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Sodium in PDB 5ghi: Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp

Enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp

All present enzymatic activity of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp:
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp, PDB code: 5ghi 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) 32.10 / 1.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.458, 47.554, 123.815, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp (pdb code 5ghi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp, PDB code: 5ghi:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5ghi

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Sodium binding site 1 out of 3 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp


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 Mutant) in Complex with 8-Oxo-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:16.2
occ:1.00
O2A A:8DG201 2.3 16.1 1.0
OE2 A:GLU56 2.3 19.0 1.0
O1B A:8DG201 2.3 17.7 1.0
O A:GLY36 2.3 13.3 1.0
O A:HOH399 2.4 16.2 1.0
O A:HOH425 2.7 28.9 1.0
NA A:NA203 3.3 21.6 1.0
CD A:GLU56 3.3 16.9 1.0
PA A:8DG201 3.4 15.2 1.0
PB A:8DG201 3.5 17.8 1.0
O3A A:8DG201 3.5 15.9 1.0
OE1 A:GLU56 3.5 15.5 1.0
C A:GLY36 3.6 11.0 1.0
NZ A:LYS23 3.7 17.0 1.0
CE A:LYS23 4.0 17.0 1.0
CA A:GLY37 4.1 12.2 1.0
O5' A:8DG201 4.2 13.7 1.0
O3B A:8DG201 4.2 19.6 1.0
N A:GLY37 4.3 11.3 1.0
OE1 A:GLU52 4.4 23.7 1.0
O A:HOH382 4.5 13.7 1.0
O A:HOH303 4.5 30.9 1.0
N A:GLY36 4.6 10.5 1.0
CG A:GLU56 4.6 17.3 1.0
O1A A:8DG201 4.7 18.1 1.0
O2G A:8DG201 4.7 28.5 1.0
CA A:GLY36 4.7 12.1 1.0
O2B A:8DG201 4.7 16.3 1.0
C4' A:8DG201 4.7 13.1 1.0
C5' A:8DG201 5.0 13.5 1.0
CG A:GLU100 5.0 28.5 1.0

Sodium binding site 2 out of 3 in 5ghi

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Sodium binding site 2 out of 3 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp


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 Mutant) in Complex with 8-Oxo-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:21.6
occ:1.00
OE1 A:GLU52 2.3 23.7 1.0
O A:HOH303 2.4 30.9 1.0
O1B A:8DG201 2.4 17.7 1.0
OE2 A:GLU56 2.5 19.0 1.0
O A:HOH301 2.5 37.0 1.0
O A:HOH310 3.1 26.5 1.0
NA A:NA202 3.3 16.2 1.0
O A:HOH471 3.3 24.1 1.0
CD A:GLU52 3.3 19.9 1.0
CD A:GLU56 3.4 16.9 1.0
OE2 A:GLU52 3.6 21.3 1.0
PB A:8DG201 3.7 17.8 1.0
CG A:GLU56 3.8 17.3 1.0
O A:GLY36 3.8 13.3 1.0
O A:HOH425 4.0 28.9 1.0
O2G A:8DG201 4.1 28.5 1.0
O2B A:8DG201 4.1 16.3 1.0
OE2 A:GLU100 4.4 34.5 1.0
OE1 A:GLU56 4.4 15.5 1.0
CA A:GLY37 4.4 12.2 1.0
C A:GLY36 4.5 11.0 1.0
OE1 A:GLU55 4.5 35.0 1.0
CG A:GLU52 4.7 17.6 1.0
CG A:GLU100 4.7 28.5 1.0
CD A:GLU100 4.7 33.1 1.0
O3B A:8DG201 4.7 19.6 1.0
N A:GLY37 4.8 11.3 1.0
O3A A:8DG201 4.8 15.9 1.0
O A:HOH445 4.9 36.1 1.0
O A:HOH460 5.0 41.5 1.0
CB A:GLU52 5.0 16.9 1.0

Sodium binding site 3 out of 3 in 5ghi

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Sodium binding site 3 out of 3 in the Crystal Structure of Human MTH1(G2K Mutant) in Complex with 8-Oxo-Dgtp


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 Mutant) in Complex with 8-Oxo-Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:31.2
occ:1.00
O1A B:8DG201 2.2 29.0 1.0
OE2 B:GLU56 2.2 22.3 1.0
O B:HOH430 2.3 30.1 1.0
O B:HOH304 2.3 35.7 1.0
O B:GLY36 2.4 16.0 1.0
O2B B:8DG201 2.6 54.3 1.0
CD B:GLU56 3.3 19.8 1.0
PA B:8DG201 3.4 25.9 1.0
C B:GLY36 3.6 13.9 1.0
OE1 B:GLU56 3.6 17.2 1.0
PB B:8DG201 3.8 44.0 1.0
O3A B:8DG201 3.8 32.1 1.0
CE B:LYS23 3.9 43.8 1.0
O B:HOH368 4.0 50.5 1.0
O5' B:8DG201 4.1 19.1 1.0
CA B:GLY37 4.2 13.9 1.0
NZ B:LYS23 4.2 46.7 1.0
OE1 B:GLU52 4.3 27.5 1.0
N B:GLY37 4.3 13.7 1.0
O B:HOH375 4.5 17.5 1.0
CG B:GLU56 4.5 20.6 1.0
CD B:LYS23 4.6 36.5 1.0
N B:GLY36 4.6 12.8 1.0
O1B B:8DG201 4.7 36.1 1.0
CA B:GLY36 4.7 12.8 1.0
O2A B:8DG201 4.7 30.1 1.0
C4' B:8DG201 4.7 16.1 1.0
O B:HOH305 4.8 54.4 1.0
C5' B:8DG201 4.9 17.2 1.0
O3B B:8DG201 5.0 48.9 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: Tue Dec 15 11:01:32 2020

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