Atomistry » Zinc » PDB 3dgl-3dsu » 3dhc
Atomistry »
  Zinc »
    PDB 3dgl-3dsu »
      3dhc »

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

Protein crystallography data

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

Zinc Binding Sites:

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 3dhc

Go back to Zinc Binding Sites List in 3dhc
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 3dhc

Go back to Zinc Binding Sites List in 3dhc
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

Reference:

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
Page generated: Wed Dec 16 04:13:13 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy