Zinc in PDB 4zo3: Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine

The structure of Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine, PDB code: 4zo3 was solved by R.Mascarenhas, P.W.Thomas, C.-X.Wu, B.P.Nocek, Q.Hoang, W.Fast, D.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.52 / 1.67
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.090, 47.870, 249.150, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.8

The binding sites of Zinc atom in the Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine (pdb code 4zo3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine, PDB code: 4zo3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.3 occ:0.84 O A:HOH523 2.0 19.8 1.0 NE2 A:HIS237 2.0 12.6 1.0 ND1 A:HIS147 2.1 12.7 1.0 NE2 A:HIS145 2.2 10.5 1.0 OD2 A:ASP258 2.3 13.0 1.0 O2 A:C6L403 2.5 21.2 0.9 CD2 A:HIS237 3.0 11.1 1.0 CD2 A:HIS145 3.0 11.1 1.0 CE1 A:HIS237 3.1 14.1 1.0 CE1 A:HIS147 3.1 13.3 1.0 CG A:HIS147 3.1 10.9 1.0 CE1 A:HIS145 3.2 10.0 1.0 ZN A:ZN402 3.3 14.0 0.7 C4 A:C6L403 3.3 27.3 0.9 CG A:ASP258 3.4 11.3 1.0 CB A:HIS147 3.4 12.2 1.0 O1 A:C6L403 3.7 19.1 0.9 CB A:ASP258 3.9 10.9 1.0 NE2 A:HIS150 4.1 11.2 1.0 CD2 A:HIS150 4.1 12.8 1.0 CG A:HIS237 4.1 12.0 1.0 ND1 A:HIS237 4.1 13.9 1.0 NE2 A:HIS147 4.2 13.9 1.0 CG A:HIS145 4.2 10.2 1.0 CD2 A:HIS147 4.2 12.3 1.0 ND1 A:HIS145 4.3 10.6 1.0 N1 A:C6L403 4.4 41.2 0.9 OD1 A:ASP258 4.4 14.7 1.0 C3 A:C6L403 4.4 40.2 0.9 OD1 A:ASP149 4.4 14.3 1.0 C5 A:C6L403 4.6 40.1 0.9 NE2 A:HIS261 4.6 12.5 1.0 OD2 A:ASP149 4.7 13.1 1.0 O4 A:C6L403 4.7 51.9 0.9 CA A:HIS147 4.9 11.7 1.0

Zinc binding site 2 out of 4 in the Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:14.0 occ:0.72 O A:HOH523 2.0 19.8 1.0 OD2 A:ASP258 2.1 13.0 1.0 NE2 A:HIS150 2.1 11.2 1.0 NE2 A:HIS305 2.1 12.1 1.0 OD2 A:ASP149 2.1 13.1 1.0 O1 A:C6L403 2.4 19.1 0.9 CG A:ASP258 2.9 11.3 1.0 CD2 A:HIS150 2.9 12.8 1.0 CE1 A:HIS305 3.0 14.1 1.0 OD1 A:ASP258 3.0 14.7 1.0 C4 A:C6L403 3.0 27.3 0.9 CG A:ASP149 3.1 16.4 1.0 CD2 A:HIS305 3.2 11.5 1.0 CE1 A:HIS150 3.2 11.2 1.0 ZN A:ZN401 3.3 14.3 0.8 OD1 A:ASP149 3.5 14.3 1.0 O2 A:C6L403 3.6 21.2 0.9 C3 A:C6L403 3.9 40.2 0.9 NE2 A:HIS145 4.1 10.5 1.0 ND1 A:HIS305 4.1 13.9 1.0 CG A:HIS150 4.1 11.6 1.0 CE1 A:HIS145 4.2 10.0 1.0 ND1 A:HIS150 4.2 11.2 1.0 NE2 A:HIS261 4.2 12.5 1.0 CG A:HIS305 4.3 14.1 1.0 CB A:ASP258 4.3 10.9 1.0 CB A:ASP149 4.4 12.1 1.0 N1 A:C6L403 4.6 41.2 0.9 NE2 A:HIS237 4.7 12.6 1.0 OG A:SER304 4.7 13.0 0.4 CD2 A:HIS261 4.9 12.8 1.0

Zinc binding site 3 out of 4 in the Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:35.2 occ:0.93 O B:HOH517 2.0 27.3 1.0 NE2 B:HIS237 2.1 31.6 1.0 ND1 B:HIS147 2.1 30.4 1.0 NE2 B:HIS145 2.1 30.2 1.0 OD2 B:ASP258 2.2 31.2 1.0 O1 B:C6L403 2.7 36.5 0.9 CD2 B:HIS237 3.0 31.9 1.0 CD2 B:HIS145 3.0 30.7 1.0 CE1 B:HIS147 3.0 30.8 1.0 CE1 B:HIS237 3.1 31.5 1.0 CG B:HIS147 3.1 30.5 1.0 CG B:ASP258 3.2 31.1 1.0 CE1 B:HIS145 3.2 30.0 1.0 ZN B:ZN402 3.3 31.3 0.8 C4 B:C6L403 3.4 44.3 0.9 CB B:HIS147 3.5 30.1 1.0 O2 B:C6L403 3.6 38.2 0.9 CB B:ASP258 3.8 31.2 1.0 NE2 B:HIS150 4.0 28.9 1.0 CD2 B:HIS150 4.0 29.1 1.0 NE2 B:HIS147 4.2 31.2 1.0 CG B:HIS237 4.2 31.8 1.0 ND1 B:HIS237 4.2 31.6 1.0 OD1 B:ASP258 4.2 31.0 1.0 CG B:HIS145 4.2 30.8 1.0 CD2 B:HIS147 4.2 31.0 1.0 ND1 B:HIS145 4.2 30.4 1.0 OD1 B:ASP149 4.3 28.9 1.0 N1 B:C6L403 4.4 49.5 0.9 C3 B:C6L403 4.5 53.9 0.9 NE2 B:HIS261 4.6 25.9 1.0 OD2 B:ASP149 4.6 28.4 1.0 C5 B:C6L403 4.7 51.6 0.9 CA B:HIS147 4.9 30.4 1.0 CG B:ASP149 4.9 28.5 1.0 CE1 B:HIS150 5.0 28.8 1.0

Zinc binding site 4 out of 4 in the Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Aidc, A Dizinc Quorum-Quenching Lactonase, in Complex with A Product N-Hexnoyl-L-Homoserine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:31.3 occ:0.78 NE2 B:HIS150 2.1 28.9 1.0 O B:HOH517 2.1 27.3 1.0 OD2 B:ASP149 2.1 28.4 1.0 NE2 B:HIS305 2.1 24.8 1.0 OD2 B:ASP258 2.1 31.2 1.0 O2 B:C6L403 2.5 38.2 0.9 CG B:ASP258 2.8 31.1 1.0 CD2 B:HIS150 2.9 29.1 1.0 OD1 B:ASP258 2.9 31.0 1.0 CE1 B:HIS305 3.0 24.5 1.0 CG B:ASP149 3.1 28.5 1.0 CD2 B:HIS305 3.1 24.8 1.0 CE1 B:HIS150 3.1 28.8 1.0 C4 B:C6L403 3.3 44.3 0.9 ZN B:ZN401 3.3 35.2 0.9 OD1 B:ASP149 3.4 28.9 1.0 O1 B:C6L403 3.8 36.5 0.9 CG B:HIS150 4.1 29.2 1.0 C3 B:C6L403 4.1 53.9 0.9 ND1 B:HIS305 4.1 24.2 1.0 NE2 B:HIS145 4.1 30.2 1.0 ND1 B:HIS150 4.2 29.0 1.0 CE1 B:HIS145 4.2 30.0 1.0 CG B:HIS305 4.2 24.4 1.0 NE2 B:HIS261 4.3 25.9 1.0 CB B:ASP258 4.3 31.2 1.0 CB B:ASP149 4.4 28.2 1.0 N1 B:C6L403 4.8 49.5 0.9 NE2 B:HIS237 4.8 31.6 1.0 CD2 B:HIS261 4.9 28.2 1.0 ND1 B:HIS147 5.0 30.4 1.0

R.Mascarenhas, P.W.Thomas, C.X.Wu, B.P.Nocek, Q.Q.Hoang, D.Liu, W.Fast. Structural and Biochemical Characterization of Aidc, A Quorum-Quenching Lactonase with Atypical Selectivity. Biochemistry V. 54 4342 2015.
ISSN: ISSN 0006-2960
PubMed: 26115006
DOI: 10.1021/ACS.BIOCHEM.5B00499