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Zinc 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:

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-001 (pdb code 5g57). 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-001, PDB code: 5g57:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5g57

Go back to Zinc Binding Sites List in 5g57
Zinc 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 Zinc with other atoms in the Zn 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:Zn1919

b:23.8
occ:1.00
OD1 A:ASP822 2.1 19.3 1.0
OD2 A:ASP710 2.1 21.1 1.0
O A:HOH2090 2.2 24.6 1.0
NE2 A:HIS673 2.2 20.4 1.0
NE2 A:HIS709 2.2 20.0 1.0
O A:HOH2070 2.3 27.1 1.0
CG A:ASP822 3.0 23.7 1.0
CD2 A:HIS709 3.1 20.3 1.0
CE1 A:HIS673 3.2 20.8 1.0
CD2 A:HIS673 3.2 21.3 1.0
CG A:ASP710 3.2 19.3 1.0
CE1 A:HIS709 3.2 19.6 1.0
OD2 A:ASP822 3.3 27.1 1.0
OD1 A:ASP710 3.6 20.6 1.0
MG A:MG1920 3.8 11.8 1.0
O A:HOH2069 4.1 25.6 1.0
CD2 A:HIS669 4.2 26.9 1.0
CG A:HIS709 4.3 18.9 1.0
ND1 A:HIS709 4.3 19.6 1.0
O A:HOH2068 4.3 30.0 1.0
ND1 A:HIS673 4.3 20.1 1.0
CG A:HIS673 4.3 21.4 1.0
NE2 A:HIS669 4.3 27.5 1.0
CB A:ASP822 4.4 23.9 1.0
CB A:ASP710 4.4 20.4 1.0
O A:HOH2089 4.8 22.1 1.0
CA A:ASP822 4.9 22.1 1.0
CG2 A:VAL677 4.9 20.6 1.0

Zinc binding site 2 out of 2 in 5g57

Go back to Zinc Binding Sites List in 5g57
Zinc 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 Zinc with other atoms in the Zn 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:Zn1919

b:25.2
occ:1.00
OD1 B:ASP822 2.2 20.9 1.0
O B:HOH2085 2.2 24.4 1.0
NE2 B:HIS673 2.2 21.1 1.0
NE2 B:HIS709 2.2 20.4 1.0
OD2 B:ASP710 2.2 20.8 1.0
O B:HOH2064 2.2 24.9 1.0
CG B:ASP822 3.1 23.6 1.0
CD2 B:HIS709 3.1 21.5 1.0
CE1 B:HIS673 3.1 20.9 1.0
CD2 B:HIS673 3.2 20.8 1.0
CG B:ASP710 3.2 20.6 1.0
CE1 B:HIS709 3.2 20.5 1.0
OD2 B:ASP822 3.3 28.9 1.0
OD1 B:ASP710 3.6 20.8 1.0
MG B:MG1920 3.8 10.4 1.0
O B:HOH2065 4.0 25.8 1.0
CD2 B:HIS669 4.2 25.8 1.0
O B:HOH2062 4.2 38.1 1.0
CG B:HIS709 4.3 20.1 1.0
ND1 B:HIS673 4.3 21.1 1.0
ND1 B:HIS709 4.3 21.6 1.0
CG B:HIS673 4.3 19.8 1.0
NE2 B:HIS669 4.4 27.5 1.0
CB B:ASP710 4.4 20.3 1.0
CB B:ASP822 4.5 21.9 1.0
O B:HOH2084 4.8 23.8 1.0
C29 B:6M51918 4.9 32.2 1.0
CA B:ASP822 4.9 21.9 1.0
CG2 B:VAL677 5.0 22.1 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 06:18:37 2020

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