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Zinc in PDB 3dhb: 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at the Catalytic Metal Center

Protein crystallography data

The structure of 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at the Catalytic Metal Center, PDB code: 3dhb 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) 18.79 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.438, 55.583, 79.866, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 18.4

Zinc Binding Sites:

The binding sites of Zinc atom in the 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at the Catalytic Metal Center (pdb code 3dhb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at the Catalytic Metal Center, PDB code: 3dhb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3dhb

Go back to Zinc Binding Sites List in 3dhb
Zinc binding site 1 out of 2 in the 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at 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 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at the Catalytic Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn251

b:13.3
occ:0.90
NE2 A:HIS235 2.0 13.0 1.0
NE2 A:HIS109 2.1 10.6 1.0
OD2 A:ASP191 2.1 11.9 1.0
O2 A:C6L253 2.1 19.6 0.9
CG A:ASP191 2.7 11.1 1.0
OD1 A:ASP191 2.7 13.8 1.0
OD1 A:ASP108 2.8 17.4 0.5
C4 A:C6L253 2.9 21.2 0.9
O1 A:C6L253 2.9 17.4 0.9
CD2 A:HIS235 3.0 13.3 1.0
CE1 A:HIS235 3.0 13.9 1.0
CD2 A:HIS109 3.0 11.2 1.0
CE1 A:HIS109 3.0 9.9 1.0
O A:HOH406 3.7 23.3 1.0
ZN A:ZN252 3.7 11.2 0.9
CG A:ASP108 3.7 13.4 0.5
OD2 A:ASP108 3.9 12.1 0.5
O3 A:C6L253 4.0 20.7 0.9
OD2 A:ASP108 4.0 14.4 0.5
ND1 A:HIS235 4.1 13.1 1.0
ND1 A:HIS109 4.1 9.2 1.0
CG A:HIS235 4.1 13.7 1.0
CG A:HIS109 4.2 10.2 1.0
CB A:ASP191 4.2 11.2 1.0
CE1 A:TYR194 4.2 15.3 1.0
CE1 A:HIS104 4.3 10.8 1.0
C3 A:C6L253 4.4 21.1 0.9
NE2 A:HIS104 4.4 10.7 1.0
O A:HOH344 4.5 26.0 1.0
CG A:ASP108 4.6 12.1 0.5
OD1 A:ASP108 4.7 14.2 0.5
C2 A:C6L253 4.8 22.5 0.9
OH A:TYR194 4.8 18.9 1.0
CZ A:TYR194 4.8 16.3 1.0
CD1 A:TYR194 4.9 14.9 1.0
NE2 A:HIS169 5.0 12.5 1.0
C1 A:C6L253 5.0 22.1 0.9

Zinc binding site 2 out of 2 in 3dhb

Go back to Zinc Binding Sites List in 3dhb
Zinc binding site 2 out of 2 in the 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at 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 1.4 Angstrom Structure of N-Acyl Homoserine Lactone Hydrolase with the Product N-Hexanoyl-L-Homoserine Bound at the Catalytic Metal Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn252

b:11.2
occ:0.90
O1 A:C6L253 2.0 17.4 0.9
NE2 A:HIS169 2.1 12.5 1.0
NE2 A:HIS104 2.1 10.7 1.0
ND1 A:HIS106 2.1 11.1 1.0
OD2 A:ASP191 2.4 11.9 1.0
CD2 A:HIS169 3.0 12.2 1.0
CD2 A:HIS104 3.0 11.2 1.0
CE1 A:HIS106 3.1 12.4 1.0
CE1 A:HIS169 3.1 13.5 1.0
CE1 A:HIS104 3.2 10.8 1.0
C4 A:C6L253 3.2 21.2 0.9
CG A:HIS106 3.2 10.5 1.0
CG A:ASP191 3.5 11.1 1.0
CB A:HIS106 3.5 10.1 1.0
ZN A:ZN251 3.7 13.3 0.9
O2 A:C6L253 3.8 19.6 0.9
CB A:ASP191 3.8 11.2 1.0
N1 A:C6L253 4.1 21.6 0.9
CG A:HIS169 4.1 10.7 1.0
CG A:HIS104 4.2 8.5 1.0
ND1 A:HIS169 4.2 11.8 1.0
NE2 A:HIS106 4.2 12.2 1.0
CD2 A:HIS109 4.2 11.2 1.0
ND1 A:HIS104 4.2 9.0 1.0
C3 A:C6L253 4.2 21.1 0.9
CD2 A:HIS106 4.3 11.8 1.0
NE2 A:HIS109 4.3 10.6 1.0
OH A:TYR194 4.4 18.9 1.0
C5 A:C6L253 4.5 21.6 0.9
OD1 A:ASP191 4.6 13.8 1.0
C8 A:C6L253 4.6 31.8 0.9
CE1 A:TYR194 4.7 15.3 1.0
OD2 A:ASP108 4.8 14.4 0.5
O4 A:C6L253 4.9 20.6 0.9
CA A:HIS106 5.0 8.9 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

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