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Sodium in PDB 9mbf: Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp

Enzymatic activity of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp

All present enzymatic activity of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp:
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp, PDB code: 9mbf was solved by K.Fujimiya, Y.Hirano, K.Kusaka, T.Tamada, T.Nakamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.386, 47.421, 123.894, 90, 90, 90
R / Rfree (%) n/a / 24.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp (pdb code 9mbf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp, PDB code: 9mbf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 9mbf

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Sodium binding site 1 out of 4 in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:17.9
occ:1.00
 O1A A:6U4201 2.3 15.3 1.0
O1B A:6U4201 2.3 14.5 1.0
O A:HOH450 2.3 34.8 1.0
O A:HOH341 2.3 12.3 1.0
O A:HOH370 2.5 20.2 1.0
O A:HOH389 2.5 22.2 1.0
O A:HOH306 3.2 9.0 0.6
PB A:6U4201 3.5 12.4 1.0
PA A:6U4201 3.5 12.3 1.0
O3A A:6U4201 3.6 11.0 1.0
O A:HOH414 3.7 28.9 1.0
D2 A:HOH311 3.8 22.6 1.0
O3B A:6U4201 4.2 11.6 1.0
OE1 A:GLU56 4.3 21.0 1.0
O A:HOH311 4.3 18.8 1.0
OE2 A:GLU56 4.4 19.3 1.0
OE1 A:GLU100 4.5 35.0 1.0
O5' A:6U4201 4.5 10.2 1.0
O3G A:6U4201 4.6 20.4 1.0
O2A A:6U4201 4.6 13.8 1.0
CD A:GLU56 4.6 21.6 1.0
O2G A:6U4201 4.7 18.8 1.0
O A:GLY36 4.7 8.3 1.0
O2B A:6U4201 4.8 10.9 1.0
O A:HOH416 4.8 18.2 0.5
O A:HOH333 4.8 22.7 1.0
PG A:6U4201 4.8 15.1 1.0
H6 A:6U4201 4.9 12.1 1.0
HA2 A:GLY37 4.9 8.4 1.0
H7 A:6U4201 4.9 9.7 1.0
O A:HOH314 4.9 19.1 1.0
D1 A:HOH311 5.0 22.6 1.0

Sodium binding site 2 out of 4 in 9mbf

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Sodium binding site 2 out of 4 in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:15.5
occ:1.00
 O A:HOH311 2.3 18.8 1.0
O A:HOH331 2.4 20.1 1.0
O A:HOH367 2.4 14.7 1.0
O2B A:6U4201 2.4 10.9 1.0
OE2 A:GLU52 2.4 12.5 1.0
O A:HOH337 2.4 18.6 1.0
D1 A:HOH367 2.4 17.6 1.0
D1 A:HOH311 2.4 22.6 1.0
D2 A:HOH367 2.8 17.6 1.0
D2 A:HOH311 3.1 22.6 1.0
D1 A:HOH337 3.2 22.3 1.0
D A:LYS38 3.4 8.8 0.8
H A:LYS38 3.4 8.8 0.2
CD A:GLU52 3.4 12.5 1.0
DH12 A:ARG51 3.4 15.9 1.0
PB A:6U4201 3.5 12.4 1.0
HE21 A:GLN40 3.6 19.0 0.4
DE21 A:GLN40 3.6 19.0 0.6
OE1 A:GLU52 3.6 13.5 1.0
O1B A:6U4201 3.8 14.5 1.0
HA3 A:GLY37 3.8 8.4 1.0
O A:HOH306 3.9 16.1 0.4
HB2 A:LYS38 4.0 11.4 1.0
N A:LYS38 4.0 7.3 1.0
DH22 A:ARG51 4.1 14.8 1.0
O A:LYS38 4.2 10.3 1.0
O2G A:6U4201 4.2 18.8 1.0
NH1 A:ARG51 4.3 13.2 1.0
NE2 A:GLN40 4.3 15.8 1.0
O A:HOH373 4.4 25.2 1.0
OE1 A:GLU55 4.4 28.6 1.0
O3B A:6U4201 4.5 11.6 1.0
HE22 A:GLN40 4.5 19.0 0.5
DE22 A:GLN40 4.5 19.0 0.5
CA A:GLY37 4.6 7.0 1.0
O A:HOH306 4.6 9.0 0.6
DH11 A:ARG51 4.7 15.9 0.3
HH11 A:ARG51 4.7 15.9 0.7
O3A A:6U4201 4.7 11.0 1.0
C A:GLY37 4.7 6.9 1.0
O A:HOH463 4.7 26.3 1.0
CG A:GLU52 4.8 11.1 1.0
CB A:LYS38 4.8 9.6 1.0
CA A:LYS38 4.8 6.4 1.0
NH2 A:ARG51 4.8 12.3 1.0
HD2 A:LYS38 4.9 11.2 1.0
HG2 A:GLU52 4.9 13.4 1.0
C A:LYS38 5.0 6.5 1.0
PG A:6U4201 5.0 15.1 1.0

