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Sodium in PDB 5ghq: Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp

Enzymatic activity of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp:
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp, PDB code: 5ghq was solved by T.Nakamura, S.Waz, K.Hirata, Y.Nakabeppu, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.06 / 1.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.368, 47.342, 123.362, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 18

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp (pdb code 5ghq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp, PDB code: 5ghq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5ghq

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Sodium binding site 1 out of 5 in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 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 Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:29.3
occ:0.49
 NA A:NA202 0.0 29.3 0.5
NA A:NA202 2.2 29.2 0.5
O A:HOH408 2.3 28.2 1.0
OE2 A:GLU56 2.4 26.1 1.0
O A:GLY36 2.5 12.8 1.0
O2A A:6U4201 2.9 30.8 1.0
CD A:GLU56 3.2 21.3 1.0
O1B A:6U4201 3.4 26.6 1.0
OE1 A:GLU56 3.7 19.6 1.0
C A:GLY36 3.7 10.8 1.0
PA A:6U4201 3.8 26.8 1.0
O3A A:6U4201 3.9 29.0 1.0
OE1 A:GLU100 3.9 41.3 0.5
O A:HOH305 4.0 32.5 1.0
O5' A:6U4201 4.0 20.7 1.0
CA A:GLY37 4.2 11.2 1.0
PB A:6U4201 4.2 25.1 1.0
CG A:GLU56 4.4 24.4 1.0
N A:GLY37 4.4 10.6 1.0
OE1 A:GLU52 4.4 23.7 1.0
OE2 A:GLU100 4.5 41.0 0.5
O A:HOH397 4.5 17.0 1.0
C4' A:6U4201 4.6 17.5 1.0
CD A:GLU100 4.6 39.6 0.5
N A:GLY36 4.7 9.2 1.0
C5' A:6U4201 4.8 20.0 1.0
CA A:GLY36 4.9 11.1 1.0
O A:HOH309 4.9 30.9 1.0

Sodium binding site 2 out of 5 in 5ghq

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Sodium binding site 2 out of 5 in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 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 Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:29.2
occ:0.51
 NA A:NA202 0.0 29.2 0.5
O1B A:6U4201 2.2 26.6 1.0
NA A:NA202 2.2 29.3 0.5
O2A A:6U4201 2.3 30.8 1.0
O A:HOH309 3.1 30.9 1.0
PB A:6U4201 3.4 25.1 1.0
PA A:6U4201 3.5 26.8 1.0
O3A A:6U4201 3.6 29.0 1.0
OE1 A:GLU100 3.6 41.3 0.5
OE2 A:GLU100 3.7 41.0 0.5
CD A:GLU100 3.8 39.6 0.5
OE2 A:GLU56 3.8 26.1 1.0
OE2 A:GLU100 4.0 41.0 0.5
O A:HOH305 4.0 32.5 1.0
O3B A:6U4201 4.1 31.3 1.0
O A:HOH408 4.1 28.2 1.0
O1G A:6U4201 4.3 43.4 1.0
O5' A:6U4201 4.5 20.7 1.0
O A:GLY36 4.5 12.8 1.0
O1A A:6U4201 4.5 32.0 1.0
O2B A:6U4201 4.7 26.0 1.0
PG A:6U4201 4.7 34.8 1.0
CG A:GLU100 4.7 34.6 0.5
O2G A:6U4201 4.8 41.5 1.0
CD A:GLU100 4.8 39.2 0.5
CD A:GLU56 5.0 21.3 1.0

Sodium binding site 3 out of 5 in 5ghq

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Sodium binding site 3 out of 5 in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 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 Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:24.8
occ:0.62
 O2B A:6U4201 2.3 26.0 1.0
O A:HOH367 2.3 21.5 1.0
O A:HOH380 2.4 40.9 1.0
OE2 A:GLU52 2.4 23.8 1.0
O A:HOH305 2.5 32.5 1.0
PB A:6U4201 3.4 25.1 1.0
CD A:GLU52 3.4 22.3 1.0
O1B A:6U4201 3.5 26.6 1.0
OE1 A:GLU52 3.7 23.7 1.0
O2G A:6U4201 3.8 41.5 1.0
NH1 A:ARG51 4.0 24.4 1.0
N A:LYS38 4.1 11.6 1.0
O A:LYS38 4.2 14.1 1.0
O A:HOH311 4.2 35.3 1.0
O A:HOH492 4.3 32.1 1.0
NE2 A:GLN40 4.4 23.0 1.0
O3B A:6U4201 4.4 31.3 1.0
OE1 A:GLU55 4.4 32.4 1.0
O A:HOH309 4.5 30.9 1.0
O3A A:6U4201 4.6 29.0 1.0
CA A:GLY37 4.7 11.2 1.0
CG A:GLU52 4.8 21.2 1.0
NH2 A:ARG51 4.8 21.7 1.0
C A:GLY37 4.8 9.9 1.0
PG A:6U4201 4.8 34.8 1.0
CB A:LYS38 4.8 11.9 1.0
CZ A:ARG51 4.9 22.5 1.0
CA A:LYS38 4.9 11.2 1.0

