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Manganese in PDB 9mbm: 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es/Ep-3M Complex

Enzymatic activity of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es/Ep-3M Complex

All present enzymatic activity of 2-Oxo-Datp 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 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es/Ep-3M Complex, PDB code: 9mbm 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) 36.93 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.091, 47.374, 123.467, 90, 90, 90
R / Rfree (%) 13.4 / 18.1

Manganese Binding Sites:

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

Manganese binding site 1 out of 5 in 9mbm

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Manganese binding site 1 out of 5 in the 2-Oxo-Datp 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 2-Oxo-Datp 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:15.7
occ:0.60
 OP2 A:IGU202 1.9 33.5 0.7
OE1 A:GLU56 2.0 21.2 1.0
O2B A:6U4201 2.1 18.2 0.3
O A:HOH374 2.1 32.4 0.7
O A:HOH398 2.2 19.9 1.0
O A:GLY36 2.3 16.7 1.0
O1A A:6U4201 2.3 17.7 0.3
O A:HOH304 2.4 37.1 1.0
MN A:MN204 3.0 15.4 0.3
CD A:GLU56 3.1 18.8 1.0
PB A:6U4201 3.3 18.6 0.3
P A:IGU202 3.4 30.7 0.7
PA A:6U4201 3.4 14.0 0.3
C A:GLY36 3.5 12.9 1.0
O3A A:6U4201 3.5 15.5 0.3
OE2 A:GLU56 3.5 17.5 1.0
OE1 A:GLU100 3.6 37.6 0.5
OP3 A:IGU202 4.0 32.0 0.7
CA A:GLY37 4.0 14.7 1.0
OE1 A:GLU52 4.0 28.5 1.0
O3B A:6U4201 4.1 23.6 0.3
N A:GLY37 4.2 12.8 1.0
O5' A:IGU202 4.2 31.1 0.7
O A:HOH332 4.3 17.2 1.0
NZ A:LYS23 4.3 26.6 1.0
O5' A:6U4201 4.3 9.7 0.3
O1G A:6U4201 4.3 28.9 0.3
OP1 A:IGU202 4.3 32.7 0.7
CE A:LYS23 4.4 25.2 1.0
CG A:GLU56 4.4 17.1 1.0
O A:HOH341 4.5 21.2 0.3
N A:GLY36 4.5 12.2 1.0
O1B A:6U4201 4.6 19.3 0.3
O A:HOH314 4.6 22.7 0.7
CA A:GLY36 4.6 13.8 1.0
O2A A:6U4201 4.6 19.8 0.3
CD A:GLU100 4.7 38.0 0.5
C4' A:IGU202 4.7 27.6 0.7
C4' A:6U4201 4.8 7.4 0.3
O A:HOH312 4.8 44.4 1.0
CD A:GLU52 4.9 23.7 1.0
PG A:6U4201 5.0 28.6 0.3

Manganese binding site 2 out of 5 in 9mbm

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Manganese binding site 2 out of 5 in the 2-Oxo-Datp 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 2-Oxo-Datp 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:Mn204

b:15.4
occ:0.30
 O A:HOH374 1.8 32.4 0.7
O A:HOH312 1.9 44.4 1.0
OE1 A:GLU52 2.1 28.5 1.0
O A:HOH341 2.2 21.2 0.3
O2B A:6U4201 2.2 18.2 0.3
OE1 A:GLU56 2.4 21.2 1.0
OE1 A:GLU100 2.5 37.6 0.5
MN A:MN203 3.0 15.7 0.6
CD A:GLU52 3.1 23.7 1.0
CD A:GLU56 3.3 18.8 1.0
CD A:GLU100 3.3 38.0 0.5
OE2 A:GLU100 3.5 40.5 0.5
OE2 A:GLU52 3.5 24.6 1.0
PB A:6U4201 3.5 18.6 0.3
O1G A:6U4201 3.6 28.9 0.3
O A:HOH304 3.6 37.1 1.0
MN A:MN205 3.6 32.4 0.3
CG A:GLU56 3.6 17.1 1.0
OE2 A:GLU100 3.7 43.1 0.5
O A:GLY36 3.9 16.7 1.0
O1B A:6U4201 3.9 19.3 0.3
OE1 A:GLU55 4.1 32.3 1.0
O A:HOH387 4.2 44.0 1.0
O A:HOH314 4.3 22.7 0.7
OP2 A:IGU202 4.4 33.5 0.7
O3B A:6U4201 4.4 23.6 0.3
OE2 A:GLU56 4.4 17.5 1.0
CG A:GLU52 4.5 19.6 1.0
CD A:GLU100 4.5 40.9 0.5
PG A:6U4201 4.6 28.6 0.3
C A:GLY36 4.6 12.9 1.0
CG A:GLU100 4.6 36.7 0.5
CA A:GLY37 4.7 14.7 1.0
O3A A:6U4201 4.7 15.5 0.3
CG A:GLU100 4.7 34.3 0.5
CB A:GLU52 4.8 18.4 1.0
O A:HOH398 4.9 19.9 1.0
O1A A:6U4201 4.9 17.7 0.3
O2G A:6U4201 4.9 30.3 0.3
N A:GLY37 5.0 12.8 1.0

Manganese binding site 3 out of 5 in 9mbm

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Manganese binding site 3 out of 5 in the 2-Oxo-Datp 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 2-Oxo-Datp 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:Mn205

b:32.4
occ:0.30
 O A:HOH356 2.2 35.6 1.0
OE2 A:GLU52 2.2 24.6 1.0
O A:HOH387 2.3 44.0 1.0
O A:HOH341 2.3 21.2 0.3
O A:HOH302 2.4 55.3 1.0
O1B A:6U4201 2.5 19.3 0.3
O A:HOH314 3.0 22.7 0.7
CD A:GLU52 3.3 23.7 1.0
PB A:6U4201 3.6 18.6 0.3
O A:HOH374 3.6 32.4 0.7
MN A:MN204 3.6 15.4 0.3
OE1 A:GLU52 3.7 28.5 1.0
O A:HOH458 3.8 42.6 1.0
O2B A:6U4201 3.9 18.2 0.3
NH1 A:ARG51 3.9 23.8 1.0
O2G A:6U4201 3.9 30.3 0.3
NE2 A:GLN40 4.1 32.5 1.0
O A:HOH312 4.2 44.4 1.0
O A:LYS38 4.2 16.4 1.0
N A:LYS38 4.3 13.3 1.0
OE1 A:GLU55 4.4 32.3 1.0
NH2 A:ARG51 4.5 23.1 1.0
O3B A:6U4201 4.6 23.6 0.3
CG A:GLU52 4.6 19.6 1.0
O1G A:6U4201 4.6 28.9 0.3
PG A:6U4201 4.7 28.6 0.3
CZ A:ARG51 4.7 23.3 1.0
CA A:GLY37 4.8 14.7 1.0
O3A A:6U4201 4.8 15.5 0.3
C A:GLY37 4.9 12.8 1.0
CB A:LYS38 4.9 13.5 1.0

