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Zinc in PDB 3lon: Hcv NS3-4A Protease Domain with Ketoamide Inhibitor Narlaprevir

Protein crystallography data

The structure of Hcv NS3-4A Protease Domain with Ketoamide Inhibitor Narlaprevir, PDB code: 3lon was solved by A.J.Prongay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 224.392, 224.392, 75.331, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Hcv NS3-4A Protease Domain with Ketoamide Inhibitor Narlaprevir (pdb code 3lon). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Hcv NS3-4A Protease Domain with Ketoamide Inhibitor Narlaprevir, PDB code: 3lon:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3lon

Go back to Zinc Binding Sites List in 3lon
Zinc binding site 1 out of 2 in the Hcv NS3-4A Protease Domain with Ketoamide Inhibitor Narlaprevir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hcv NS3-4A Protease Domain with Ketoamide Inhibitor Narlaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:44.9
occ:1.00
O A:HOH190 2.0 12.4 1.0
SG A:CYS97 2.1 31.8 1.0
SG A:CYS99 2.2 49.6 1.0
SG A:CYS145 2.4 41.9 1.0
CB A:CYS145 3.3 38.1 1.0
CB A:CYS99 3.3 47.3 1.0
CB A:CYS97 3.5 36.0 1.0
N A:CYS99 3.6 51.0 1.0
CA A:CYS97 3.8 39.4 1.0
N A:THR98 3.8 46.6 1.0
CA A:CYS99 4.0 48.8 1.0
C A:CYS97 4.3 44.2 1.0
CB A:HIS149 4.3 33.2 1.0
CB A:ALA147 4.4 34.3 1.0
C A:THR98 4.6 51.8 1.0
C A:CYS99 4.6 49.0 1.0
CG A:HIS149 4.7 36.8 1.0
CA A:CYS145 4.7 35.4 1.0
N A:GLY100 4.8 47.0 1.0
CD2 A:HIS149 4.8 40.5 1.0
CA A:THR98 4.8 49.2 1.0

Zinc binding site 2 out of 2 in 3lon

Go back to Zinc Binding Sites List in 3lon
Zinc binding site 2 out of 2 in the Hcv NS3-4A Protease Domain with Ketoamide Inhibitor Narlaprevir


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hcv NS3-4A Protease Domain with Ketoamide Inhibitor Narlaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn902

b:42.9
occ:1.00
SG C:CYS145 2.1 37.4 1.0
SG C:CYS97 2.2 33.1 1.0
SG C:CYS99 2.3 40.7 1.0
O C:HOH190 2.3 11.0 1.0
CB C:CYS145 3.3 32.3 1.0
CB C:CYS99 3.4 35.3 1.0
CB C:CYS97 3.5 32.8 1.0
N C:CYS99 3.7 38.7 1.0
CA C:CYS97 3.9 33.9 1.0
N C:THR98 3.9 37.1 1.0
CA C:CYS99 4.1 38.4 1.0
CB C:HIS149 4.3 22.4 1.0
C C:CYS97 4.4 35.1 1.0
CB C:ALA147 4.4 26.8 1.0
C C:CYS99 4.7 40.1 1.0
C C:THR98 4.7 39.2 1.0
N C:GLY100 4.7 41.3 1.0
CA C:CYS145 4.8 30.1 1.0
CG C:HIS149 4.8 20.5 1.0
ND1 C:HIS149 4.9 28.4 1.0
N C:ALA147 4.9 31.1 1.0
CA C:THR98 4.9 37.8 1.0

Reference:

A.Arasappan, F.Bennett, S.L.Bogen, M.Blackman, K.Chen, S.Hendrata, Y.Huang, R.M.Huelgas, L.Nair, A.I.Padilla, W.Pan, R.Pike, P.Pinto, S.Ruan, M.Sannigrahi, F.Velaquez, B.Vibulbhan, W.Wu, W.Yang, A.K.Saksena, V.Girijavallabhan, N.Y.Shih, J.Kong, T.Meng, Y.Jin, J.Wong, P.Mcnamara, A.Prongay, V.Madison, J.J.Piwinski, K.C.Cheng, R.Morrison, B.Malcolm, X.Tong, R.Ralston, F.G.Njoroge. Candidate Selection and Preclinical Evaluation Culminating in the Discovery of Narlaprevir (Sch 900518): A Potent, Selective and Orally Efficacious Second Generation Hcv NS3 Serine Protease Inhibitor To Be Published.
Page generated: Wed Dec 16 04:32:40 2020

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