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Zinc in PDB 3udj: Crystal Structure of Bace with Compound 5

Enzymatic activity of Crystal Structure of Bace with Compound 5

All present enzymatic activity of Crystal Structure of Bace with Compound 5:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace with Compound 5, PDB code: 3udj 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) 31.48 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 75.113, 104.016, 100.847, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bace with Compound 5 (pdb code 3udj). 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 Crystal Structure of Bace with Compound 5, PDB code: 3udj:

Zinc binding site 1 out of 1 in 3udj

Go back to Zinc Binding Sites List in 3udj
Zinc binding site 1 out of 1 in the Crystal Structure of Bace with Compound 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:24.0
occ:0.70
ND1 A:HIS396 2.0 32.4 1.0
NE2 A:HIS398 2.0 30.5 1.0
CE1 A:HIS396 2.9 29.0 1.0
CE1 A:HIS398 2.9 33.5 1.0
CG A:HIS396 3.0 33.0 1.0
CD2 A:HIS398 3.1 31.9 1.0
CB A:HIS396 3.4 34.6 1.0
NE2 A:HIS396 4.0 33.8 1.0
ND1 A:HIS398 4.1 33.7 1.0
CD2 A:HIS396 4.1 31.8 1.0
CG A:HIS398 4.2 35.5 1.0
CA A:HIS396 4.9 35.4 1.0

Reference:

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
Page generated: Wed Dec 16 04:54:06 2020

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