 28.8 0.5
HG3 A:GLU52 4.8 19.1 1.0
C A:GLY37 4.8 9.9 1.0
CB A:LYS38 4.9 12.3 0.6
CA A:LYS38 5.0 11.1 0.6
CB A:LYS38 5.0 9.7 0.4
CA A:LYS38 5.0 10.1 0.4

Manganese binding site 4 out of 6 in 9mbi

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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/Ep-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/Ep-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn203

b:11.9
occ:0.40
 O1A B:8DG201 2.1 29.3 0.5
O B:HOH365 2.1 14.2 0.5
O B:HOH395 2.1 18.5 1.0
OE2 B:GLU56 2.1 17.4 1.0
O B:GLY36 2.2 13.1 1.0
O2B B:8DG201 2.3 30.2 0.5
OP1 B:8OG202 2.3 14.7 0.5
OE2 B:GLU100 2.6 39.5 1.0
MN B:MN204 3.1 16.2 0.3
CD B:GLU56 3.2 14.5 1.0
CD B:GLU100 3.3 39.4 1.0
OE1 B:GLU100 3.4 40.5 1.0
C B:GLY36 3.4 10.8 1.0
P B:8OG202 3.4 12.7 0.5
PA B:8DG201 3.4 28.8 0.5
HE3 B:LYS23 3.4 42.9 1.0
OP3 B:8OG202 3.5 16.7 0.5
OE1 B:GLU56 3.5 13.7 1.0
PB B:8DG201 3.5 28.9 0.5
H B:GLY36 3.7 11.6 1.0
HA3 B:GLY37 3.7 13.1 1.0
O3A B:8DG201 3.7 29.5 0.5
HZ2 B:LYS23 3.8 44.4 1.0
HA2 B:GLY37 3.8 13.1 1.0
HZ1 B:LYS23 3.9 44.4 1.0
CA B:GLY37 4.1 10.9 1.0
O5' B:8OG202 4.1 12.5 0.5
NZ B:LYS23 4.1 37.0 1.0
OE1 B:GLU52 4.1 21.4 1.0
O5' B:8DG201 4.2 25.9 0.5
N B:GLY37 4.2 10.4 1.0
CE B:LYS23 4.2 35.7 1.0
O B:HOH354 4.3 14.1 1.0
N B:GLY36 4.4 9.6 1.0
O1B B:8DG201 4.5 29.3 0.5
CG B:GLU56 4.5 13.9 1.0
CA B:GLY36 4.5 10.3 1.0
O2G B:8DG201 4.5 33.9 0.5
HG2 B:GLU56 4.6 16.7 1.0
CG B:GLU100 4.6 37.0 1.0
O2A B:8DG201 4.6 29.5 0.5
O3B B:8DG201 4.7 30.7 0.5
HB3 B:GLU100 4.7 39.9 1.0
OP2 B:8OG202 4.7 14.6 0.5
C4' B:8DG201 4.7 20.1 0.5
C4' B:8OG202 4.7 10.4 0.5
HG2 B:GLU100 4.7 44.4 1.0
HG3 B:GLU56 4.8 16.7 1.0
O B:HOH369 4.8 38.9 1.0
O B:HOH346 4.8 19.7 0.5
HD3 B:LYS23 4.8 39.5 1.0
HE2 B:LYS23 4.9 42.9 1.0
O1G B:8DG201 4.9 34.4 0.5
C5' B:8OG202 4.9 11.1 0.5
C5' B:8DG201 4.9 22.9 0.5
HZ3 B:LYS23 5.0 44.4 1.0

