Zinc in PDB 2r2d: Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens

The structure of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens, PDB code: 2r2d was solved by D.Liu, P.W.Thomas, J.Momb, Q.Hoang, G.A.Petsko, D.Ringe, W.Fast, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.10 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.146, 158.033, 80.439, 90.00, 104.48, 90.00
R / Rfree (%)	15.9 / 21.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens (pdb code 2r2d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens, PDB code: 2r2d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn277 b:24.1 occ:1.00 O3 A:PO4279 1.9 25.2 1.0 NE2 A:HIS259 2.0 22.7 1.0 NE2 A:HIS116 2.0 21.9 1.0 OD1 A:ASP213 2.3 25.0 1.0 OD2 A:ASP213 2.3 23.1 1.0 CG A:ASP213 2.6 25.5 1.0 CE1 A:HIS259 3.0 19.9 1.0 CE1 A:HIS116 3.0 22.1 1.0 CD2 A:HIS116 3.0 20.2 1.0 CD2 A:HIS259 3.0 18.9 1.0 P A:PO4279 3.1 24.5 1.0 O1 A:PO4279 3.3 24.0 1.0 OD2 A:ASP115 3.4 27.6 1.0 OD1 A:ASP115 3.8 35.6 1.0 O2 A:PO4279 3.8 28.3 1.0 CG A:ASP115 4.0 26.2 1.0 O1 A:GOL280 4.0 41.0 1.0 CE1 A:TYR216 4.1 22.6 1.0 ND1 A:HIS259 4.1 21.6 1.0 ND1 A:HIS116 4.1 24.1 1.0 CB A:ASP213 4.1 22.6 1.0 CG A:HIS259 4.2 21.3 1.0 CG A:HIS116 4.2 22.9 1.0 ZN A:ZN278 4.3 23.2 1.0 O4 A:PO4279 4.3 22.8 1.0 CE1 A:HIS111 4.6 23.1 1.0 CD1 A:TYR216 4.7 21.9 1.0 C1 A:GOL280 4.8 43.4 1.0 NE2 A:HIS111 4.8 20.1 1.0 CA A:ASP213 5.0 21.6 1.0

Zinc binding site 2 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn278 b:23.2 occ:1.00 O1 A:PO4279 1.9 24.0 1.0 NE2 A:HIS111 2.0 20.1 1.0 NE2 A:HIS191 2.1 21.6 1.0 ND1 A:HIS113 2.2 22.3 1.0 OD1 A:ASP213 2.5 25.0 1.0 CD2 A:HIS111 2.9 22.0 1.0 CD2 A:HIS191 3.0 22.5 1.0 CE1 A:HIS111 3.1 23.1 1.0 CE1 A:HIS191 3.1 23.2 1.0 CG A:HIS113 3.1 20.3 1.0 P A:PO4279 3.1 24.5 1.0 CE1 A:HIS113 3.2 23.1 1.0 O2 A:PO4279 3.3 28.3 1.0 CB A:HIS113 3.4 20.5 1.0 CG A:ASP213 3.6 25.5 1.0 CB A:ASP213 4.0 22.6 1.0 O3 A:PO4279 4.0 25.2 1.0 CG A:HIS111 4.1 22.6 1.0 CG A:HIS191 4.1 22.4 1.0 ND1 A:HIS111 4.2 22.7 1.0 ND1 A:HIS191 4.2 23.6 1.0 ZN A:ZN277 4.3 24.1 1.0 NE2 A:HIS113 4.3 21.9 1.0 CD2 A:HIS113 4.3 20.8 1.0 O4 A:PO4279 4.3 22.8 1.0 CD2 A:HIS116 4.4 20.2 1.0 NE2 A:HIS116 4.6 21.9 1.0 OD2 A:ASP213 4.7 23.1 1.0 O A:HOH326 4.8 26.9 1.0 CA A:HIS113 4.9 20.9 1.0

