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

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

All present enzymatic activity of 8-Oxo-Dgtp 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 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M Complex, PDB code: 9mbj 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) 44.56 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.592, 47.737, 124.198, 90, 90, 90
R / Rfree (%) 13.9 / 20.8

Manganese Binding Sites:

The binding sites of Manganese atom in the 8-Oxo-Dgtp Hydrolysis in Human MTH1(G2K Mutant) Crystal Using MN2+: the Ep-M Complex (pdb code 9mbj). 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 Ep-M Complex, PDB code: 9mbj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 9mbj

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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 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 8-Oxo-Dgtp 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:18.9
occ:0.50
 OE2 A:GLU56 2.0 29.3 1.0
OP2 A:8OG201 2.0 42.7 1.0
O A:HOH367 2.1 33.6 0.8
O A:HOH346 2.2 33.6 1.0
O A:GLY36 2.3 22.1 1.0
O A:HOH368 2.3 55.8 1.0
MN A:MN203 3.0 28.4 0.2
CD A:GLU56 3.0 26.7 1.0
P A:8OG201 3.3 40.7 1.0
OE1 A:GLU56 3.5 27.0 1.0
C A:GLY36 3.5 20.4 1.0
OP3 A:8OG201 3.7 42.8 1.0
OE1 A:GLU52 4.1 44.0 1.0
CA A:GLY37 4.2 19.1 1.0
O5' A:8OG201 4.2 37.0 1.0
NZ A:LYS23 4.3 33.3 1.0
N A:GLY37 4.3 17.8 1.0
CG A:GLU56 4.3 27.0 1.0
OP1 A:8OG201 4.4 40.1 1.0
O A:HOH350 4.4 24.9 1.0
CE A:LYS23 4.4 33.9 1.0
N A:GLY36 4.5 17.2 1.0
CA A:GLY36 4.6 19.5 1.0
OE2 A:GLU100 4.7 63.7 1.0
O A:HOH305 4.8 41.7 1.0
C4' A:8OG201 4.8 33.6 1.0
C5' A:8OG201 5.0 36.0 1.0

Manganese binding site 2 out of 6 in 9mbj

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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 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 8-Oxo-Dgtp 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:28.4
occ:0.20
 O A:HOH367 1.8 33.6 0.8
OE2 A:GLU56 2.4 29.3 1.0
OE1 A:GLU52 2.5 44.0 1.0
OE2 A:GLU100 2.8 63.7 1.0
MN A:MN202 3.0 18.9 0.5
CD A:GLU56 3.4 26.7 1.0
CD A:GLU52 3.5 39.4 1.0
O A:HOH368 3.5 55.8 1.0
CG A:GLU56 3.6 27.0 1.0
MN A:MN204 3.7 35.7 0.2
OE2 A:GLU52 3.8 43.3 1.0
CD A:GLU100 3.9 61.5 1.0
O A:GLY36 3.9 22.1 1.0
OE1 A:GLU55 4.2 49.5 1.0
O A:HOH305 4.4 41.7 1.0
OE1 A:GLU56 4.5 27.0 1.0
CG A:GLU100 4.6 52.5 1.0
OP2 A:8OG201 4.6 42.7 1.0
C A:GLY36 4.7 20.4 1.0
OE1 A:GLU100 4.8 63.5 1.0
CA A:GLY37 4.8 19.1 1.0
CG A:GLU52 4.8 31.3 1.0
O A:HOH346 4.8 33.6 1.0
OP3 A:8OG201 4.9 42.8 1.0

Manganese binding site 3 out of 6 in 9mbj

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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 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 8-Oxo-Dgtp 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:35.7
occ:0.20
 O A:HOH330 2.1 40.7 1.0
OE2 A:GLU52 2.3 43.3 1.0
O A:HOH305 3.0 41.7 1.0
CD A:GLU52 3.3 39.4 1.0
O A:HOH367 3.6 33.6 0.8
OE1 A:GLU52 3.6 44.0 1.0
MN A:MN203 3.7 28.4 0.2
NH1 A:ARG51 4.0 31.5 1.0
OE1 A:GLU55 4.3 49.5 1.0
N A:LYS38 4.3 19.1 0.4
N A:LYS38 4.3 20.1 0.6
O A:LYS38 4.4 20.8 0.4
O A:LYS38 4.4 24.2 0.6
CA A:GLY37 4.7 19.1 1.0
NE2 A:GLN40 4.7 38.2 1.0
CG A:GLU52 4.7 31.3 1.0
NH2 A:ARG51 4.8 29.1 1.0
C A:GLY37 4.9 19.7 1.0
CZ A:ARG51 4.9 30.1 1.0

