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Zinc in PDB 5l8y: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-937

Protein crystallography data

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-937, PDB code: 5l8y was solved by A.K.Singh, E.S.Anthonyrajah, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.97 / 2.14
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.820, 115.940, 68.510, 90.00, 107.43, 90.00
R / Rfree (%) 18.1 / 21.7

Other elements in 5l8y:

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-937 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-937 (pdb code 5l8y). 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-937, PDB code: 5l8y:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5l8y

Go back to Zinc Binding Sites List in 5l8y
Zinc binding site 1 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-937


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-937 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:43.9
occ:1.00
OD2 A:ASP710 2.1 36.8 1.0
O A:HOH1122 2.2 46.6 1.0
NE2 A:HIS709 2.2 42.5 1.0
OD1 A:ASP822 2.2 38.3 1.0
NE2 A:HIS673 2.2 41.5 1.0
O A:HOH1163 2.4 56.1 1.0
CD2 A:HIS709 3.0 36.6 1.0
CD2 A:HIS673 3.1 40.6 1.0
CG A:ASP710 3.1 38.3 1.0
CG A:ASP822 3.2 40.4 1.0
CE1 A:HIS709 3.2 39.9 1.0
CE1 A:HIS673 3.3 40.6 1.0
OD2 A:ASP822 3.4 44.7 1.0
OD1 A:ASP710 3.5 40.0 1.0
MG A:MG1002 3.9 30.0 1.0
O A:HOH1177 4.2 51.2 1.0
CD2 A:HIS669 4.2 41.5 1.0
CG A:HIS709 4.2 40.9 1.0
ND1 A:HIS709 4.3 38.7 1.0
CG A:HIS673 4.3 40.7 1.0
ND1 A:HIS673 4.4 43.2 1.0
CB A:ASP710 4.4 36.3 1.0
CB A:ASP822 4.5 42.0 1.0
NE2 A:HIS669 4.5 38.6 1.0
CG2 A:VAL677 4.8 37.7 1.0
CA A:ASP822 4.9 38.6 1.0

Zinc binding site 2 out of 2 in 5l8y

Go back to Zinc Binding Sites List in 5l8y
Zinc binding site 2 out of 2 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-937


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-937 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:40.5
occ:1.00
OD1 B:ASP710 2.2 34.1 1.0
OD1 B:ASP822 2.2 32.0 1.0
O B:HOH1169 2.3 37.8 1.0
NE2 B:HIS673 2.3 34.2 1.0
NE2 B:HIS709 2.3 30.1 1.0
O B:HOH1116 2.4 33.4 1.0
CG B:ASP822 3.1 34.3 1.0
CD2 B:HIS709 3.1 31.3 1.0
CG B:ASP710 3.2 36.1 1.0
CD2 B:HIS673 3.2 32.9 1.0
OD2 B:ASP822 3.3 37.2 1.0
CE1 B:HIS673 3.3 34.6 1.0
CE1 B:HIS709 3.4 32.3 1.0
OD2 B:ASP710 3.5 34.3 1.0
MG B:MG1002 3.8 23.4 1.0
CD2 B:HIS669 4.1 39.3 1.0
O B:HOH1223 4.2 43.9 1.0
CG B:HIS709 4.3 31.5 1.0
CG B:HIS673 4.4 34.4 1.0
NE2 B:HIS669 4.4 38.8 1.0
ND1 B:HIS673 4.4 33.4 1.0
ND1 B:HIS709 4.4 32.0 1.0
CB B:ASP710 4.4 34.1 1.0
CB B:ASP822 4.5 35.3 1.0
O B:HOH1130 4.7 31.9 1.0
CG2 B:VAL677 4.9 35.8 1.0
CA B:ASP822 4.9 33.6 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: Sun Oct 27 20:51:16 2024

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