Sodium binding site 3 out of 4 in 9mbf

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Sodium binding site 3 out of 4 in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:28.8
occ:1.00
 OE2 B:GLU52 2.4 24.7 1.0
O2B B:6U4201 2.6 17.6 1.0
O B:HOH342 2.8 23.2 1.0
CD B:GLU52 3.3 16.9 1.0
PB B:6U4201 3.4 83.0 1.0
OE1 B:GLU52 3.4 21.0 1.0
O1B B:6U4201 3.4 74.7 1.0
HH12 B:ARG51 3.5 22.8 0.3
DH11 B:ARG51 3.5 22.8 0.8
O B:HOH387 3.5 29.3 1.0
HA3 B:GLY37 3.5 9.7 1.0
D B:LYS38 3.6 13.9 1.0
O1G B:6U4201 4.2 101.2 1.0
N B:LYS38 4.2 11.6 1.0
NH1 B:ARG51 4.3 19.0 1.0
HB2 B:LYS38 4.3 13.7 1.0
CA B:GLY37 4.4 8.1 1.0
DH22 B:ARG51 4.5 20.5 1.0
O3B B:6U4201 4.5 102.1 1.0
HE21 B:GLN40 4.5 27.6 0.4
DE22 B:GLN40 4.5 27.6 0.8
O3A B:6U4201 4.5 32.1 1.0
O B:LYS38 4.6 13.3 1.0
HH11 B:ARG51 4.6 22.8 0.2
DH12 B:ARG51 4.6 22.8 0.7
DZ2 B:LYS38 4.7 78.3 0.4
HZ1 B:LYS38 4.7 78.3 0.3
CG B:GLU52 4.7 17.4 1.0
OE1 B:GLU55 4.7 34.4 1.0
C B:GLY37 4.7 12.6 1.0
HA2 B:GLY37 4.9 9.7 1.0
HG2 B:GLU52 5.0 20.9 1.0
PG B:6U4201 5.0 92.7 1.0
HG3 B:GLU52 5.0 20.9 1.0

Sodium binding site 4 out of 4 in 9mbf

Go back to Sodium Binding Sites List in 9mbf
Sodium binding site 4 out of 4 in the Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Neutron Crystal Structure of Human MTH1(G2K/C87A/C104S Mutant) in Complex with 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:31.4
occ:1.00
 O1A B:6U4201 2.2 19.5 1.0
O B:HOH361 2.2 22.3 1.0
OE2 B:GLU56 2.3 28.8 1.0
O B:GLY36 2.4 12.7 1.0
O1B B:6U4201 2.6 74.7 1.0
DZ3 B:LYS23 3.2 55.9 0.2
HZ3 B:LYS23 3.2 55.9 0.8
PA B:6U4201 3.4 29.8 1.0
H7 B:6U4201 3.4 15.1 1.0
CD B:GLU56 3.4 41.5 1.0
O3A B:6U4201 3.5 32.1 1.0
C B:GLY36 3.6 10.4 1.0
HA3 B:GLY37 3.6 9.7 1.0
PB B:6U4201 3.6 83.0 1.0
HE3 B:LYS23 3.6 49.8 1.0
HA2 B:GLY37 3.7 9.7 1.0
O5' B:6U4201 3.9 23.9 1.0
OE1 B:GLU56 3.9 23.4 1.0
NZ B:LYS23 4.0 46.6 1.0
CA B:GLY37 4.0 8.1 1.0
CE B:LYS23 4.1 41.5 1.0
H B:GLY36 4.1 16.1 0.2
D B:GLY36 4.1 16.1 0.8
HE2 B:LYS23 4.2 49.8 1.0
O B:HOH344 4.2 19.7 1.0
N B:GLY37 4.3 8.5 1.0
OE1 B:GLU52 4.3 21.0 1.0
C4' B:6U4201 4.3 12.6 1.0
HZ2 B:LYS23 4.4 55.9 0.3
DZ2 B:LYS23 4.4 55.9 0.7
DZ1 B:LYS23 4.5 55.9 0.5
HZ1 B:LYS23 4.6 55.9 0.5
C5' B:6U4201 4.6 14.5 1.0
O2B B:6U4201 4.6 17.6 1.0
H5 B:6U4201 4.6 17.4 1.0
CG B:GLU56 4.6 30.9 1.0
N B:GLY36 4.7 13.4 1.0
HG2 B:GLU56 4.7 37.1 1.0
O2A B:6U4201 4.7 34.7 1.0
CA B:GLY36 4.8 10.5 1.0
O3B B:6U4201 4.8 102.1 1.0
HG3 B:GLU56 4.8 37.1 1.0
O2G B:6U4201 4.8 76.8 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: Mon Aug 18 17:23:35 2025

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