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Zinc in PDB 3udp: Crystal Structure of Bace with Compound 12

Enzymatic activity of Crystal Structure of Bace with Compound 12

All present enzymatic activity of Crystal Structure of Bace with Compound 12:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Bace with Compound 12, PDB code: 3udp 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) 24.75 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 74.504, 103.865, 98.462, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 27.5

Other elements in 3udp:

The structure of Crystal Structure of Bace with Compound 12 also contains other interesting chemical elements:

Bromine (Br) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bace with Compound 12 (pdb code 3udp). 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 12, PDB code: 3udp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3udp

Go back to Zinc Binding Sites List in 3udp
Zinc binding site 1 out of 2 in the Crystal Structure of Bace with Compound 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:45.7
occ:0.40
OD2 A:ASP131 2.0 45.8 1.0
ND1 A:HIS397 2.3 44.5 1.0
CG A:HIS397 2.8 42.5 1.0
O A:HOH822 2.8 48.9 1.0
CB A:HIS397 2.8 41.1 1.0
CG A:ASP131 2.9 37.5 1.0
O A:HOH898 2.9 49.9 1.0
OD1 A:ASP131 3.2 39.9 1.0
CE1 A:HIS397 3.4 45.3 1.0
CA A:HIS397 3.8 40.8 1.0
CD2 A:HIS397 4.0 39.5 1.0
NE2 A:HIS397 4.3 43.6 1.0
CB A:ASP131 4.3 35.5 1.0
C A:HIS397 4.5 41.1 1.0
O A:HOH876 4.6 57.6 1.0
O A:HIS397 4.8 42.1 1.0
N A:HIS397 5.0 40.1 1.0

Zinc binding site 2 out of 2 in 3udp

Go back to Zinc Binding Sites List in 3udp
Zinc binding site 2 out of 2 in the Crystal Structure of Bace with Compound 12


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 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:24.2
occ:0.70
ND1 A:HIS396 2.0 36.8 1.0
NE2 A:HIS398 2.0 32.7 1.0
CE1 A:HIS396 2.9 37.4 1.0
CE1 A:HIS398 3.0 33.4 1.0
CD2 A:HIS398 3.0 30.6 1.0
CG A:HIS396 3.0 39.9 1.0
CB A:HIS396 3.4 38.0 1.0
NE2 A:HIS396 4.1 37.4 1.0
ND1 A:HIS398 4.1 29.7 1.0
CD2 A:HIS396 4.1 36.9 1.0
CG A:HIS398 4.1 36.0 1.0
O A:HOH694 4.5 48.6 1.0
CA A:HIS396 4.9 39.5 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 04:54:09 2020

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