Atomistry » Sodium » PDB 5g3c-5gtl » 5ghm
Atomistry »
  Sodium »
    PDB 5g3c-5gtl »
      5ghm »

Sodium in PDB 5ghm: Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0

Enzymatic activity of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0

All present enzymatic activity of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0:
3.6.1.55; 3.6.1.56;

Protein crystallography data

The structure of Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0, PDB code: 5ghm 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) 37.80 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.790, 47.778, 123.610, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0 (pdb code 5ghm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0, PDB code: 5ghm:

Sodium binding site 1 out of 1 in 5ghm

Go back to Sodium Binding Sites List in 5ghm
Sodium binding site 1 out of 1 in the Crystal Structure of Human MTH1(G2K/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0


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/D120N Mutant) in Complex with 8- Oxo-Dgtp at pH 7.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:48.0
occ:1.00
O A:HOH310 2.3 26.8 1.0
O A:HOH337 2.4 33.3 1.0
O1B A:8DG201 2.5 0.8 1.0
OE2 A:GLU56 2.6 29.1 1.0
O A:GLY36 2.8 15.3 1.0
O2A A:8DG201 2.9 0.8 1.0
O3A A:8DG201 3.6 0.2 1.0
PB A:8DG201 3.6 0.7 1.0
CD A:GLU56 3.7 28.3 1.0
O A:HOH448 3.8 66.5 1.0
PA A:8DG201 3.8 0.7 1.0
C A:GLY36 3.9 12.2 1.0
CA A:GLY37 4.1 14.3 1.0
OE1 A:GLU56 4.2 23.2 1.0
O5' A:8DG201 4.5 0.6 1.0
N A:GLY37 4.5 13.1 1.0
OE1 A:GLU52 4.6 28.4 1.0
O3G A:8DG201 4.6 1.0 1.0
O2B A:8DG201 4.6 0.5 1.0
O3B A:8DG201 4.8 0.8 1.0
OE1 A:GLU100 4.8 65.5 1.0
CG A:GLU56 4.8 22.5 1.0
C5' A:8DG201 4.8 91.9 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 11:01:34 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy