Zinc in PDB 4zo2: Aidc, A Dizinc Quorum-Quenching Lactonase

The structure of Aidc, A Dizinc Quorum-Quenching Lactonase, PDB code: 4zo2 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)	21.12 / 1.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.257, 97.880, 110.871, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 16.2

The binding sites of Zinc atom in the Aidc, A Dizinc Quorum-Quenching Lactonase (pdb code 4zo2). 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, PDB code: 4zo2:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:15.4 occ:0.76 O A:HOH538 1.9 18.8 1.0 NE2 A:HIS237 2.1 15.7 1.0 NE2 A:HIS145 2.1 15.3 1.0 ND1 A:HIS147 2.2 16.4 1.0 OD2 A:ASP258 2.4 15.6 1.0 O A:HOH775 2.7 39.6 1.0 CD2 A:HIS237 3.0 16.5 1.0 CD2 A:HIS145 3.1 14.5 1.0 CE1 A:HIS237 3.1 16.3 1.0 CE1 A:HIS147 3.1 17.0 1.0 CG A:HIS147 3.2 16.1 1.0 CE1 A:HIS145 3.2 14.2 1.0 ZN A:ZN402 3.3 14.9 0.8 CG A:ASP258 3.4 15.3 1.0 CB A:HIS147 3.5 15.3 1.0 O A:HOH746 3.6 28.8 1.0 CB A:ASP258 3.9 16.4 1.0 NE2 A:HIS150 4.0 14.3 1.0 CD2 A:HIS150 4.1 14.0 1.0 CG A:HIS237 4.2 16.4 1.0 ND1 A:HIS237 4.2 16.4 1.0 NE2 A:HIS147 4.2 17.7 1.0 CG A:HIS145 4.2 14.6 1.0 ND1 A:HIS145 4.3 14.0 1.0 CD2 A:HIS147 4.3 16.8 1.0 OD1 A:ASP149 4.4 18.1 1.0 OD1 A:ASP258 4.4 17.2 1.0 OD2 A:ASP149 4.7 16.4 1.0 NE2 A:HIS261 4.7 18.5 1.0 CA A:HIS147 4.9 15.7 1.0 CE1 A:HIS150 5.0 14.1 1.0

Zinc binding site 2 out of 4 in the Aidc, A Dizinc Quorum-Quenching Lactonase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:14.9 occ:0.75 O A:HOH538 2.0 18.8 1.0 OD2 A:ASP258 2.1 15.6 1.0 NE2 A:HIS305 2.1 14.9 1.0 NE2 A:HIS150 2.1 14.3 1.0 OD2 A:ASP149 2.2 16.4 1.0 O A:HOH746 2.5 28.8 1.0 CG A:ASP258 2.9 15.3 1.0 CD2 A:HIS150 3.0 14.0 1.0 CE1 A:HIS305 3.0 15.3 1.0 OD1 A:ASP258 3.1 17.2 1.0 CG A:ASP149 3.1 16.1 1.0 CD2 A:HIS305 3.1 14.3 1.0 CE1 A:HIS150 3.1 14.1 1.0 ZN A:ZN401 3.3 15.4 0.8 OD1 A:ASP149 3.4 18.1 1.0 O A:HOH775 3.7 39.6 1.0 O A:HOH836 3.7 46.2 1.0 NE2 A:HIS145 4.1 15.3 1.0 ND1 A:HIS305 4.2 15.0 1.0 CG A:HIS150 4.2 14.3 1.0 CE1 A:HIS145 4.2 14.2 1.0 ND1 A:HIS150 4.2 14.5 1.0 CG A:HIS305 4.3 14.2 1.0 CB A:ASP258 4.4 16.4 1.0 NE2 A:HIS261 4.4 18.5 1.0 CB A:ASP149 4.4 16.2 1.0 NE2 A:HIS237 4.8 15.7 1.0

Zinc binding site 3 out of 4 in the Aidc, A Dizinc Quorum-Quenching Lactonase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:15.5 occ:0.81 O B:HOH538 1.9 17.6 1.0 NE2 B:HIS237 2.1 15.2 1.0 NE2 B:HIS145 2.1 15.0 1.0 ND1 B:HIS147 2.2 15.2 1.0 OD2 B:ASP258 2.4 15.4 1.0 O B:HOH779 2.6 29.8 1.0 CD2 B:HIS145 3.0 14.7 1.0 CD2 B:HIS237 3.0 15.9 1.0 CE1 B:HIS237 3.1 15.9 1.0 CE1 B:HIS147 3.1 16.4 1.0 CE1 B:HIS145 3.1 14.0 1.0 CG B:HIS147 3.2 15.1 1.0 ZN B:ZN402 3.3 15.1 0.8 CG B:ASP258 3.4 15.1 1.0 CB B:HIS147 3.5 15.5 1.0 O B:HOH699 3.8 28.4 1.0 CB B:ASP258 3.9 15.8 1.0 NE2 B:HIS150 4.0 14.5 1.0 CD2 B:HIS150 4.1 13.9 1.0 ND1 B:HIS237 4.2 15.5 1.0 CG B:HIS237 4.2 14.9 1.0 CG B:HIS145 4.2 13.8 1.0 ND1 B:HIS145 4.2 13.9 1.0 NE2 B:HIS147 4.2 16.0 1.0 CD2 B:HIS147 4.3 15.5 1.0 OD1 B:ASP149 4.4 17.8 1.0 OD1 B:ASP258 4.4 17.2 1.0 O B:HOH859 4.7 47.6 1.0 NE2 B:HIS261 4.7 18.6 1.0 OD2 B:ASP149 4.7 16.6 1.0 CA B:HIS147 5.0 15.8 1.0 CE1 B:HIS150 5.0 14.1 1.0 CG B:ASP149 5.0 15.8 1.0

Zinc binding site 4 out of 4 in the Aidc, A Dizinc Quorum-Quenching Lactonase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:15.1 occ:0.75 O B:HOH538 2.0 17.6 1.0 NE2 B:HIS150 2.1 14.5 1.0 NE2 B:HIS305 2.1 15.2 1.0 OD2 B:ASP258 2.1 15.4 1.0 OD2 B:ASP149 2.1 16.6 1.0 O B:HOH699 2.4 28.4 1.0 CG B:ASP258 2.9 15.1 1.0 CD2 B:HIS150 3.0 13.9 1.0 CE1 B:HIS305 3.0 15.2 1.0 OD1 B:ASP258 3.1 17.2 1.0 CG B:ASP149 3.1 15.8 1.0 CE1 B:HIS150 3.1 14.1 1.0 CD2 B:HIS305 3.1 14.9 1.0 ZN B:ZN401 3.3 15.5 0.8 OD1 B:ASP149 3.4 17.8 1.0 O B:HOH779 3.9 29.8 1.0 NE2 B:HIS145 4.1 15.0 1.0 ND1 B:HIS305 4.2 15.1 1.0 CG B:HIS150 4.2 13.5 1.0 CE1 B:HIS145 4.2 14.0 1.0 ND1 B:HIS150 4.2 14.7 1.0 CG B:HIS305 4.3 14.3 1.0 NE2 B:HIS261 4.3 18.6 1.0 CB B:ASP258 4.4 15.8 1.0 CB B:ASP149 4.4 15.7 1.0 NE2 B:HIS237 4.8 15.2 1.0 CD2 B:HIS261 5.0 17.8 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