Zinc in PDB 5dro: Structure of the Aquifex Aeolicus Lpxc/Lpc-011 Complex

The structure of Structure of the Aquifex Aeolicus Lpxc/Lpc-011 Complex, PDB code: 5dro was solved by C.-J.Lee, J.Najeeb, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.94 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.820, 74.680, 135.870, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.6

The binding sites of Zinc atom in the Structure of the Aquifex Aeolicus Lpxc/Lpc-011 Complex (pdb code 5dro). 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 Aquifex Aeolicus Lpxc/Lpc-011 Complex, PDB code: 5dro:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Aquifex Aeolicus Lpxc/Lpc-011 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 Aquifex Aeolicus Lpxc/Lpc-011 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.5 occ:1.00 OD1 A:ASP230 2.1 12.3 1.0 O01 A:ZH2402 2.1 12.8 1.0 NE2 A:HIS74 2.1 11.6 1.0 NE2 A:HIS226 2.1 10.7 1.0 O04 A:ZH2402 2.2 17.5 1.0 CG A:ASP230 2.7 11.4 1.0 OD2 A:ASP230 2.7 10.0 1.0 C02 A:ZH2402 2.8 15.6 1.0 N03 A:ZH2402 2.9 16.0 1.0 CD2 A:HIS74 3.0 10.9 1.0 CD2 A:HIS226 3.0 12.3 1.0 CE1 A:HIS226 3.1 10.0 1.0 CE1 A:HIS74 3.1 15.7 1.0 OG1 A:THR179 4.1 14.2 1.0 O A:HOH660 4.1 23.1 1.0 CG A:HIS226 4.1 10.3 1.0 ND1 A:HIS226 4.2 8.8 1.0 C05 A:ZH2402 4.2 18.7 1.0 CG A:HIS74 4.2 14.8 1.0 ND1 A:HIS74 4.2 13.0 1.0 CB A:ASP230 4.2 11.0 1.0 CB A:THR179 4.3 12.0 1.0 O27 A:ZH2402 4.3 34.2 1.0 OE2 A:GLU73 4.3 12.4 1.0 CG A:GLU73 4.3 10.9 1.0 C26 A:ZH2402 4.7 28.7 1.0 CA A:THR179 4.8 10.2 1.0 N06 A:ZH2402 4.8 18.0 1.0 O A:HIS226 4.8 10.6 1.0 CA A:ASP230 4.8 8.8 1.0 CD A:GLU73 4.9 12.8 1.0 C28 A:ZH2402 4.9 27.7 1.0 O A:HOH504 5.0 25.6 1.0 NE2 A:HIS253 5.0 16.8 1.0

Zinc binding site 2 out of 2 in the Structure of the Aquifex Aeolicus Lpxc/Lpc-011 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 Aquifex Aeolicus Lpxc/Lpc-011 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:8.7 occ:0.92 NE2 B:HIS74 2.0 11.7 1.0 NE2 B:HIS226 2.1 9.7 1.0 O04 B:ZH2402 2.1 16.2 1.0 OD1 B:ASP230 2.2 10.9 1.0 O01 B:ZH2402 2.2 11.7 1.0 OD2 B:ASP230 2.7 14.2 1.0 CG B:ASP230 2.8 13.2 1.0 N03 B:ZH2402 2.8 17.0 1.0 C02 B:ZH2402 2.9 17.4 1.0 CD2 B:HIS74 3.0 11.9 1.0 CE1 B:HIS74 3.0 17.5 1.0 CD2 B:HIS226 3.0 8.4 1.0 CE1 B:HIS226 3.1 13.0 1.0 ND1 B:HIS74 4.1 17.5 1.0 OG1 B:THR179 4.1 12.3 1.0 CG B:HIS74 4.1 12.3 1.0 ND1 B:HIS226 4.1 12.1 1.0 CG B:HIS226 4.2 11.4 1.0 C05 B:ZH2402 4.2 18.2 1.0 OE2 B:GLU73 4.2 11.4 1.0 CB B:ASP230 4.2 10.0 1.0 CG B:GLU73 4.3 12.3 1.0 CB B:THR179 4.4 10.7 1.0 O27 B:ZH2402 4.4 32.3 1.0 C26 B:ZH2402 4.7 27.4 1.0 CD B:GLU73 4.8 14.7 1.0 C28 B:ZH2402 4.8 29.0 1.0 N06 B:ZH2402 4.8 13.4 1.0 O B:HIS226 4.9 8.9 1.0 NE2 B:HIS253 4.9 15.4 1.0 CA B:THR179 4.9 12.0 1.0 CA B:ASP230 4.9 9.3 1.0 O B:HOH520 4.9 30.2 1.0 CE1 B:HIS253 5.0 13.2 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