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Zinc in PDB 3pvk: Secreted Aspartic Protease 2 in Complex with Benzamidine

Enzymatic activity of Secreted Aspartic Protease 2 in Complex with Benzamidine

All present enzymatic activity of Secreted Aspartic Protease 2 in Complex with Benzamidine:
3.4.23.24;

Protein crystallography data

The structure of Secreted Aspartic Protease 2 in Complex with Benzamidine, PDB code: 3pvk was solved by H.Koester, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 1.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.380, 63.580, 98.410, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 18.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Secreted Aspartic Protease 2 in Complex with Benzamidine (pdb code 3pvk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Secreted Aspartic Protease 2 in Complex with Benzamidine, PDB code: 3pvk:

Zinc binding site 1 out of 1 in 3pvk

Go back to Zinc Binding Sites List in 3pvk
Zinc binding site 1 out of 1 in the Secreted Aspartic Protease 2 in Complex with Benzamidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Secreted Aspartic Protease 2 in Complex with Benzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:9.3
occ:1.00
OD2 A:ASP57 2.0 8.6 1.0
N1 A:IMD4003 2.1 12.8 1.0
N3 A:IMD4002 2.1 11.4 1.0
CG A:ASP57 2.8 8.1 1.0
OD1 A:ASP57 2.9 7.6 1.0
C4 A:IMD4002 2.9 17.2 1.0
C5 A:IMD4003 3.0 20.6 1.0
C2 A:IMD4003 3.1 18.6 1.0
C2 A:IMD4002 3.2 15.1 1.0
C5 A:IMD4002 4.1 20.5 1.0
CB A:ASP57 4.2 8.8 1.0
C4 A:IMD4003 4.2 19.8 1.0
N3 A:IMD4003 4.2 18.2 1.0
N1 A:IMD4002 4.3 21.4 1.0
OG1 A:THR55 4.3 10.3 1.0
NE2 A:GLN61 4.5 11.8 1.0
CB A:THR55 4.8 9.3 1.0
O A:HOH519 4.8 28.0 1.0

Reference:

J.Behnen, H.Koster, G.Neudert, T.Craan, A.Heine, G.Klebe. Experimental and Computational Active Site Mapping As A Starting Point to Fragment-Based Lead Discovery. Chemmedchem V. 7 248 2012.
ISSN: ISSN 1860-7179
PubMed: 22213702
DOI: 10.1002/CMDC.201100490
Page generated: Wed Dec 16 04:44:05 2020

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