Zinc in PDB 3dha: An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site

The structure of An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site, PDB code: 3dha 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)	45.00 / 0.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.929, 55.604, 78.703, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 16.9

The binding sites of Zinc atom in the An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site (pdb code 3dha). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site, PDB code: 3dha:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn255 b:13.4 occ:1.00 NE2 A:HIS239 2.0 12.7 1.0 O A:HOH307 2.0 13.4 1.0 NE2 A:HIS113 2.0 12.1 1.0 OD2 A:ASP195 2.1 13.3 1.0 OD1 A:ASP112 2.3 14.5 1.0 CE1 A:HIS239 3.0 13.7 1.0 CD2 A:HIS113 3.0 11.6 1.0 CG A:ASP195 3.0 13.4 1.0 CE1 A:HIS113 3.1 12.5 1.0 CD2 A:HIS239 3.1 13.1 1.0 CG A:ASP112 3.2 12.4 1.0 OD1 A:ASP195 3.3 14.8 1.0 ZN A:ZN256 3.3 12.4 1.0 OD2 A:ASP112 3.5 13.7 1.0 O A:HOH289 3.6 23.9 1.0 O A:HOH340 3.9 17.0 1.0 NE2 A:HIS108 4.1 11.3 1.0 ND1 A:HIS239 4.1 14.4 1.0 CE1 A:HIS108 4.1 11.2 1.0 O A:HOH404 4.2 33.9 1.0 CG A:HIS113 4.2 11.2 1.0 CG A:HIS239 4.2 13.9 1.0 ND1 A:HIS113 4.2 12.2 1.0 CB A:ASP195 4.4 13.8 1.0 CE1 A:TYR198 4.6 17.7 1.0 CB A:ASP112 4.6 12.8 1.0 O A:HOH361 4.6 20.2 1.0 NE2 A:HIS173 4.6 12.3 1.0

Zinc binding site 2 out of 2 in the An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of An Ultral High Resolution Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at An Alternative Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn256 b:12.4 occ:1.00 O A:HOH307 1.9 13.4 1.0 NE2 A:HIS173 2.0 12.3 1.0 NE2 A:HIS108 2.0 11.3 1.0 ND1 A:HIS110 2.1 12.2 1.0 OD2 A:ASP195 2.6 13.3 1.0 CD2 A:HIS173 3.0 12.4 1.0 CD2 A:HIS108 3.0 11.5 1.0 CE1 A:HIS110 3.0 12.8 1.0 CE1 A:HIS108 3.1 11.2 1.0 CE1 A:HIS173 3.1 12.6 1.0 CG A:HIS110 3.2 11.6 1.0 ZN A:ZN255 3.3 13.4 1.0 CB A:HIS110 3.6 12.1 1.0 CG A:ASP195 3.7 13.4 1.0 CB A:ASP195 4.0 13.8 1.0 NE2 A:HIS113 4.0 12.1 1.0 O A:HOH289 4.0 23.9 1.0 CD2 A:HIS113 4.1 11.6 1.0 CG A:HIS173 4.2 12.8 1.0 ND1 A:HIS173 4.2 13.3 1.0 CG A:HIS108 4.2 10.8 1.0 ND1 A:HIS108 4.2 11.5 1.0 NE2 A:HIS110 4.2 14.3 1.0 CD2 A:HIS110 4.3 13.3 1.0 OD2 A:ASP112 4.3 13.7 1.0 C6 A:C6L257 4.4 20.9 0.7 OH A:TYR198 4.7 19.5 1.0 O A:HOH447 4.8 25.5 1.0 CE1 A:TYR198 4.8 17.7 1.0 OD1 A:ASP195 4.8 14.8 1.0 OD1 A:ASP112 4.8 14.5 1.0 CE1 A:HIS113 5.0 12.5 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