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Magnesium in PDB 5g5v: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-038

Protein crystallography data

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-038, PDB code: 5g5v 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) 88.58 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 147.690, 114.781, 64.009, 90.00, 109.40, 90.00
R / Rfree (%) 17.6 / 19.9

Other elements in 5g5v:

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-038 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-038 (pdb code 5g5v). 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-038, PDB code: 5g5v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5g5v

Go back to Magnesium Binding Sites List in 5g5v
Magnesium binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-038


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-038 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1919

b:2.0
occ:1.00
O A:HOH2095 2.1 11.2 1.0
OD1 A:ASP710 2.2 7.0 1.0
O A:HOH2094 2.2 8.7 1.0
O A:HOH2071 2.2 15.8 1.0
O A:HOH2096 2.2 8.5 1.0
O A:HOH2121 2.3 10.0 1.0
CG A:ASP710 3.2 7.2 1.0
OD2 A:ASP710 3.5 7.3 1.0
ZN A:ZN1918 3.7 11.1 1.0
O A:HOH2073 4.0 12.6 1.0
NE2 A:HIS745 4.2 7.9 1.0
OE2 A:GLU742 4.2 13.2 1.0
OG1 A:THR783 4.2 9.3 1.0
O A:HIS709 4.2 6.6 1.0
O A:HOH2097 4.3 13.8 1.0
CD2 A:HIS709 4.3 6.9 1.0
OD2 A:ASP822 4.4 10.4 1.0
CD2 A:HIS713 4.4 9.0 1.0
CD2 A:HIS745 4.5 7.9 1.0
CB A:ASP710 4.5 7.3 1.0
NE2 A:HIS713 4.6 8.7 1.0
NE2 A:HIS709 4.7 6.9 1.0
CB A:THR783 4.7 9.6 1.0
C25 A:8Z41936 4.8 26.7 1.0
CA A:ASP710 4.9 7.3 1.0
O A:HOH2120 4.9 32.5 1.0
O A:THR783 4.9 10.4 1.0
CD2 A:HIS669 5.0 9.4 1.0

Magnesium binding site 2 out of 2 in 5g5v

Go back to Magnesium Binding Sites List in 5g5v
Magnesium binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-038


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-038 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1920

b:2.0
occ:1.00
O B:HOH2104 2.0 14.5 1.0
OD1 B:ASP710 2.1 9.6 1.0
O B:HOH2083 2.1 12.1 1.0
O B:HOH2060 2.2 16.7 1.0
O B:HOH2085 2.2 10.5 1.0
O B:HOH2084 2.2 12.2 1.0
CG B:ASP710 3.2 8.9 1.0
OD2 B:ASP710 3.5 8.2 1.0
ZN B:ZN1919 3.8 12.4 1.0
NE2 B:HIS745 4.1 10.2 1.0
O B:HOH2062 4.1 15.3 1.0
OG1 B:THR783 4.1 10.3 1.0
OE2 B:GLU742 4.2 16.7 1.0
O B:HIS709 4.2 8.4 1.0
CD2 B:HIS709 4.3 8.1 1.0
O B:HOH2148 4.3 30.2 1.0
CD2 B:HIS745 4.4 10.0 1.0
OD2 B:ASP822 4.4 10.7 1.0
O B:HOH2087 4.5 20.2 1.0
CB B:ASP710 4.5 9.1 1.0
CD2 B:HIS713 4.5 14.1 1.0
CB B:THR783 4.7 11.2 1.0
NE2 B:HIS709 4.7 8.1 1.0
NE2 B:HIS713 4.8 14.4 1.0
CA B:ASP710 4.8 9.1 1.0
CD2 B:HIS669 4.9 13.2 1.0
NE2 B:HIS669 5.0 13.2 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 20:20:33 2020

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