Atomistry » Magnesium » PDB 6gtr-6h4m » 6gxq
Atomistry »
  Magnesium »
    PDB 6gtr-6h4m »
      6gxq »

Magnesium in PDB 6gxq: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335

Protein crystallography data

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335, PDB code: 6gxq was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.28 / 1.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.876, 114.424, 68.232, 90.00, 108.36, 90.00
R / Rfree (%) 20 / 24.4

Other elements in 6gxq:

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335 (pdb code 6gxq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335, PDB code: 6gxq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6gxq

Go back to Magnesium Binding Sites List in 6gxq
Magnesium binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:27.3
occ:1.00
OD1 A:ASP710 2.0 29.1 1.0
O A:HOH1259 2.0 35.2 1.0
O A:HOH1203 2.0 26.6 1.0
O A:HOH1134 2.1 27.4 1.0
O A:HOH1127 2.1 32.6 1.0
O A:HOH1227 2.1 32.1 1.0
CG A:ASP710 3.1 27.2 1.0
OD2 A:ASP710 3.5 29.9 1.0
ZN A:ZN1002 3.8 36.0 1.0
O A:HOH1175 3.9 37.3 1.0
NE2 A:HIS745 4.0 30.4 1.0
O A:HIS709 4.0 27.3 1.0
OG1 A:THR783 4.1 26.5 1.0
OE2 A:GLU742 4.2 30.4 1.0
CD2 A:HIS709 4.3 23.7 1.0
CD2 A:HIS745 4.3 28.0 1.0
CB A:ASP710 4.4 29.5 1.0
O A:HOH1200 4.4 30.9 1.0
OD2 A:ASP822 4.4 36.3 1.0
CD2 A:HIS713 4.5 31.1 1.0
O A:HOH1103 4.5 47.0 1.0
CB A:THR783 4.6 24.2 1.0
CA A:ASP710 4.6 29.1 1.0
NE2 A:HIS709 4.7 25.8 1.0
C25 A:FFZ1005 4.7 39.5 1.0
CD2 A:HIS669 4.8 27.9 1.0
NE2 A:HIS713 4.9 30.0 1.0
C A:HIS709 4.9 26.1 1.0
NE2 A:HIS669 4.9 29.0 1.0
CE1 A:HIS745 5.0 30.9 1.0

Magnesium binding site 2 out of 2 in 6gxq

Go back to Magnesium Binding Sites List in 6gxq
Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:29.9
occ:1.00
OD1 B:ASP710 2.0 28.3 1.0
O B:HOH1185 2.0 33.3 1.0
O B:HOH1242 2.0 27.4 1.0
O B:HOH1170 2.0 26.2 1.0
O B:HOH1112 2.1 27.3 1.0
O B:HOH1154 2.2 28.6 1.0
CG B:ASP710 3.0 28.9 1.0
OD2 B:ASP710 3.5 32.1 1.0
O B:HOH1199 3.6 30.6 1.0
ZN B:ZN1003 3.8 36.9 1.0
NE2 B:HIS745 3.9 23.6 1.0
O B:HIS709 3.9 27.4 1.0
OG1 B:THR783 4.2 32.6 1.0
OE2 B:GLU742 4.2 34.0 1.0
CD2 B:HIS709 4.2 25.0 1.0
O B:HOH1235 4.3 29.2 1.0
CD2 B:HIS745 4.3 24.0 1.0
CB B:ASP710 4.3 27.9 1.0
CD2 B:HIS713 4.5 27.4 1.0
OD2 B:ASP822 4.5 35.0 1.0
CA B:ASP710 4.6 25.9 1.0
NE2 B:HIS709 4.6 26.5 1.0
CB B:THR783 4.7 29.7 1.0
NE2 B:HIS713 4.8 28.5 1.0
CD2 B:HIS669 4.8 30.6 1.0
C B:HIS709 4.9 26.0 1.0
NE2 B:HIS669 5.0 31.7 1.0
CE1 B:HIS745 5.0 24.1 1.0

Reference:

E.De Heuvel, A.K.Singh, P.Boronat, A.J.Kooistra, T.Van Der Meer, P.Sadek, A.R.Blaazer, N.C.Shaner, D.S.Bindels, G.Caljon, L.Maes, G.J.Sterk, M.Siderius, M.Oberholzer, I.J.P.De Esch, D.G.Brown, R.Leurs. Alkynamide Phthalazinones As A New Class of TBRPDEB1 Inhibitors (Part 2). Bioorg.Med.Chem. V. 27 4013 2019.
ISSN: ESSN 1464-3391
PubMed: 31378593
DOI: 10.1016/J.BMC.2019.06.026
Page generated: Tue Oct 1 01:27:53 2024

Last articles

Sr in 3BNQ
Sr in 2X53
Sr in 2SPT
Sr in 2QJY
Sr in 2XRM
Sr in 2WOH
Sr in 2RIO
Sr in 2PN4
Sr in 2QJP
Sr in 2HMP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy