Atomistry » Magnesium » PDB 5fsc-5g5t » 5g57
Atomistry »
  Magnesium »
    PDB 5fsc-5g5t »
      5g57 »

Magnesium in PDB 5g57: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-001

Protein crystallography data

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-001, PDB code: 5g57 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) 79.77 / 1.73
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.420, 115.090, 68.760, 90.00, 108.08, 90.00
R / Rfree (%) 15.9 / 18.3

Other elements in 5g57:

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-001 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-001 (pdb code 5g57). 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-001, PDB code: 5g57:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5g57

Go back to Magnesium Binding Sites List in 5g57
Magnesium binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-001


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-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1920

b:11.8
occ:1.00
O A:HOH2091 2.1 22.0 1.0
O A:HOH2113 2.1 22.6 1.0
OD1 A:ASP710 2.1 20.6 1.0
O A:HOH2069 2.1 25.6 1.0
O A:HOH2089 2.1 22.1 1.0
O A:HOH2090 2.1 24.6 1.0
CG A:ASP710 3.2 19.3 1.0
OD2 A:ASP710 3.5 21.1 1.0
ZN A:ZN1919 3.8 23.8 1.0
O A:HOH2070 4.1 27.1 1.0
NE2 A:HIS745 4.1 22.2 1.0
OG1 A:THR783 4.1 21.7 1.0
O A:HIS709 4.2 20.1 1.0
OE2 A:GLU742 4.2 29.0 1.0
CD2 A:HIS709 4.3 20.3 1.0
O A:HOH2093 4.4 26.0 1.0
OD2 A:ASP822 4.4 27.1 1.0
O A:HOH2100 4.5 51.3 1.0
CD2 A:HIS745 4.5 20.8 1.0
CB A:ASP710 4.5 20.4 1.0
CD2 A:HIS713 4.6 24.0 1.0
NE2 A:HIS709 4.7 20.0 1.0
CB A:THR783 4.7 21.2 1.0
NE2 A:HIS669 4.7 27.5 1.0
CA A:ASP710 4.8 20.9 1.0
CD2 A:HIS669 4.8 26.9 1.0
NE2 A:HIS713 4.9 23.4 1.0
C29 A:6M51931 4.9 30.0 1.0

Magnesium binding site 2 out of 2 in 5g57

Go back to Magnesium Binding Sites List in 5g57
Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-001


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-001 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1920

b:10.4
occ:1.00
O B:HOH2085 2.0 24.4 1.0
OD1 B:ASP710 2.0 20.8 1.0
O B:HOH2065 2.0 25.8 1.0
O B:HOH2084 2.1 23.8 1.0
O B:HOH2086 2.1 19.8 1.0
O B:HOH2115 2.1 22.2 1.0
CG B:ASP710 3.1 20.6 1.0
OD2 B:ASP710 3.5 20.8 1.0
ZN B:ZN1919 3.8 25.2 1.0
O B:HOH2064 4.1 24.9 1.0
NE2 B:HIS745 4.1 20.0 1.0
OE2 B:GLU742 4.1 25.9 1.0
O B:HIS709 4.1 21.4 1.0
OG1 B:THR783 4.2 22.6 1.0
CD2 B:HIS709 4.2 21.5 1.0
O B:HOH2089 4.3 25.2 1.0
OD2 B:ASP822 4.4 28.9 1.0
CD2 B:HIS745 4.5 19.4 1.0
CB B:ASP710 4.5 20.3 1.0
CD2 B:HIS713 4.5 22.0 1.0
NE2 B:HIS709 4.6 20.4 1.0
C29 B:6M51918 4.7 32.2 1.0
CB B:THR783 4.8 22.7 1.0
C28 B:6M51918 4.8 35.5 1.0
NE2 B:HIS669 4.8 27.5 1.0
CA B:ASP710 4.8 20.5 1.0
CD2 B:HIS669 4.8 25.8 1.0
O B:HOH2098 4.8 44.5 1.0
NE2 B:HIS713 4.8 22.2 1.0
CD B:GLU742 5.0 26.5 1.0

Reference:

A.R.Blaazer, A.K.Singh, E.De Heuvel, E.Edink, K.M.Orrling, J.J.N.Veerman, T.Van Den Bergh, C.Jansen, E.Balasubramaniam, W.J.Mooij, H.Custers, M.Sijm, D.N.A.Tagoe, T.D.Kalejaiye, J.C.Munday, H.Tenor, A.Matheeussen, M.Wijtmans, M.Siderius, C.De Graaf, L.Maes, H.P.De Koning, D.S.Bailey, G.J.Sterk, I.J.P.De Esch, D.G.Brown, R.Leurs. Targeting A Subpocket in Trypanosoma Brucei Phosphodiesterase B1 (TBRPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J. Med. Chem. V. 61 3870 2018.
ISSN: ISSN 1520-4804
PubMed: 29672041
DOI: 10.1021/ACS.JMEDCHEM.7B01670
Page generated: Mon Dec 14 20:20:27 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