Manganese binding site 4 out of 5 in 9mbm

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Manganese binding site 4 out of 5 in the 2-Oxo-Datp 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 2-Oxo-Datp 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:19.9
occ:0.40
 OE1 B:GLU56 2.0 30.2 1.0
O B:HOH350 2.0 18.9 0.3
O B:HOH378 2.1 28.6 1.0
O1A B:6U4201 2.2 51.9 0.5
O B:GLY36 2.2 19.9 1.0
O B:HOH318 2.2 37.8 1.0
O2B B:6U4201 2.3 52.8 0.5
OP2 B:IGU202 2.4 27.9 0.5
CD B:GLU56 3.1 28.2 1.0
MN B:MN204 3.1 22.9 0.2
C B:GLY36 3.4 15.1 1.0
PA B:6U4201 3.5 51.2 0.5
OE2 B:GLU56 3.5 25.8 1.0
PB B:6U4201 3.6 52.6 0.5
P B:IGU202 3.6 26.5 0.5
OP3 B:IGU202 3.7 29.3 0.5
O3A B:6U4201 3.9 52.4 0.5
O2G B:6U4201 3.9 55.3 0.5
CA B:GLY37 4.1 17.4 1.0
OE1 B:GLU52 4.1 37.4 1.0
O B:HOH357 4.1 23.3 1.0
O5' B:6U4201 4.2 48.5 0.5
N B:GLY37 4.2 14.9 1.0
O5' B:IGU202 4.2 18.9 0.5
CG B:GLU56 4.4 25.4 1.0
N B:GLY36 4.4 15.1 1.0
NZ B:LYS23 4.5 34.4 0.5
O1G B:6U4201 4.5 54.3 0.5
CA B:GLY36 4.5 14.2 1.0
CE B:LYS23 4.6 32.7 0.5
OE1 B:GLU100 4.6 38.9 0.5
O3B B:6U4201 4.6 53.4 0.5
C4' B:6U4201 4.6 44.2 0.5
C4' B:IGU202 4.6 12.6 0.5
PG B:6U4201 4.6 54.9 0.5
O1B B:6U4201 4.6 52.7 0.5
O2A B:6U4201 4.7 52.1 0.5
O B:HOH348 4.8 16.7 0.3
C5' B:6U4201 4.8 45.9 0.5
O B:HOH337 4.9 58.0 1.0
OP1 B:IGU202 4.9 30.0 0.5
O B:HOH360 4.9 57.1 1.0
O3' B:6U4201 5.0 43.9 0.5
OE2 B:GLU100 5.0 39.9 0.5
C5' B:IGU202 5.0 16.4 0.5

Manganese binding site 5 out of 5 in 9mbm

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Manganese binding site 5 out of 5 in the 2-Oxo-Datp 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 2-Oxo-Datp 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:22.9
occ:0.20
 O B:HOH350 1.9 18.9 0.3
O B:HOH360 1.9 57.1 1.0
OE1 B:GLU52 2.3 37.4 1.0
OE1 B:GLU56 2.4 30.2 1.0
O2B B:6U4201 2.5 52.8 0.5
O B:HOH337 2.5 58.0 1.0
MN B:MN203 3.1 19.9 0.4
O1G B:6U4201 3.2 54.3 0.5
CD B:GLU56 3.2 28.2 1.0
CD B:GLU52 3.3 35.1 1.0
O B:HOH318 3.4 37.8 1.0
CG B:GLU56 3.5 25.4 1.0
OE2 B:GLU52 3.6 38.7 1.0
PB B:6U4201 3.7 52.6 0.5
O B:GLY36 3.9 19.9 1.0
O1B B:6U4201 4.0 52.7 0.5
PG B:6U4201 4.3 54.9 0.5
OE1 B:GLU55 4.3 55.0 1.0
O B:HOH348 4.3 16.7 0.3
OE2 B:GLU56 4.4 25.8 1.0
O3B B:6U4201 4.4 53.4 0.5
O2G B:6U4201 4.5 55.3 0.5
CG B:GLU52 4.6 30.1 1.0
C B:GLY36 4.6 15.1 1.0
O1A B:6U4201 4.7 51.9 0.5
OE2 B:GLU100 4.7 39.9 0.5
CA B:GLY37 4.8 17.4 1.0
O B:HOH378 4.8 28.6 1.0
CB B:GLU52 4.9 27.1 1.0
O3A B:6U4201 5.0 52.4 0.5
OP3 B:IGU202 5.0 29.3 0.5

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 02:44:52 2025

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