Manganese binding site 5 out of 6 in 9mbi

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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/Ep-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/Ep-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn204

b:16.2
occ:0.30
 O B:HOH369 1.8 38.9 1.0
O B:HOH365 1.9 14.2 0.5
OE1 B:GLU52 2.2 21.4 1.0
OE2 B:GLU56 2.4 17.4 1.0
OE1 B:GLU100 2.5 40.5 1.0
O2B B:8DG201 2.6 30.2 0.5
MN B:MN203 3.1 11.9 0.4
CD B:GLU52 3.2 21.0 1.0
CD B:GLU56 3.3 14.5 1.0
MN B:MN205 3.4 25.9 0.2
HG3 B:GLU56 3.5 16.7 1.0
CD B:GLU100 3.5 39.4 1.0
HG2 B:GLU56 3.5 16.7 1.0
O1G B:8DG201 3.5 34.4 0.5
OE2 B:GLU52 3.5 23.3 1.0
PB B:8DG201 3.7 28.9 0.5
CG B:GLU56 3.7 13.9 1.0
O B:GLY36 3.7 13.1 1.0
OE2 B:GLU100 3.7 39.5 1.0
HA3 B:GLY37 3.7 13.1 1.0
O1B B:8DG201 3.8 29.3 0.5
O B:HOH405 4.0 47.6 1.0
O B:HOH346 4.1 19.7 0.5
HB3 B:GLU52 4.3 19.3 1.0
OE1 B:GLU55 4.4 30.9 1.0
OE1 B:GLU56 4.4 13.7 1.0
C B:GLY36 4.5 10.8 1.0
CG B:GLU52 4.6 18.7 1.0
PG B:8DG201 4.6 33.1 0.5
CA B:GLY37 4.6 10.9 1.0
HA B:GLU52 4.6 17.1 1.0
O3B B:8DG201 4.7 30.7 0.5
O1A B:8DG201 4.7 29.3 0.5
OP3 B:8OG202 4.7 16.7 0.5
HB2 B:GLU55 4.8 24.5 1.0
O2G B:8DG201 4.8 33.9 0.5
CB B:GLU52 4.9 16.1 1.0
CG B:GLU100 4.9 37.0 1.0
O3A B:8DG201 4.9 29.5 0.5
HA2 B:GLY37 4.9 13.1 1.0
O B:HOH395 4.9 18.5 1.0
N B:GLY37 4.9 10.4 1.0
H B:GLY36 5.0 11.6 1.0
HG3 B:GLU52 5.0 22.5 1.0

Manganese binding site 6 out of 6 in 9mbi

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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/Ep-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/Ep-3M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn205

b:25.9
occ:0.20
 O B:HOH405 2.0 47.6 1.0
O B:HOH366 2.4 25.7 1.0
O1B B:8DG201 2.4 29.3 0.5
OE2 B:GLU52 2.5 23.3 1.0
O B:HOH346 2.5 19.7 0.5
HH12 B:ARG51 3.3 24.4 1.0
MN B:MN204 3.4 16.2 0.3
CD B:GLU52 3.4 21.0 1.0
O1G B:8DG201 3.4 34.4 0.5
O B:HOH365 3.5 14.2 0.5
PB B:8DG201 3.5 28.9 0.5
OE1 B:GLU52 3.6 21.4 1.0
H B:LYS38 3.7 12.9 1.0
HA3 B:GLY37 3.8 13.1 1.0
O B:HOH369 3.8 38.9 1.0
O2B B:8DG201 3.9 30.2 0.5
NH1 B:ARG51 4.1 20.4 1.0
O3B B:8DG201 4.2 30.7 0.5
HB2 B:LYS38 4.3 16.4 1.0
N B:LYS38 4.3 10.7 1.0
HH22 B:ARG51 4.4 21.2 1.0
OE1 B:GLU55 4.5 30.9 1.0
HH11 B:ARG51 4.5 24.4 1.0
PG B:8DG201 4.5 33.1 0.5
O B:LYS38 4.5 13.4 1.0
HE21 B:GLN40 4.6 34.1 1.0
CA B:GLY37 4.7 10.9 1.0
CG B:GLU52 4.8 18.7 1.0
O3A B:8DG201 4.9 29.5 0.5
C B:GLY37 4.9 10.8 1.0
OP3 B:8OG202 4.9 16.7 0.5
HG2 B:GLU52 4.9 22.5 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 02:41:39 2025

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