Manganese binding site 4 out of 6 in 9mbj

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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 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 8-Oxo-Dgtp 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:27.8
occ:0.30
 OP1 B:8OG201 1.9 75.8 1.0
OE2 B:GLU56 2.1 35.1 1.0
O B:HOH369 2.2 32.3 1.0
O B:HOH314 2.3 60.4 1.0
O B:GLY36 2.3 23.1 1.0
MN B:MN204 2.5 42.1 0.2
CD B:GLU56 3.1 31.1 1.0
P B:8OG201 3.4 74.2 1.0
OE1 B:GLU56 3.4 30.7 1.0
C B:GLY36 3.5 21.1 1.0
O5' B:8OG201 3.8 69.5 1.0
OE1 B:GLU52 4.0 49.5 1.0
OP3 B:8OG201 4.1 76.7 1.0
CA B:GLY37 4.1 18.4 1.0
N B:GLY37 4.3 19.1 1.0
CG B:GLU56 4.4 30.0 1.0
OP2 B:8OG201 4.4 76.1 1.0
O B:HOH332 4.5 32.2 1.0
N B:GLY36 4.5 19.5 1.0
NZ B:LYS23 4.5 50.4 1.0
CE B:LYS23 4.6 48.8 1.0
C5' B:8OG201 4.6 65.4 1.0
CA B:GLY36 4.6 20.1 1.0
O B:HOH304 4.6 37.3 1.0
C4' B:8OG201 4.7 61.7 1.0
CD B:GLU52 4.8 46.3 1.0

Manganese binding site 5 out of 6 in 9mbj

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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 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 8-Oxo-Dgtp 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:44.7
occ:0.20
 O B:HOH304 2.5 37.3 1.0
OE2 B:GLU52 2.5 49.5 1.0
O B:HOH354 2.5 57.0 1.0
MN B:MN204 3.0 42.1 0.2
CD B:GLU52 3.4 46.3 1.0
OE1 B:GLU52 3.7 49.5 1.0
N B:LYS38 4.3 21.1 1.0
CA B:GLY37 4.4 18.4 1.0
NH1 B:ARG51 4.5 38.9 1.0
OP3 B:8OG201 4.6 76.7 1.0
OE1 B:GLU55 4.6 62.1 1.0
O B:LYS38 4.8 25.7 1.0
C B:GLY37 4.8 17.8 1.0
CG B:GLU52 4.8 40.7 1.0

Manganese binding site 6 out of 6 in 9mbj

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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 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 8-Oxo-Dgtp 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:42.1
occ:0.20
 MN B:MN202 2.5 27.8 0.3
OE1 B:GLU52 2.6 49.5 1.0
OE2 B:GLU56 2.6 35.1 1.0
O B:HOH314 2.9 60.4 1.0
MN B:MN203 3.0 44.7 0.2
CD B:GLU52 3.4 46.3 1.0
O B:GLY36 3.4 23.1 1.0
OE2 B:GLU52 3.5 49.5 1.0
OP1 B:8OG201 3.5 75.8 1.0
CD B:GLU56 3.5 31.1 1.0
O B:HOH304 3.8 37.3 1.0
CG B:GLU56 4.0 30.0 1.0
CA B:GLY37 4.3 18.4 1.0
C B:GLY36 4.3 21.1 1.0
OE1 B:GLU56 4.4 30.7 1.0
OP3 B:8OG201 4.5 76.7 1.0
O B:HOH369 4.6 32.3 1.0
P B:8OG201 4.6 74.2 1.0
N B:GLY37 4.7 19.1 1.0
CG B:GLU52 4.8 40.7 1.0
OE1 B:GLU55 4.9 62.1 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 02:42:59 2025

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