Zinc binding site 3 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn277 b:27.6 occ:1.00 O4 B:PO4279 1.8 26.7 1.0 NE2 B:HIS259 2.0 25.8 1.0 NE2 B:HIS116 2.0 22.5 1.0 OD1 B:ASP213 2.3 26.9 1.0 OD2 B:ASP213 2.4 25.9 1.0 CG B:ASP213 2.7 26.7 1.0 CE1 B:HIS116 2.9 25.2 1.0 CD2 B:HIS259 3.0 25.3 1.0 CE1 B:HIS259 3.0 27.8 1.0 CD2 B:HIS116 3.1 23.0 1.0 P B:PO4279 3.1 26.5 1.0 O3 B:PO4279 3.4 27.7 1.0 OD2 B:ASP115 3.5 33.5 1.0 OD1 B:ASP115 3.6 35.2 1.0 O2 B:PO4279 3.8 29.4 1.0 CG B:ASP115 3.9 29.9 1.0 O1 B:GOL281 4.0 51.7 1.0 ND1 B:HIS116 4.1 26.5 1.0 ND1 B:HIS259 4.1 25.3 1.0 CG B:HIS259 4.1 26.8 1.0 CE1 B:TYR216 4.1 25.8 1.0 CB B:ASP213 4.1 25.4 1.0 CG B:HIS116 4.2 24.7 1.0 ZN B:ZN278 4.3 26.3 1.0 O1 B:PO4279 4.3 28.9 1.0 CE1 B:HIS111 4.7 21.5 1.0 CD1 B:TYR216 4.7 22.6 1.0 NE2 B:HIS111 4.9 21.7 1.0 CA B:ASP213 4.9 25.2 1.0

Zinc binding site 4 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn278 b:26.3 occ:1.00 O3 B:PO4279 1.9 27.7 1.0 NE2 B:HIS111 2.1 21.7 1.0 NE2 B:HIS191 2.1 21.6 1.0 ND1 B:HIS113 2.2 24.7 1.0 OD1 B:ASP213 2.6 26.9 1.0 CD2 B:HIS111 3.0 22.3 1.0 CD2 B:HIS191 3.0 22.1 1.0 P B:PO4279 3.1 26.5 1.0 CE1 B:HIS111 3.1 21.5 1.0 CE1 B:HIS191 3.1 23.0 1.0 CG B:HIS113 3.1 22.4 1.0 CE1 B:HIS113 3.3 24.6 1.0 O2 B:PO4279 3.3 29.4 1.0 CB B:HIS113 3.4 23.9 1.0 CG B:ASP213 3.6 26.7 1.0 O4 B:PO4279 3.9 26.7 1.0 CB B:ASP213 4.0 25.4 1.0 CG B:HIS111 4.2 23.1 1.0 O1 B:PO4279 4.2 28.9 1.0 CG B:HIS191 4.2 22.6 1.0 ND1 B:HIS111 4.2 22.6 1.0 ND1 B:HIS191 4.2 23.1 1.0 CD2 B:HIS113 4.3 23.2 1.0 ZN B:ZN277 4.3 27.6 1.0 CD2 B:HIS116 4.3 23.0 1.0 NE2 B:HIS113 4.3 24.1 1.0 NE2 B:HIS116 4.6 22.5 1.0 O B:HOH350 4.7 31.3 1.0 OD2 B:ASP213 4.8 25.9 1.0 CA B:HIS113 4.8 24.3 1.0

Zinc binding site 5 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn277 b:24.7 occ:1.00 O1 C:PO4279 1.9 25.6 1.0 NE2 C:HIS116 2.0 22.5 1.0 NE2 C:HIS259 2.1 23.5 1.0 OD1 C:ASP213 2.3 25.5 1.0 OD2 C:ASP213 2.4 24.2 1.0 CG C:ASP213 2.6 21.9 1.0 CE1 C:HIS116 2.9 22.5 1.0 CD2 C:HIS259 3.0 20.4 1.0 CE1 C:HIS259 3.1 23.7 1.0 CD2 C:HIS116 3.1 21.5 1.0 P C:PO4279 3.1 23.4 1.0 O3 C:PO4279 3.3 21.6 1.0 OD2 C:ASP115 3.4 30.8 1.0 OD1 C:ASP115 3.6 35.5 1.0 O1 C:GOL281 3.8 40.2 1.0 O4 C:PO4279 3.8 25.6 1.0 CG C:ASP115 3.9 26.5 1.0 CE1 C:TYR216 4.1 22.1 1.0 ND1 C:HIS116 4.1 24.3 1.0 CB C:ASP213 4.1 22.7 1.0 ND1 C:HIS259 4.2 21.8 1.0 CG C:HIS259 4.2 22.7 1.0 CG C:HIS116 4.2 23.4 1.0 ZN C:ZN278 4.2 23.5 1.0 O2 C:PO4279 4.3 23.9 1.0 CE1 C:HIS111 4.6 21.0 1.0 NE2 C:HIS111 4.7 22.0 1.0 CD1 C:TYR216 4.8 21.1 1.0 C1 C:GOL281 4.9 43.0 1.0 CA C:ASP213 5.0 21.7 1.0

