Magnesium in PDB 6g2m: Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau, PDB code: 6g2m was solved by P.Pachl, P.Rezacova, J.Brynda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.86 / 1.37
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.858, 73.858, 106.121, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 15.1

Other elements in 6g2m:

The structure of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau (pdb code 6g2m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau, PDB code: 6g2m:

Magnesium binding site 1 out of 1 in 6g2m

Go back to Magnesium Binding Sites List in 6g2m
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Mitochondrial 5'(3')-Deoxyribonucleotidase in Complex with the Inhibitor Pb-Pau within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:9.5
occ:1.00
O A:HOH455 2.0 13.3 1.0
O A:HOH422 2.1 12.6 1.0
OD1 A:ASP176 2.1 12.3 1.0
O A:ASP43 2.1 12.5 1.0
OD2 A:ASP41 2.1 12.2 1.0
O11 A:O84305 2.1 14.0 1.0
CG A:ASP41 3.1 12.6 1.0
CG A:ASP176 3.1 13.0 1.0
C A:ASP43 3.2 11.5 1.0
OD1 A:ASP41 3.4 13.1 1.0
P2 A:O84305 3.5 13.2 1.0
OD2 A:ASP176 3.5 13.9 1.0
O10 A:O84305 3.7 13.4 1.0
OD1 A:ASP175 3.9 12.6 1.0
N A:GLY44 4.1 11.7 1.0
CA A:ASP43 4.1 11.1 1.0
CB A:ASP43 4.2 11.1 1.0
CA A:GLY44 4.3 11.8 1.0
N A:ASP176 4.3 12.1 1.0
C18 A:O84305 4.3 18.4 1.0
CB A:ASP176 4.4 12.0 1.0
CB A:ASP41 4.4 12.4 1.0
N A:ASP43 4.4 10.8 1.0
O9 A:O84305 4.5 13.5 1.0
CG A:ASP175 4.5 11.9 1.0
C19 A:O84305 4.5 14.9 1.0
CE1 A:PHE75 4.5 17.0 1.0
O6 A:O84305 4.6 19.8 1.0
CZ A:PHE75 4.6 16.0 1.0
CG2 A:VAL45 4.8 13.7 1.0
OD2 A:ASP175 4.8 13.4 1.0
N A:ARG177 4.8 12.5 1.0
C A:GLY44 4.8 12.9 1.0
CA A:ASP176 4.8 12.5 1.0
O A:HOH420 4.9 13.2 1.0

Reference:

P.Pachl, O.Simak, M.Budesinsky, J.Brynda, I.Rosenberg, P.Rezacova. Structure-Based Optimization of Bisphosphonate Nucleoside Inhibitors of Human 5'(3')-Deoxyribonucleotidases Eur.J.Org.Chem. 2018.
ISSN: ISSN 1434-193X
DOI: 10.1002/EJOC.201800515
Page generated: Mon Dec 14 22:43:31 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy