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

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

All present enzymatic activity of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M 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 Ep-M Complex, PDB code: 9mbn 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) 33.26 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.488, 47.595, 124.06, 90, 90, 90
R / Rfree (%) 17 / 20.7

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 9mbn

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Manganese binding site 1 out of 6 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M 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 Ep-M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:19.4
occ:0.70
 OP1 A:IGU201 2.0 30.3 1.0
OE2 A:GLU56 2.1 22.4 1.0
O A:HOH411 2.2 26.1 0.8
O A:HOH356 2.2 20.7 1.0
O A:GLY36 2.2 19.8 1.0
O A:HOH432 2.3 26.9 0.4
OE2 A:GLU100 2.3 27.2 0.6
MN A:MN203 2.7 24.2 0.2
CD A:GLU56 3.1 18.9 1.0
P A:IGU201 3.4 25.7 1.0
C A:GLY36 3.4 17.3 1.0
CD A:GLU100 3.5 31.2 0.6
OE1 A:GLU56 3.6 20.7 1.0
OP2 A:IGU201 3.9 32.2 1.0
CA A:GLY37 4.0 16.9 1.0
CG A:GLU100 4.0 27.0 0.6
OE1 A:GLU52 4.0 29.3 1.0
N A:GLY37 4.2 16.1 1.0
O A:HOH432 4.2 29.4 0.6
NZ A:LYS23 4.3 23.9 1.0
O A:HOH398 4.3 33.9 1.0
O5' A:IGU201 4.3 23.2 1.0
O A:HOH317 4.4 19.0 1.0
CG A:GLU56 4.4 19.1 1.0
CE A:LYS23 4.4 24.7 1.0
OP3 A:IGU201 4.4 30.3 1.0
N A:GLY36 4.5 15.3 1.0
OE1 A:GLU100 4.5 35.8 0.6
CA A:GLY36 4.6 15.4 1.0
O A:HOH305 4.6 25.5 1.0
C4' A:IGU201 4.8 20.5 1.0
CD A:GLU52 4.8 23.5 1.0

Manganese binding site 2 out of 6 in 9mbn

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Manganese binding site 2 out of 6 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M 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 Ep-M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:24.2
occ:0.20
 O A:HOH411 1.5 26.1 0.8
O A:HOH432 2.2 29.4 0.6
OE1 A:GLU52 2.3 29.3 1.0
OE2 A:GLU56 2.3 22.4 1.0
MN A:MN202 2.7 19.4 0.7
CD A:GLU52 3.2 23.5 1.0
CD A:GLU56 3.3 18.9 1.0
O A:HOH432 3.5 26.9 0.4
OE2 A:GLU100 3.5 27.2 0.6
OE2 A:GLU52 3.5 28.0 1.0
OE1 A:GLU100 3.5 41.9 0.4
O A:GLY36 3.6 19.8 1.0
MN A:MN204 3.6 24.2 0.2
CG A:GLU56 3.7 19.1 1.0
CD A:GLU100 4.2 31.2 0.6
OE1 A:GLU56 4.3 20.7 1.0
C A:GLY36 4.4 17.3 1.0
OP1 A:IGU201 4.4 30.3 1.0
O A:HOH305 4.4 25.5 1.0
OE1 A:GLU55 4.5 37.6 1.0
CD A:GLU100 4.5 44.4 0.4
O A:HOH398 4.5 33.9 1.0
O A:HOH356 4.5 20.7 1.0
CA A:GLY37 4.5 16.9 1.0
CG A:GLU52 4.6 19.2 1.0
CG A:GLU100 4.7 27.0 0.6
CG A:GLU100 4.7 33.6 0.4
N A:GLY37 4.9 16.1 1.0
CB A:GLU52 4.9 17.7 1.0
OE1 A:GLU100 4.9 35.8 0.6

Manganese binding site 3 out of 6 in 9mbn

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Manganese binding site 3 out of 6 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M 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 Ep-M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn204

b:24.2
occ:0.20
 O A:HOH343 2.2 35.8 1.0
OE2 A:GLU52 2.3 28.0 1.0
O A:HOH305 3.0 25.5 1.0
O A:HOH411 3.3 26.1 0.8
CD A:GLU52 3.4 23.5 1.0
MN A:MN203 3.6 24.2 0.2
OE1 A:GLU52 3.8 29.3 1.0
NH1 A:ARG51 3.9 25.0 1.0
O A:HOH451 4.2 42.5 1.0
N A:LYS38 4.2 15.7 1.0
O A:LYS38 4.3 18.8 1.0
NE2 A:GLN40 4.4 27.4 1.0
OE1 A:GLU55 4.5 37.6 1.0
CA A:GLY37 4.6 16.9 1.0
CG A:GLU52 4.7 19.2 1.0
NH2 A:ARG51 4.7 23.6 1.0
CZ A:ARG51 4.8 23.4 1.0
O A:HOH432 4.8 29.4 0.6
C A:GLY37 4.8 16.1 1.0
O A:HOH398 4.9 33.9 1.0
CB A:LYS38 5.0 17.7 1.0