Zinc binding site 6 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn278 b:23.5 occ:1.00 O3 C:PO4279 1.9 21.6 1.0 NE2 C:HIS191 2.1 20.5 1.0 NE2 C:HIS111 2.1 22.0 1.0 ND1 C:HIS113 2.2 22.2 1.0 OD1 C:ASP213 2.5 25.5 1.0 CD2 C:HIS111 3.0 22.4 1.0 CD2 C:HIS191 3.0 22.4 1.0 CE1 C:HIS191 3.0 22.6 1.0 P C:PO4279 3.1 23.4 1.0 CG C:HIS113 3.1 21.6 1.0 CE1 C:HIS113 3.2 22.6 1.0 CE1 C:HIS111 3.2 21.0 1.0 O4 C:PO4279 3.3 25.6 1.0 CB C:HIS113 3.3 21.0 1.0 CG C:ASP213 3.6 21.9 1.0 O1 C:PO4279 4.0 25.6 1.0 CB C:ASP213 4.0 22.7 1.0 ND1 C:HIS191 4.1 21.3 1.0 CG C:HIS111 4.2 22.5 1.0 CG C:HIS191 4.2 21.5 1.0 O2 C:PO4279 4.2 23.9 1.0 ZN C:ZN277 4.2 24.7 1.0 CD2 C:HIS113 4.3 24.0 1.0 NE2 C:HIS113 4.3 24.5 1.0 ND1 C:HIS111 4.3 22.2 1.0 CD2 C:HIS116 4.4 21.5 1.0 NE2 C:HIS116 4.6 22.5 1.0 OD2 C:ASP213 4.7 24.2 1.0 O C:HOH319 4.7 29.3 1.0 CA C:HIS113 4.8 22.0 1.0

Zinc binding site 7 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn277 b:30.7 occ:1.00 O4 D:PO4279 1.9 31.9 1.0 NE2 D:HIS116 2.0 28.6 1.0 NE2 D:HIS259 2.1 31.8 1.0 OD2 D:ASP213 2.2 29.5 1.0 OD1 D:ASP213 2.2 31.1 1.0 CG D:ASP213 2.6 30.2 1.0 CD2 D:HIS259 2.9 28.6 1.0 CE1 D:HIS116 3.0 28.9 1.0 CD2 D:HIS116 3.1 29.6 1.0 P D:PO4279 3.1 29.6 1.0 CE1 D:HIS259 3.1 29.1 1.0 O2 D:PO4279 3.3 30.1 1.0 OD2 D:ASP115 3.4 34.4 1.0 OD1 D:ASP115 3.6 40.0 1.0 O1 D:PO4279 3.8 30.5 1.0 CG D:ASP115 3.9 32.1 1.0 O1 D:GOL280 4.0 47.5 1.0 CE1 D:TYR216 4.1 29.5 1.0 CB D:ASP213 4.1 30.8 1.0 ND1 D:HIS116 4.1 28.7 1.0 CG D:HIS259 4.1 30.1 1.0 ND1 D:HIS259 4.2 28.2 1.0 CG D:HIS116 4.2 29.1 1.0 O3 D:PO4279 4.3 29.4 1.0 ZN D:ZN278 4.3 28.8 1.0 CE1 D:HIS111 4.7 24.5 1.0 C1 D:GOL280 4.8 48.7 1.0 CD1 D:TYR216 4.8 28.5 1.0 NE2 D:HIS111 4.9 24.2 1.0 CA D:ASP213 4.9 29.7 1.0

Zinc binding site 8 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn278 b:28.8 occ:1.00 O2 D:PO4279 1.9 30.1 1.0 NE2 D:HIS191 2.0 26.5 1.0 NE2 D:HIS111 2.1 24.2 1.0 ND1 D:HIS113 2.2 27.8 1.0 OD1 D:ASP213 2.6 31.1 1.0 CD2 D:HIS191 3.0 28.0 1.0 CD2 D:HIS111 3.0 24.8 1.0 CE1 D:HIS191 3.0 27.1 1.0 P D:PO4279 3.1 29.6 1.0 CG D:HIS113 3.1 25.8 1.0 O1 D:PO4279 3.2 30.5 1.0 CE1 D:HIS111 3.2 24.5 1.0 CE1 D:HIS113 3.2 28.4 1.0 CB D:HIS113 3.4 25.9 1.0 CG D:ASP213 3.6 30.2 1.0 O4 D:PO4279 4.0 31.9 1.0 CB D:ASP213 4.0 30.8 1.0 ND1 D:HIS191 4.1 29.9 1.0 CG D:HIS191 4.1 27.7 1.0 O3 D:PO4279 4.2 29.4 1.0 CG D:HIS111 4.2 25.5 1.0 ND1 D:HIS111 4.3 24.9 1.0 CD2 D:HIS113 4.3 26.7 1.0 ZN D:ZN277 4.3 30.7 1.0 NE2 D:HIS113 4.3 27.5 1.0 CD2 D:HIS116 4.4 29.6 1.0 NE2 D:HIS116 4.6 28.6 1.0 O D:HOH335 4.7 36.7 1.0 OD2 D:ASP213 4.7 29.5 1.0 CA D:HIS113 4.8 26.0 1.0

