Zinc in PDB 6jst: Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl, PDB code: 6jst was solved by B.Xue, W.S.Yew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.73
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.991, 51.187, 134.473, 90.99, 91.33, 96.33
R / Rfree (%)	21.9 / 26.4

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl (pdb code 6jst). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl, PDB code: 6jst:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:16.5 occ:0.79 ND1 A:HIS178 1.7 23.3 1.0 OQ1 A:KCX145 1.9 20.5 1.0 NE2 A:HIS206 2.1 17.2 1.0 O A:OH403 2.2 20.7 1.0 CE1 A:HIS178 2.5 26.1 1.0 CG A:HIS178 2.8 18.9 1.0 CX A:KCX145 3.0 25.4 1.0 CD2 A:HIS206 3.0 16.2 1.0 CE1 A:HIS206 3.1 18.2 1.0 OQ2 A:KCX145 3.3 15.6 1.0 CB A:HIS178 3.3 16.2 1.0 FE A:FE401 3.6 10.6 0.9 NE2 A:HIS178 3.7 32.7 1.0 CD2 A:HIS178 3.8 29.0 1.0 NZ A:KCX145 4.1 25.6 1.0 CE1 A:HIS23 4.2 19.5 1.0 ND1 A:HIS206 4.2 16.7 1.0 CG A:HIS206 4.2 18.4 1.0 O A:HOH503 4.3 38.0 1.0 CA A:HIS178 4.3 10.1 1.0 NE2 A:HIS23 4.3 15.8 1.0 ND2 A:ASN266 4.5 17.5 1.0 O A:HOH698 4.6 31.5 1.0 CE A:KCX145 4.6 21.9 1.0 OD1 A:ASN266 4.7 9.4 1.0 O A:HOH653 5.0 15.3 1.0 CG A:ASN266 5.0 16.6 1.0

Zinc binding site 2 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:21.0 occ:0.80 OQ2 B:KCX145 2.0 38.3 1.0 NE2 B:HIS206 2.1 21.3 1.0 ND1 B:HIS178 2.1 11.4 1.0 O B:OH403 2.2 20.5 1.0 CX B:KCX145 3.0 29.7 1.0 CD2 B:HIS206 3.0 22.2 1.0 CE1 B:HIS178 3.0 12.0 1.0 CG B:HIS178 3.1 7.9 1.0 CE1 B:HIS206 3.1 21.8 1.0 OQ1 B:KCX145 3.3 18.9 1.0 CB B:HIS178 3.5 9.2 1.0 FE B:FE401 3.6 12.1 1.0 NZ B:KCX145 4.1 21.8 1.0 NE2 B:HIS178 4.1 18.4 1.0 CG B:HIS206 4.2 13.3 1.0 CE1 B:HIS23 4.2 19.9 1.0 ND1 B:HIS206 4.2 13.3 1.0 CD2 B:HIS178 4.2 17.2 1.0 NH1 B:ARG230 4.3 34.6 1.0 NE2 B:HIS23 4.3 13.4 1.0 CA B:HIS178 4.4 10.4 1.0 CE B:KCX145 4.5 25.9 1.0 ND2 B:ASN266 4.6 18.9 1.0 O B:HOH720 4.6 37.7 1.0 O B:HOH679 4.7 25.9 1.0 OD1 B:ASN266 4.7 10.0 1.0 O B:HOH636 4.9 35.5 1.0 CG B:ASN266 5.0 16.6 1.0 O B:HOH656 5.0 18.5 1.0

Zinc binding site 3 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:35.5 occ:0.80 OQ1 C:KCX145 2.0 45.6 1.0 ND1 C:HIS178 2.0 53.9 1.0 NE2 C:HIS206 2.1 46.3 1.0 O C:OH403 2.3 34.4 1.0 CE1 C:HIS178 2.9 52.0 1.0 CD2 C:HIS206 3.0 44.5 1.0 CG C:HIS178 3.1 50.3 1.0 CX C:KCX145 3.1 42.8 1.0 CE1 C:HIS206 3.1 43.8 1.0 OQ2 C:KCX145 3.4 37.3 1.0 CB C:HIS178 3.5 46.9 1.0 FE C:FE401 3.5 29.2 0.8 NE2 C:HIS178 4.0 52.9 1.0 CD2 C:HIS178 4.1 52.0 1.0 CG C:HIS206 4.1 45.0 1.0 ND1 C:HIS206 4.2 44.5 1.0 NZ C:KCX145 4.2 43.2 1.0 NE2 C:HIS23 4.2 35.3 1.0 CE1 C:HIS23 4.3 36.6 1.0 ND2 C:ASN266 4.4 25.8 1.0 CE C:KCX145 4.6 44.0 1.0 CA C:HIS178 4.6 43.0 1.0 NH2 C:ARG230 4.7 43.4 1.0 OD1 C:ASN266 4.9 40.7 1.0 CG C:ASN266 4.9 29.1 1.0

Zinc binding site 4 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Geobacillus Kaustophilus Lactonase, Y99P/D266N Double Mutant with Bound 3-Oxo-C8-Hsl within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:31.7 occ:0.67 ND1 D:HIS178 2.0 37.6 1.0 NE2 D:HIS206 2.1 34.3 1.0 OQ1 D:KCX145 2.1 46.8 1.0 O D:HOH574 2.4 45.1 1.0 CE1 D:HIS178 2.9 33.9 1.0 CE1 D:HIS206 3.0 33.1 1.0 CD2 D:HIS206 3.1 34.8 1.0 CX D:KCX145 3.1 38.6 1.0 CG D:HIS178 3.1 34.6 1.0 O D:HOH587 3.4 42.8 1.0 OQ2 D:KCX145 3.4 38.3 1.0 CB D:HIS178 3.5 31.4 1.0 FE D:FE401 3.7 30.0 0.9 NE2 D:HIS178 4.1 33.6 1.0 ND1 D:HIS206 4.2 30.2 1.0 CD2 D:HIS178 4.2 35.1 1.0 NZ D:KCX145 4.2 34.9 1.0 CG D:HIS206 4.2 32.6 1.0 CE1 D:HIS23 4.2 34.0 1.0 NE2 D:HIS23 4.4 39.0 1.0 ND2 D:ASN266 4.4 32.7 1.0 CA D:HIS178 4.5 33.2 1.0 CE D:KCX145 4.6 32.1 1.0 OD1 D:ASN266 4.7 39.3 1.0 CG D:ASN266 4.9 36.8 1.0

M.K.Go, L.N.Zhao, B.Xue, S.Supekar, R.C.Robinson, H.Fan, W.S.Yew. Directed Computational Evolution of Quorum-Quenching Lactonases From the Amidohydrolase Superfamily Structure 2020.
ISSN: ISSN 0969-2126