Manganese binding site 4 out of 6 in 9mbn

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Manganese binding site 4 out of 6 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M 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 Ep-M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:21.8
occ:0.40
 OP1 B:IGU201 2.1 42.3 1.0
OE2 B:GLU56 2.1 30.9 1.0
O B:HOH409 2.2 35.5 0.8
O B:HOH370 2.2 27.4 1.0
O B:GLY36 2.3 20.4 1.0
OE1 B:GLU100 2.4 35.7 0.5
MN B:MN203 2.7 30.5 0.2
CD B:GLU56 3.2 34.2 1.0
P B:IGU201 3.4 38.5 1.0
C B:GLY36 3.5 19.6 1.0
OE1 B:GLU56 3.6 26.1 1.0
CD B:GLU100 3.7 45.8 0.5
O B:HOH371 3.8 40.6 1.0
OP2 B:IGU201 3.8 44.1 1.0
OE1 B:GLU52 4.0 32.8 1.0
CA B:GLY37 4.0 17.6 1.0
O5' B:IGU201 4.2 27.5 1.0
N B:GLY37 4.2 18.4 1.0
O B:HOH350 4.3 24.5 1.0
CG B:GLU56 4.4 29.7 1.0
OE2 B:GLU100 4.5 47.1 0.5
OP3 B:IGU201 4.6 48.4 1.0
O B:HOH304 4.6 32.5 1.0
N B:GLY36 4.6 20.2 1.0
CE B:LYS23 4.6 77.3 1.0
CG B:GLU100 4.6 47.4 0.5
C4' B:IGU201 4.6 23.6 1.0
CA B:GLY36 4.7 17.3 1.0
NZ B:LYS23 4.9 68.1 1.0
MN B:MN204 4.9 35.6 0.2
O B:HOH342 4.9 38.6 1.0
CD B:GLU52 4.9 32.6 1.0
C5' B:IGU201 4.9 25.2 1.0

Manganese binding site 5 out of 6 in 9mbn

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Manganese binding site 5 out of 6 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M 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 Ep-M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn203

b:30.5
occ:0.20
 O B:HOH409 1.8 35.5 0.8
OE2 B:GLU56 2.1 30.9 1.0
O B:HOH342 2.3 38.6 1.0
O B:HOH371 2.3 40.6 1.0
OE1 B:GLU52 2.5 32.8 1.0
MN B:MN202 2.7 21.8 0.4
CD B:GLU56 3.1 34.2 1.0
OE1 B:GLU100 3.1 35.7 0.5
MN B:MN204 3.2 35.6 0.2
CG B:GLU56 3.4 29.7 1.0
CD B:GLU52 3.5 32.6 1.0
O B:GLY36 3.7 20.4 1.0
OE2 B:GLU52 3.8 39.5 1.0
CD B:GLU100 4.0 45.8 0.5
O B:HOH408 4.1 51.1 1.0
OE1 B:GLU56 4.1 26.1 1.0
OE2 B:GLU100 4.4 47.1 0.5
OP1 B:IGU201 4.4 42.3 1.0
O B:HOH304 4.5 32.5 1.0
O B:HOH370 4.5 27.4 1.0
C B:GLY36 4.5 19.6 1.0
CG B:GLU52 4.8 31.2 1.0
CA B:GLY37 4.8 17.6 1.0
CB B:GLU56 4.9 28.6 1.0
OP2 B:IGU201 5.0 44.1 1.0
OE1 B:GLU55 5.0 66.2 1.0

Manganese binding site 6 out of 6 in 9mbn

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn204

b:35.6
occ:0.20
 OE2 B:GLU52 2.2 39.5 1.0
O B:HOH408 2.4 51.1 1.0
O B:HOH325 2.6 36.1 1.0
O B:HOH409 2.7 35.5 0.8
O B:HOH304 2.8 32.5 1.0
CD B:GLU52 3.0 32.6 1.0
OE1 B:GLU52 3.2 32.8 1.0
MN B:MN203 3.2 30.5 0.2
O B:HOH342 3.5 38.6 1.0
O B:HOH371 3.7 40.6 1.0
NH1 B:ARG51 4.2 33.5 1.0
N B:LYS38 4.3 20.6 1.0
CG B:GLU52 4.4 31.2 1.0
CA B:GLY37 4.4 17.6 1.0
OE1 B:GLU55 4.6 66.2 1.0
O B:LYS38 4.6 25.8 1.0
OP2 B:IGU201 4.7 44.1 1.0
C B:GLY37 4.7 21.5 1.0
MN B:MN202 4.9 21.8 0.4

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 02:45:59 2025

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