Zinc binding site 9 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn277 b:32.8 occ:1.00 O1 E:PO4279 1.8 35.8 1.0 NE2 E:HIS116 2.1 27.0 1.0 NE2 E:HIS259 2.1 34.0 1.0 OD2 E:ASP213 2.3 31.4 1.0 OD1 E:ASP213 2.3 27.0 1.0 CG E:ASP213 2.7 29.2 1.0 CD2 E:HIS259 3.0 32.0 1.0 CD2 E:HIS116 3.0 27.1 1.0 CE1 E:HIS116 3.1 28.4 1.0 CE1 E:HIS259 3.1 31.6 1.0 P E:PO4279 3.2 33.9 1.0 OD2 E:ASP115 3.4 36.6 1.0 O3 E:PO4279 3.5 32.3 1.0 OD1 E:ASP115 3.7 42.1 1.0 O4 E:PO4279 3.9 36.3 1.0 CG E:ASP115 3.9 35.7 1.0 O1 E:GOL281 4.0 49.7 1.0 CG E:HIS259 4.1 34.2 1.0 CB E:ASP213 4.2 26.2 1.0 ND1 E:HIS116 4.2 28.0 1.0 CE1 E:TYR216 4.2 28.1 1.0 CG E:HIS116 4.2 27.7 1.0 ND1 E:HIS259 4.2 33.1 1.0 ZN E:ZN278 4.3 29.3 1.0 O2 E:PO4279 4.3 35.8 1.0 CE1 E:HIS111 4.6 25.8 1.0 CD1 E:TYR216 4.8 28.0 1.0 NE2 E:HIS111 4.8 24.4 1.0 C1 E:GOL281 4.8 52.6 1.0 CA E:ASP213 5.0 27.5 1.0

Zinc binding site 10 out of 12 in the Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn278 b:29.3 occ:1.00 O3 E:PO4279 1.9 32.3 1.0 NE2 E:HIS191 2.1 28.8 1.0 NE2 E:HIS111 2.1 24.4 1.0 ND1 E:HIS113 2.1 27.1 1.0 OD1 E:ASP213 2.5 27.0 1.0 CD2 E:HIS111 2.9 24.3 1.0 CD2 E:HIS191 2.9 26.8 1.0 CE1 E:HIS113 3.0 30.9 1.0 P E:PO4279 3.1 33.9 1.0 CG E:HIS113 3.1 26.6 1.0 CE1 E:HIS191 3.1 27.4 1.0 CE1 E:HIS111 3.1 25.8 1.0 O4 E:PO4279 3.3 36.3 1.0 CB E:HIS113 3.4 28.2 1.0 CG E:ASP213 3.6 29.2 1.0 O1 E:PO4279 3.8 35.8 1.0 CB E:ASP213 4.0 26.2 1.0 CG E:HIS191 4.1 26.4 1.0 CG E:HIS111 4.1 25.8 1.0 NE2 E:HIS113 4.1 29.0 1.0 ND1 E:HIS191 4.2 28.8 1.0 ND1 E:HIS111 4.2 26.8 1.0 CD2 E:HIS113 4.2 28.4 1.0 O2 E:PO4279 4.2 35.8 1.0 ZN E:ZN277 4.3 32.8 1.0 CD2 E:HIS116 4.4 27.1 1.0 NE2 E:HIS116 4.7 27.0 1.0 OD2 E:ASP213 4.7 31.4 1.0 O E:HOH347 4.8 36.9 1.0 CA E:HIS113 4.9 27.5 1.0

D.Liu, P.W.Thomas, J.Momb, Q.Q.Hoang, G.A.Petsko, D.Ringe, W.Fast. Structure and Specificity of A Quorum-Quenching Lactonase (Aiib) From Agrobacterium Tumefaciens. Biochemistry V. 46 11789 2007.
ISSN: ISSN 0006-2960
PubMed: 17900178
DOI: 10.1021/BI7012849