Zinc in PDB 3dhc: 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to the Catalytic Metal Center

The structure of 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to the Catalytic Metal Center, PDB code: 3dhc was solved by D.Liu, J.Momb, P.W.Thomas, A.Moulin, G.A.Petsko, W.Fast, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.62 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.775, 55.460, 79.191, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 18.3

The binding sites of Zinc atom in the 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to the Catalytic Metal Center (pdb code 3dhc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to the Catalytic Metal Center, PDB code: 3dhc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to the Catalytic Metal Center


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to the Catalytic Metal Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn251 b:10.6 occ:0.80 O1 A:CYK253 1.9 22.1 0.8 NE2 A:HIS169 2.0 11.5 1.0 NE2 A:HIS104 2.1 10.7 1.0 ND1 A:HIS106 2.2 11.6 1.0 OD2 A:ASP191 2.4 12.4 1.0 C4 A:CYK253 2.8 18.6 0.8 O2 A:CYK253 2.9 20.4 0.8 CD2 A:HIS169 3.0 12.5 1.0 CD2 A:HIS104 3.0 11.8 1.0 CE1 A:HIS106 3.1 12.0 1.0 CE1 A:HIS169 3.1 13.4 1.0 CE1 A:HIS104 3.2 11.0 1.0 CG A:HIS106 3.2 10.9 1.0 CG A:ASP191 3.5 12.5 1.0 CB A:HIS106 3.6 10.3 1.0 ZN A:ZN252 3.7 12.7 0.8 CB A:ASP191 3.8 11.9 1.0 CG A:HIS169 4.1 12.3 1.0 ND1 A:HIS169 4.2 13.7 1.0 C3 A:CYK253 4.2 17.0 0.8 NE2 A:HIS106 4.2 12.9 1.0 CG A:HIS104 4.2 10.0 1.0 ND1 A:HIS104 4.3 11.2 1.0 CD2 A:HIS106 4.3 12.0 1.0 CD2 A:HIS109 4.3 11.7 1.0 NE2 A:HIS109 4.4 10.3 1.0 OH A:TYR194 4.5 18.2 1.0 N1 A:CYK253 4.6 17.4 0.8 O3 A:CYK253 4.6 18.2 0.8 OD1 A:ASP191 4.6 14.8 1.0 C5 A:CYK253 4.7 17.6 0.8 C8 A:CYK253 4.8 32.5 0.8 CE1 A:TYR194 4.8 15.4 1.0 C7 A:CYK253 5.0 28.4 0.8

Zinc binding site 2 out of 2 in the 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to the Catalytic Metal Center


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.3 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homocysteine Bound to the Catalytic Metal Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn252 b:12.7 occ:0.80 O2 A:CYK253 2.0 20.4 0.8 OD2 A:ASP191 2.0 12.4 1.0 NE2 A:HIS109 2.1 10.3 1.0 NE2 A:HIS235 2.1 14.0 1.0 CG A:ASP191 2.7 12.5 1.0 OD1 A:ASP191 2.8 14.8 1.0 C4 A:CYK253 3.0 18.6 0.8 CD2 A:HIS109 3.0 11.7 1.0 CE1 A:HIS235 3.0 15.3 1.0 CD2 A:HIS235 3.0 13.6 1.0 CE1 A:HIS109 3.1 12.7 1.0 OD1 A:ASP108 3.3 24.9 1.0 O1 A:CYK253 3.4 22.1 0.8 ZN A:ZN251 3.7 10.6 0.8 O A:HOH426 3.7 24.7 1.0 OD2 A:ASP108 3.9 16.0 1.0 CG A:ASP108 4.0 17.4 1.0 C3 A:CYK253 4.1 17.0 0.8 ND1 A:HIS235 4.1 14.9 1.0 CE1 A:HIS104 4.2 11.0 1.0 CG A:HIS109 4.2 10.4 1.0 ND1 A:HIS109 4.2 10.5 1.0 CG A:HIS235 4.2 14.4 1.0 CB A:ASP191 4.2 11.9 1.0 C2 A:CYK253 4.2 21.4 0.8 NE2 A:HIS104 4.2 10.7 1.0 C1 A:CYK253 4.4 26.3 0.8 CE1 A:TYR194 4.5 15.4 1.0 O A:HOH319 4.6 46.4 1.0 NE2 A:HIS169 4.9 11.5 1.0

D.Liu, J.Momb, P.W.Thomas, A.Moulin, G.A.Petsko, W.Fast, D.Ringe. Mechanism of the Quorum-Quenching Lactonase (Aiia) From Bacillus Thuringiensis. 1. Product-Bound Structures. Biochemistry V. 47 7706 2008.
ISSN: ISSN 0006-2960
PubMed: 18627129
DOI: 10.1021/BI800368Y