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

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

All present enzymatic activity of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-2M 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-2M Complex, PDB code: 9mbl 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) 44.22 / 1.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.503, 47.357, 123.631, 90, 90, 90
R / Rfree (%) 13.4 / 18.1

Other elements in 9mbl:

The structure of 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-2M Complex also contains other interesting chemical elements:

Sodium (Na) 4 atoms

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

Manganese binding site 1 out of 4 in 9mbl

Go back to Manganese Binding Sites List in 9mbl
Manganese binding site 1 out of 4 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-2M 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-2M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:16.3
occ:0.30
 O A:HOH304 0.2 42.8 0.7
O1A A:6U4201 2.0 22.2 0.3
OE2 A:GLU56 2.0 17.1 0.4
O A:HOH355 2.1 17.4 0.5
NA A:NA205 2.4 17.9 0.7
O A:GLY36 2.4 13.6 1.0
O2B A:6U4201 2.5 28.2 0.3
OE1 A:GLU56 2.8 22.8 0.6
CD A:GLU56 3.0 16.4 0.4
O1A A:6U4201 3.1 13.5 0.7
MN A:MN203 3.2 35.8 0.3
CD A:GLU56 3.3 25.3 0.6
PA A:6U4201 3.4 22.3 0.3
O2B A:6U4201 3.4 17.2 0.7
O A:HOH334 3.4 30.5 0.6
OE1 A:GLU56 3.4 13.7 0.4
O A:HOH308 3.5 39.9 1.0
O A:HOH355 3.6 15.3 0.5
C A:GLY36 3.6 11.4 1.0
OE2 A:GLU56 3.7 26.5 0.6
PB A:6U4201 3.7 27.8 0.3
O3A A:6U4201 3.9 25.1 0.3
O3A A:6U4201 4.0 13.6 0.7
PA A:6U4201 4.0 12.9 0.7
O A:HOH317 4.1 24.5 0.7
O A:HOH371 4.2 16.3 1.0
NZ A:LYS23 4.2 30.0 0.6
CA A:GLY37 4.2 10.8 1.0
O5' A:6U4201 4.2 11.6 0.7
CE A:LYS23 4.2 29.4 0.6
O5' A:6U4201 4.2 19.0 0.3
PB A:6U4201 4.3 14.5 0.7
CG A:GLU56 4.3 25.3 0.6
CG A:GLU56 4.3 18.3 0.4
N A:GLY37 4.4 11.1 1.0
OE1 A:GLU52 4.5 21.1 1.0
O2A A:6U4201 4.5 21.1 0.3
C4' A:6U4201 4.6 13.1 1.0
N A:GLY36 4.7 10.8 1.0
OE2 A:GLU100 4.7 28.3 0.4
O3B A:6U4201 4.8 30.0 0.3
CA A:GLY36 4.8 10.3 1.0
O1B A:6U4201 4.8 28.2 0.3
O A:HOH350 4.8 28.5 0.7
C5' A:6U4201 4.9 12.2 0.7
O A:HOH310 4.9 28.1 1.0
C5' A:6U4201 4.9 16.1 0.3
O1G A:6U4201 4.9 32.2 0.3

Manganese binding site 2 out of 4 in 9mbl

Go back to Manganese Binding Sites List in 9mbl
Manganese binding site 2 out of 4 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-2M 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-2M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn203

b:35.8
occ:0.30
 O A:HOH317 1.4 24.5 0.7
OE2 A:GLU56 2.3 26.5 0.6
OE2 A:GLU56 2.4 17.1 0.4
O2B A:6U4201 2.5 28.2 0.3
O A:HOH348 2.5 34.7 1.0
O A:HOH308 2.6 39.9 1.0
OE1 A:GLU52 2.6 21.1 1.0
CD A:GLU56 2.9 25.3 0.6
O A:HOH304 3.0 42.8 0.7
O2B A:6U4201 3.1 17.2 0.7
MN A:MN202 3.2 16.3 0.3
CD A:GLU56 3.4 16.4 0.4
O1G A:6U4201 3.4 32.2 0.3
CG A:GLU56 3.6 25.3 0.6
CG A:GLU56 3.6 18.3 0.4
OE1 A:GLU56 3.6 22.8 0.6
PB A:6U4201 3.6 27.8 0.3
CD A:GLU52 3.6 20.0 1.0
NA A:NA205 3.7 17.9 0.7
NA A:NA204 3.8 21.1 1.0
O1B A:6U4201 3.9 28.2 0.3
O A:GLY36 3.9 13.6 1.0
O A:HOH342 3.9 32.3 0.7
OE2 A:GLU52 4.0 20.5 1.0
PB A:6U4201 4.1 14.5 0.7
O1B A:6U4201 4.2 15.4 0.7
O A:HOH361 4.4 28.6 1.0
OE1 A:GLU56 4.5 13.7 0.4
OE1 A:GLU55 4.5 28.1 1.0
O1A A:6U4201 4.6 22.2 0.3
CA A:GLY37 4.6 10.8 1.0
PG A:6U4201 4.6 32.4 0.3
O3B A:6U4201 4.6 30.0 0.3
C A:GLY36 4.6 11.4 1.0
O3A A:6U4201 4.8 25.1 0.3
O3A A:6U4201 4.9 13.6 0.7
CG A:GLU52 5.0 18.5 1.0
N A:GLY37 5.0 11.1 1.0

