Zinc in PDB 3udk: Crystal Structure of Bace with Compound 6

All present enzymatic activity of Crystal Structure of Bace with Compound 6:
3.4.23.46;

The structure of Crystal Structure of Bace with Compound 6, PDB code: 3udk was solved by I.V.Efremov, F.F.Vajdos, K.Borzilleri, S.Capetta, P.Dorff, J.Dutra, M.Mansour, C.Oborski, T.O'connell, T.J.O'sullivan, J.Pandit, H.Wang, J.Withka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.14 / 2.51
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	74.797, 104.425, 101.333, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 30.6

The binding sites of Zinc atom in the Crystal Structure of Bace with Compound 6 (pdb code 3udk). 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 Bace with Compound 6, PDB code: 3udk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Bace with Compound 6


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 Bace with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:47.1 occ:0.40 OD2 A:ASP131 1.8 39.4 1.0 ND1 A:HIS397 2.2 49.7 1.0 CG A:ASP131 2.5 39.3 1.0 OD1 A:ASP131 2.6 44.4 1.0 CG A:HIS397 2.9 49.2 1.0 CB A:HIS397 3.1 47.9 1.0 CE1 A:HIS397 3.3 49.5 1.0 O A:HOH632 3.3 31.7 1.0 CA A:HIS397 3.6 47.1 1.0 CB A:ASP131 4.0 37.7 1.0 CD2 A:HIS397 4.1 48.8 1.0 NE2 A:HIS397 4.2 49.0 1.0 O A:HIS396 4.6 47.0 1.0 N A:HIS397 4.6 46.9 1.0 C A:HIS397 4.7 46.3 1.0 C A:HIS396 5.0 46.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Bace with Compound 6


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 Bace with Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:29.4 occ:0.70 ND1 A:HIS396 2.1 40.4 1.0 NE2 A:HIS398 2.2 34.6 1.0 CE1 A:HIS396 3.0 40.1 1.0 CE1 A:HIS398 3.0 33.4 1.0 CG A:HIS396 3.1 41.9 1.0 CD2 A:HIS398 3.2 34.8 1.0 CB A:HIS396 3.4 45.1 1.0 NE2 A:HIS396 4.1 39.2 1.0 CD2 A:HIS396 4.2 38.8 1.0 ND1 A:HIS398 4.2 35.2 1.0 CG A:HIS398 4.3 39.8 1.0 CA A:HIS396 4.9 45.6 1.0

I.V.Efremov, F.F.Vajdos, K.A.Borzilleri, S.Capetta, H.Chen, P.H.Dorff, J.K.Dutra, S.W.Goldstein, M.Mansour, A.Mccoll, S.Noell, C.E.Oborski, T.N.O'connell, T.J.O'sullivan, J.Pandit, H.Wang, B.Wei, J.M.Withka. Discovery and Optimization of A Novel Spiropyrrolidine Inhibitor of {Beta}-Secretase (BACE1) Through Fragment-Based Drug Design. J.Med.Chem. V. 55 9069 2012.
ISSN: ISSN 0022-2623
PubMed: 22468999
DOI: 10.1021/JM201715D