Zinc in PDB 5drp: Structure of the Aalpxc/Lpc-023 Complex

The structure of Structure of the Aalpxc/Lpc-023 Complex, PDB code: 5drp was solved by J.Najeeb, C.-J.Lee, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.81 / 1.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.657, 50.419, 61.730, 80.26, 71.71, 88.90
R / Rfree (%)	15.6 / 19.2

The structure of Structure of the Aalpxc/Lpc-023 Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of the Aalpxc/Lpc-023 Complex (pdb code 5drp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Aalpxc/Lpc-023 Complex, PDB code: 5drp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Aalpxc/Lpc-023 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Aalpxc/Lpc-023 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:22.4 occ:1.00 OD1 A:ASP230 2.0 20.9 1.0 O01 A:5EP402 2.0 23.6 1.0 NE2 A:HIS226 2.1 22.0 1.0 NE2 A:HIS74 2.1 25.3 1.0 O04 A:5EP402 2.2 25.2 1.0 CG A:ASP230 2.7 20.3 1.0 OD2 A:ASP230 2.8 22.9 1.0 C02 A:5EP402 2.8 32.6 1.0 N03 A:5EP402 2.8 28.1 1.0 CE1 A:HIS226 3.0 24.6 1.0 CD2 A:HIS226 3.1 20.8 1.0 CD2 A:HIS74 3.1 22.8 1.0 CE1 A:HIS74 3.1 35.3 1.0 OE2 A:GLU73 4.1 28.3 1.0 ND1 A:HIS226 4.1 25.2 1.0 OG1 A:THR179 4.1 28.1 1.0 C05 A:5EP402 4.2 31.7 1.0 CG A:HIS226 4.2 25.1 1.0 ND1 A:HIS74 4.2 38.1 1.0 CB A:ASP230 4.2 19.2 1.0 CG A:GLU73 4.2 26.6 1.0 CG A:HIS74 4.2 28.3 1.0 CB A:THR179 4.3 26.4 1.0 O A:HOH537 4.6 43.6 1.0 C29 A:5EP402 4.7 38.8 1.0 CD A:GLU73 4.7 26.4 1.0 C26 A:5EP402 4.7 36.9 1.0 C27 A:5EP402 4.7 35.2 1.0 N06 A:5EP402 4.8 31.1 1.0 CA A:ASP230 4.8 20.5 1.0 NE2 A:HIS253 4.9 28.7 1.0 CA A:THR179 4.9 24.1 1.0 CE1 A:HIS253 4.9 26.6 1.0 O A:HIS226 5.0 22.3 1.0

Zinc binding site 2 out of 2 in the Structure of the Aalpxc/Lpc-023 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Aalpxc/Lpc-023 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:19.3 occ:1.00 NE2 B:HIS74 2.0 23.5 1.0 OD1 B:ASP230 2.0 13.1 1.0 NE2 B:HIS226 2.0 15.6 1.0 O01 B:5EP402 2.1 20.4 1.0 O04 B:5EP402 2.3 24.1 1.0 CG B:ASP230 2.7 19.7 1.0 OD2 B:ASP230 2.7 21.6 1.0 C02 B:5EP402 2.9 22.9 1.0 N03 B:5EP402 2.9 26.9 1.0 CE1 B:HIS226 3.0 19.4 1.0 CE1 B:HIS74 3.0 28.6 1.0 CD2 B:HIS74 3.0 20.4 1.0 CD2 B:HIS226 3.0 18.6 1.0 OE2 B:GLU73 4.0 23.9 1.0 ND1 B:HIS226 4.1 19.3 1.0 CG B:GLU73 4.1 22.7 1.0 ND1 B:HIS74 4.1 30.2 1.0 CG B:HIS74 4.1 22.3 1.0 CG B:HIS226 4.1 20.2 1.0 CB B:ASP230 4.2 17.9 1.0 C05 B:5EP402 4.2 27.0 1.0 OG1 B:THR179 4.3 20.9 1.0 C27 B:5EP402 4.5 35.9 1.0 CB B:THR179 4.6 19.9 1.0 CD B:GLU73 4.6 25.2 1.0 C26 B:5EP402 4.7 34.6 1.0 O B:HOH507 4.7 57.4 1.0 C29 B:5EP402 4.8 37.7 1.0 CA B:ASP230 4.8 16.6 1.0 O B:HIS226 4.8 17.5 1.0 N06 B:5EP402 4.9 25.4 1.0

C.J.Lee, X.Liang, Q.Wu, J.Najeeb, J.Zhao, R.Gopalaswamy, M.Titecat, F.Sebbane, N.Lemaitre, E.J.Toone, P.Zhou. Drug Design From the Cryptic Inhibitor Envelope. Nat Commun V. 7 10638 2016.
ISSN: ESSN 2041-1723
PubMed: 26912110
DOI: 10.1038/NCOMMS10638