Sodium binding site 4 out of 5 in 5ghq

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Sodium binding site 4 out of 5 in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 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 Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:24.7
occ:0.46
 NA B:NA202 0.0 24.7 0.5
NA B:NA202 1.6 26.4 0.5
O B:HOH323 2.3 27.5 1.0
O B:GLY36 2.4 13.7 1.0
OE2 B:GLU56 2.4 24.2 1.0
O1A B:6U4201 2.7 54.6 1.0
O2A B:6U4201 2.9 53.9 1.0
PA B:6U4201 3.1 51.8 1.0
CD B:GLU56 3.5 20.5 1.0
C B:GLY36 3.6 11.3 1.0
O5' B:6U4201 3.7 41.6 1.0
OE1 B:GLU56 3.9 18.8 1.0
CA B:GLY37 4.0 11.6 1.0
N B:GLY37 4.3 11.1 1.0
OE1 B:GLU52 4.3 27.5 1.0
O B:HOH305 4.4 24.7 1.0
O B:HOH378 4.5 19.5 1.0
CE B:LYS23 4.5 41.2 1.0
C4' B:6U4201 4.6 24.6 1.0
C5' B:6U4201 4.6 33.0 1.0
CG B:GLU56 4.6 19.8 1.0
O3A B:6U4201 4.6 59.5 1.0
N B:GLY36 4.7 10.3 1.0
NZ B:LYS23 4.7 41.7 1.0
CA B:GLY36 4.8 11.2 1.0
O B:HOH309 4.8 42.3 1.0
O1B B:6U4201 4.8 68.4 1.0

Sodium binding site 5 out of 5 in 5ghq

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Sodium binding site 5 out of 5 in the Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human MTH1(G2K/D120A Mutant) in Complex with 2- Oxo-Datp Under High Concentrations of 2-Oxo-Datp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:26.4
occ:0.54
 NA B:NA202 0.0 26.4 0.5
NA B:NA202 1.6 24.7 0.5
OE2 B:GLU56 2.3 24.2 1.0
O B:GLY36 2.4 13.7 1.0
OE1 B:GLU52 2.9 27.5 1.0
O1A B:6U4201 3.1 54.6 1.0
CD B:GLU56 3.1 20.5 1.0
C B:GLY36 3.5 11.3 1.0
O B:HOH323 3.5 27.5 1.0
O B:HOH309 3.5 42.3 1.0
CA B:GLY37 3.7 11.6 1.0
CD B:GLU52 3.7 24.9 1.0
O B:HOH311 3.9 36.1 1.0
CG B:GLU56 3.9 19.8 1.0
OE1 B:GLU56 3.9 18.8 1.0
O B:HOH305 3.9 24.7 1.0
N B:GLY37 4.0 11.1 1.0
OE2 B:GLU52 4.1 28.0 1.0
PA B:6U4201 4.1 51.8 1.0
O2A B:6U4201 4.3 53.9 1.0
CA B:GLY36 4.6 11.2 1.0
N B:GLY36 4.7 10.3 1.0
O5' B:6U4201 4.7 41.6 1.0
CG B:GLU52 4.9 23.4 1.0

Reference:

S.Waz, T.Nakamura, K.Hirata, Y.Koga-Ogawa, M.Chirifu, T.Arimori, T.Tamada, S.Ikemizu, Y.Nakabeppu, Y.Yamagata. Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism For Its Broad Substrate Specificity J. Biol. Chem. V. 292 2785 2017.
ISSN: ESSN 1083-351X
PubMed: 28035004
DOI: 10.1074/JBC.M116.749713
Page generated: Mon Oct 7 21:11:59 2024

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