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Zinc 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:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-038, PDB code: 5g5v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5g5v

Go back to Zinc Binding Sites List in 5g5v
Zinc 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 Zinc with other atoms in the Zn 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:Zn1918

b:11.1
occ:1.00
O A:HOH2095 2.1 11.2 1.0
OD2 A:ASP710 2.1 7.3 1.0
OD1 A:ASP822 2.1 8.8 1.0
O A:HOH2073 2.2 12.6 1.0
NE2 A:HIS673 2.3 8.2 1.0
NE2 A:HIS709 2.3 6.9 1.0
CG A:ASP822 3.1 9.5 1.0
CG A:ASP710 3.1 7.2 1.0
CD2 A:HIS709 3.1 6.9 1.0
CD2 A:HIS673 3.2 7.7 1.0
CE1 A:HIS673 3.3 7.6 1.0
CE1 A:HIS709 3.4 7.0 1.0
OD2 A:ASP822 3.4 10.4 1.0
OD1 A:ASP710 3.6 7.0 1.0
MG A:MG1919 3.7 2.0 1.0
O A:HOH2071 3.9 15.8 1.0
O A:HOH2072 4.1 21.9 1.0
CD2 A:HIS669 4.3 9.4 1.0
CG A:HIS709 4.3 6.8 1.0
CB A:ASP710 4.4 7.3 1.0
ND1 A:HIS673 4.4 7.8 1.0
CG A:HIS673 4.4 7.8 1.0
ND1 A:HIS709 4.4 6.9 1.0
CB A:ASP822 4.4 9.1 1.0
NE2 A:HIS669 4.7 9.8 1.0
O A:HOH2094 4.9 8.7 1.0
CA A:ASP822 4.9 9.1 1.0

Zinc binding site 2 out of 2 in 5g5v

Go back to Zinc Binding Sites List in 5g5v
Zinc 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 Zinc with other atoms in the Zn 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:Zn1919

b:12.4
occ:1.00
O B:HOH2084 1.9 12.2 1.0
OD2 B:ASP710 2.2 8.2 1.0
OD1 B:ASP822 2.2 8.9 1.0
O B:HOH2062 2.2 15.3 1.0
NE2 B:HIS673 2.2 8.5 1.0
NE2 B:HIS709 2.2 8.1 1.0
CG B:ASP822 3.1 9.7 1.0
CD2 B:HIS709 3.1 8.1 1.0
CG B:ASP710 3.1 8.9 1.0
CD2 B:HIS673 3.2 8.4 1.0
CE1 B:HIS673 3.2 8.6 1.0
CE1 B:HIS709 3.3 7.8 1.0
OD2 B:ASP822 3.4 10.7 1.0
OD1 B:ASP710 3.6 9.6 1.0
MG B:MG1920 3.8 2.0 1.0
O B:HOH2060 4.0 16.7 1.0
O B:HOH2061 4.1 24.3 1.0
CG B:HIS709 4.3 7.8 1.0
CD2 B:HIS669 4.3 13.2 1.0
ND1 B:HIS709 4.3 7.8 1.0
ND1 B:HIS673 4.3 8.8 1.0
CG B:HIS673 4.4 8.5 1.0
CB B:ASP710 4.4 9.1 1.0
CB B:ASP822 4.5 9.2 1.0
NE2 B:HIS669 4.6 13.2 1.0
O B:HOH2083 4.8 12.1 1.0
CA B:ASP822 5.0 8.9 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: Wed Dec 16 06:18:39 2020

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