Manganese binding site 3 out of 4 in 9mbl

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Manganese binding site 3 out of 4 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-2M 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-2M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn202

b:11.2
occ:0.20
 NA B:NA205 0.3 68.7 0.8
OE2 B:GLU56 2.1 27.4 1.0
O B:HOH426 2.3 23.8 1.0
O B:GLY36 2.3 13.7 1.0
OE2 B:GLU100 2.4 36.6 0.6
O B:HOH396 2.5 51.2 0.5
O1A B:6U4201 2.5 30.9 1.0
O2B B:6U4201 2.5 49.1 1.0
CD B:GLU56 3.2 23.5 1.0
MN B:MN203 3.2 17.7 0.2
C B:GLY36 3.5 11.8 1.0
CD B:GLU100 3.5 36.6 0.6
OE1 B:GLU56 3.6 21.1 1.0
PA B:6U4201 3.6 26.8 1.0
PB B:6U4201 3.7 45.2 1.0
O3A B:6U4201 3.7 34.8 1.0
O B:HOH417 3.7 36.8 0.5
CG B:GLU100 4.0 33.0 0.6
CA B:GLY37 4.1 10.6 1.0
O5' B:6U4201 4.2 18.9 1.0
NZ B:LYS23 4.2 29.9 0.5
NZ B:LYS23 4.2 33.8 0.5
CE B:LYS23 4.2 29.1 0.5
N B:GLY37 4.2 10.8 1.0
OE1 B:GLU52 4.2 24.5 1.0
O B:HOH354 4.3 18.2 1.0
CG B:GLU56 4.5 20.3 1.0
N B:GLY36 4.5 10.5 1.0
OE1 B:GLU100 4.6 38.4 0.6
O3B B:6U4201 4.6 56.5 1.0
CA B:GLY36 4.6 11.5 1.0
C4' B:6U4201 4.6 14.1 1.0
O1B B:6U4201 4.8 43.3 1.0
C5' B:6U4201 4.9 15.4 1.0
O2A B:6U4201 5.0 28.6 1.0

Manganese binding site 4 out of 4 in 9mbl

Go back to Manganese Binding Sites List in 9mbl
Manganese binding site 4 out of 4 in the 2-Oxo-Datp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Es-2M 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-2M Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn203

b:17.7
occ:0.20
 O B:HOH346 2.2 44.5 1.0
OE1 B:GLU52 2.3 24.5 1.0
O2B B:6U4201 2.4 49.1 1.0
O B:HOH417 2.5 36.8 0.5
OE2 B:GLU56 2.6 27.4 1.0
NA B:NA204 2.8 47.3 1.0
MN B:MN202 3.2 11.2 0.2
NA B:NA205 3.2 68.7 0.8
CD B:GLU52 3.3 24.1 1.0
CD B:GLU56 3.5 23.5 1.0
OE2 B:GLU52 3.5 25.6 1.0
PB B:6U4201 3.7 45.2 1.0
CG B:GLU56 3.7 20.3 1.0
OE2 B:GLU100 3.8 36.6 0.6
O B:HOH396 3.8 51.2 0.5
O B:GLY36 3.9 13.7 1.0
O B:HOH351 4.0 50.1 1.0
O1B B:6U4201 4.1 43.3 1.0
CD B:GLU100 4.3 36.6 0.6
O2G B:6U4201 4.3 66.5 1.0
OE1 B:GLU55 4.4 35.9 1.0
OE1 B:GLU56 4.6 21.1 1.0
C B:GLY36 4.6 11.8 1.0
CA B:GLY37 4.6 10.6 1.0
CG B:GLU52 4.7 20.9 1.0
O3A B:6U4201 4.7 34.8 1.0
O3B B:6U4201 4.8 56.5 1.0
CG B:GLU100 4.8 33.0 0.6
OE1 B:GLU100 4.9 38.4 0.6
N B:GLY37 5.0 10.8 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 02:44:02 2025

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