Zinc in PDB 6jss: Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant, PDB code: 6jss 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)	19.71 / 2.16
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.491, 51.648, 135.291, 91.83, 91.49, 95.78
R / Rfree (%)	17.5 / 22.9

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant (pdb code 6jss). 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 Mutant, PDB code: 6jss:
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 Mutant


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:24.0 occ:1.00 NE2 A:HIS206 2.0 27.9 1.0 OQ1 A:KCX145 2.1 21.7 1.0 O A:OH403 2.1 19.6 1.0 ND1 A:HIS178 2.1 14.7 1.0 CE1 A:HIS206 2.9 26.3 1.0 CX A:KCX145 3.0 21.4 1.0 CD2 A:HIS206 3.0 28.1 1.0 CE1 A:HIS178 3.1 16.3 1.0 CG A:HIS178 3.1 17.8 1.0 OQ2 A:KCX145 3.2 15.9 1.0 FE A:FE401 3.3 15.4 1.0 CB A:HIS178 3.5 14.0 1.0 NH2 A:ARG230 3.8 45.0 1.0 CE1 A:HIS23 4.0 20.3 1.0 ND1 A:HIS206 4.1 30.2 1.0 OD2 A:ASP266 4.1 16.6 1.0 NE2 A:HIS23 4.1 23.2 1.0 CG A:HIS206 4.1 24.3 1.0 NZ A:KCX145 4.2 14.6 1.0 NE2 A:HIS178 4.2 17.5 1.0 CD2 A:HIS178 4.2 18.5 1.0 CA A:HIS178 4.4 12.1 1.0 CZ A:ARG230 4.5 35.6 1.0 CE A:KCX145 4.6 16.2 1.0 OD1 A:ASP266 4.7 19.4 1.0 NE A:ARG230 4.7 29.0 1.0 CG A:ASP266 4.8 22.8 1.0

Zinc binding site 2 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:25.1 occ:1.00 OQ2 B:KCX145 2.1 20.3 1.0 NE2 B:HIS206 2.1 30.0 1.0 ND1 B:HIS178 2.2 21.7 1.0 O B:OH403 2.2 21.4 1.0 CE1 B:HIS206 3.0 29.6 1.0 CX B:KCX145 3.1 25.6 1.0 CG B:HIS178 3.1 20.2 1.0 CE1 B:HIS178 3.2 13.7 1.0 CD2 B:HIS206 3.2 29.3 1.0 FE B:FE401 3.3 18.3 1.0 OQ1 B:KCX145 3.3 17.3 1.0 O B:HOH508 3.3 33.6 1.0 CB B:HIS178 3.4 16.5 1.0 O B:HOH624 3.7 56.6 1.0 NH2 B:ARG230 3.9 27.2 1.0 CE1 B:HIS23 3.9 21.8 1.0 NE2 B:HIS23 4.0 25.8 1.0 OD2 B:ASP266 4.1 18.4 1.0 ND1 B:HIS206 4.2 25.3 1.0 NZ B:KCX145 4.3 25.0 1.0 NE2 B:HIS178 4.3 21.6 1.0 CD2 B:HIS178 4.3 22.4 1.0 CG B:HIS206 4.3 25.5 1.0 CA B:HIS178 4.4 17.6 1.0 O B:HOH517 4.5 37.1 1.0 CZ B:ARG230 4.6 27.1 1.0 CE B:KCX145 4.6 27.2 1.0 OD1 B:ASP266 4.7 18.0 1.0 CG B:ASP266 4.8 26.3 1.0

Zinc binding site 3 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:28.3 occ:0.96 OQ2 C:KCX145 2.0 32.3 1.0 NE2 C:HIS206 2.1 20.8 1.0 ND1 C:HIS178 2.1 23.1 1.0 O C:OH403 2.2 15.5 1.0 CE1 C:HIS178 2.9 19.3 1.0 CE1 C:HIS206 3.0 20.8 1.0 CX C:KCX145 3.1 30.5 1.0 CD2 C:HIS206 3.1 17.9 1.0 CG C:HIS178 3.2 19.5 1.0 OQ1 C:KCX145 3.5 26.4 1.0 FE C:FE401 3.5 20.4 1.0 CB C:HIS178 3.7 24.1 1.0 NH2 C:ARG230 3.9 28.4 1.0 OD2 C:ASP266 4.0 26.7 1.0 CE1 C:HIS23 4.0 31.5 1.0 NE2 C:HIS178 4.1 21.1 1.0 ND1 C:HIS206 4.1 22.8 1.0 NE2 C:HIS23 4.2 24.2 1.0 NZ C:KCX145 4.2 28.0 1.0 CG C:HIS206 4.2 24.4 1.0 CD2 C:HIS178 4.3 14.5 1.0 O C:HOH514 4.4 40.3 1.0 CZ C:ARG230 4.4 36.8 1.0 CE C:KCX145 4.6 21.4 1.0 CA C:HIS178 4.6 23.3 1.0 NE C:ARG230 4.8 31.9 1.0 CG C:ASP266 4.8 25.6 1.0 OD1 C:ASP266 4.9 26.4 1.0

Zinc binding site 4 out of 4 in the Structure of Geobacillus Kaustophilus Lactonase, Y99P Mutant


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 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:49.6 occ:1.00 OQ2 D:KCX145 1.9 29.0 1.0 ND1 D:HIS178 2.0 41.0 1.0 NE2 D:HIS206 2.1 39.4 1.0 O D:OH403 2.2 40.0 1.0 CX D:KCX145 3.0 23.8 1.0 CE1 D:HIS178 3.0 38.1 1.0 CG D:HIS178 3.0 32.7 1.0 CE1 D:HIS206 3.0 31.3 1.0 CD2 D:HIS206 3.1 31.3 1.0 CB D:HIS178 3.3 26.4 1.0 OQ1 D:KCX145 3.4 27.5 1.0 FE D:FE401 3.5 25.0 1.0 NH2 D:ARG230 3.7 41.9 1.0 CE1 D:HIS23 4.0 24.2 1.0 NE2 D:HIS178 4.1 35.6 1.0 CD2 D:HIS178 4.1 34.0 1.0 NZ D:KCX145 4.1 28.8 1.0 ND1 D:HIS206 4.2 32.2 1.0 NE2 D:HIS23 4.2 24.1 1.0 OD2 D:ASP266 4.2 23.7 1.0 CG D:HIS206 4.2 33.2 1.0 CZ D:ARG230 4.3 38.5 1.0 CA D:HIS178 4.3 29.6 1.0 CE D:KCX145 4.6 28.6 1.0 O D:HOH567 4.7 45.4 1.0 NE D:ARG230 4.8 32.9 1.0 OD1 D:ASP266 4.8 34.7 1.0 O D:HOH560 4.9 34.8 1.0 CG D:ASP266 4.9 26.3 1.0 NH1 D:ARG230 5.0 37.1 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