Zinc in PDB 3qg6: Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody

The structure of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody, PDB code: 3qg6 was solved by R.N.Kirchdoerfer, J.D.Janda, G.F.Kaufmann, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.74 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.360, 98.498, 73.670, 90.00, 114.03, 90.00
R / Rfree (%)	18.4 / 23.9

The structure of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody (pdb code 3qg6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody, PDB code: 3qg6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn214 b:36.5 occ:1.00 O A:ASP1 2.2 36.0 1.0 N A:ASP1 2.2 35.0 1.0 OXT L:GLU213 2.8 48.7 1.0 O A:HOH247 3.0 11.7 1.0 C A:ASP1 3.0 34.6 1.0 CA A:ASP1 3.1 34.0 1.0 C L:GLU213 3.6 41.1 1.0 O L:GLU213 3.8 42.5 1.0 CB A:ASP1 4.0 33.8 1.0 O L:ASN212 4.2 41.1 1.0 N A:VAL2 4.3 32.6 1.0 CG A:ASP1 4.9 39.1 1.0 CA L:GLU213 4.9 34.4 1.0 NE2 A:GLN27 4.9 43.6 1.0 CG2 A:VAL3 4.9 33.6 1.0 O A:HOH264 5.0 19.0 1.0 CA A:VAL2 5.0 32.0 1.0

Zinc binding site 2 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn216 b:23.5 occ:1.00 NE2 A:HIS189 2.0 27.9 1.0 OE2 H:GLU85 2.1 37.0 1.0 OE2 A:GLU185 2.2 24.0 1.0 OE1 H:GLU85 2.5 29.1 1.0 CD H:GLU85 2.7 30.2 1.0 CE1 A:HIS189 2.8 27.7 1.0 O H:HOH292 2.9 2.0 1.0 CD2 A:HIS189 3.1 27.3 1.0 CD A:GLU185 3.3 33.4 1.0 CG A:GLU185 3.9 29.8 1.0 ND1 A:HIS189 4.0 27.0 1.0 CG H:GLU85 4.1 24.9 1.0 CG A:HIS189 4.2 26.2 1.0 OE1 A:GLU185 4.3 33.2 1.0 NH1 A:ARG155 4.6 32.6 1.0 CB A:GLU185 4.8 26.1 1.0 O A:HOH223 4.9 17.8 1.0 O A:GLU185 4.9 23.8 1.0

Zinc binding site 3 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn217 b:73.8 occ:1.00 ND1 A:HIS93 2.2 34.5 1.0 O A:HOH271 2.4 29.5 1.0 CG A:HIS93 3.1 31.3 1.0 CE1 A:HIS93 3.2 35.7 1.0 CB A:HIS93 3.4 28.3 1.0 CA A:HIS93 3.9 27.5 1.0 NE2 A:HIS93 4.3 34.8 1.0 CD2 A:HIS93 4.3 33.2 1.0 N A:VAL94 4.8 26.6 1.0 C A:HIS93 4.9 27.9 1.0 N A:HIS93 4.9 27.2 1.0

Zinc binding site 4 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn229 b:77.1 occ:1.00 OD1 B:ASP72 2.0 37.2 1.0 OG B:SER74 2.6 33.8 1.0 CG B:ASP72 2.9 33.8 1.0 OD2 B:ASP72 3.2 42.4 1.0 CB B:SER74 3.4 29.0 1.0 N B:SER74 4.1 26.9 1.0 CA B:SER74 4.3 27.5 1.0 CB B:ASP72 4.3 27.0 1.0 CA B:ASP72 4.6 25.8 1.0 N B:LYS75 4.6 27.3 1.0 C B:ASP72 4.8 26.1 1.0 C B:SER74 4.8 28.3 1.0 N B:THR73 5.0 25.6 1.0

Zinc binding site 5 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn229 b:52.3 occ:1.00 NE2 H:HIS82A 2.4 39.0 1.0 CD2 H:HIS82A 3.3 36.3 1.0 CE1 H:HIS82A 3.4 40.1 1.0 NH1 H:ARG66 3.9 74.4 1.0 CG H:HIS82A 4.4 32.6 1.0 ND1 H:HIS82A 4.5 37.1 1.0 CB H:SER82B 4.5 31.4 1.0 OG H:SER82B 5.0 37.1 1.0

Zinc binding site 6 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn215 b:30.4 occ:1.00 OE2 B:GLU85 2.1 41.6 1.0 NE2 L:HIS189 2.1 30.4 1.0 OE2 L:GLU185 2.2 31.4 1.0 OE1 B:GLU85 2.5 33.5 1.0 CD B:GLU85 2.6 34.8 1.0 O B:HOH291 3.0 2.0 1.0 CE1 L:HIS189 3.0 30.2 1.0 CD2 L:HIS189 3.2 29.7 1.0 CD L:GLU185 3.3 37.8 1.0 CG L:GLU185 3.9 33.5 1.0 O L:HOH287 3.9 22.4 1.0 CG B:GLU85 4.1 29.2 1.0 ND1 L:HIS189 4.2 30.2 1.0 O B:HOH292 4.2 28.3 1.0 OE1 L:GLU185 4.3 40.3 1.0 CG L:HIS189 4.3 28.7 1.0 NH1 L:ARG155 4.6 34.8 1.0 CB L:GLU185 4.7 30.0 1.0

Zinc binding site 7 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn216 b:62.6 occ:1.00 ND1 L:HIS93 2.1 30.7 1.0 O L:HOH278 2.8 37.2 1.0 O L:HOH279 2.8 26.1 1.0 O L:HOH232 2.9 10.3 1.0 CE1 L:HIS93 3.0 32.4 1.0 CG L:HIS93 3.2 27.4 1.0 CB L:HIS93 3.7 23.6 1.0 CA L:HIS93 4.1 22.7 1.0 NE2 L:HIS93 4.2 31.8 1.0 CD2 L:HIS93 4.3 30.3 1.0 O L:HOH295 4.5 14.4 1.0

Zinc binding site 8 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn217 b:64.1 occ:1.00 O L:HOH251 2.9 13.1 1.0 OD2 L:ASP60 3.6 64.8 1.0 CG L:ASP60 4.1 56.3 1.0 OD1 L:ASP60 4.4 60.9 1.0 CB L:ASP60 4.9 46.5 1.0

Zinc binding site 9 out of 9 in the Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structural Basis For Ligand Recognition and Discrimination of A Quorum Quenching Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn218 b:34.2 occ:1.00 N L:ASP1 2.0 25.0 1.0 O L:ASP1 2.3 24.2 1.0 O L:HOH277 3.0 11.2 1.0 C L:ASP1 3.0 23.2 1.0 CA L:ASP1 3.0 23.9 1.0 OXT A:GLU213 3.0 41.5 1.0 C A:GLU213 3.8 31.0 1.0 O A:GLU213 3.9 31.5 1.0 CB L:ASP1 4.0 24.2 1.0 O A:ASN212 4.2 33.0 1.0 N L:VAL2 4.3 19.6 1.0 NE2 L:GLN27 4.7 41.6 1.0 CG L:ASP1 4.8 26.6 1.0 OD1 L:ASP1 4.9 27.5 1.0

R.N.Kirchdoerfer, A.L.Garner, C.E.Flack, J.M.Mee, A.R.Horswill, K.D.Janda, G.F.Kaufmann, I.A.Wilson. Structural Basis For Ligand Recognition and Discrimination of A Quorum-Quenching Antibody. J.Biol.Chem. V. 286 17351 2011.
ISSN: ISSN 0021-9258
PubMed: 21454495
DOI: 10.1074/JBC.M111.231258