Zinc in PDB 6jsu: Structure of Geobacillus Kaustophilus Lactonase, Y99C/D266N Double Mutant

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99C/D266N Double Mutant, PDB code: 6jsu 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)	19.87 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.600, 157.487, 50.618, 90.00, 117.06, 90.00
R / Rfree (%)	16 / 19

The structure of Structure of Geobacillus Kaustophilus Lactonase, Y99C/D266N Double Mutant also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Structure of Geobacillus Kaustophilus Lactonase, Y99C/D266N Double Mutant (pdb code 6jsu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Geobacillus Kaustophilus Lactonase, Y99C/D266N Double Mutant, PDB code: 6jsu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Y99C/D266N Double 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, Y99C/D266N Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:22.4 occ:0.82 OQ1 A:KCX145 2.0 21.3 1.0 O A:OH403 2.1 23.0 1.0 NE2 A:HIS206 2.1 23.1 1.0 ND1 A:HIS178 2.1 23.4 1.0 O A:HOH654 2.8 43.4 1.0 CX A:KCX145 3.0 22.5 1.0 CE1 A:HIS206 3.0 22.9 1.0 CG A:HIS178 3.1 23.4 1.0 CE1 A:HIS178 3.1 25.8 1.0 CD2 A:HIS206 3.1 22.4 1.0 OQ2 A:KCX145 3.3 23.4 1.0 CB A:HIS178 3.4 20.2 1.0 FE A:FE401 3.4 18.8 1.0 NE2 A:HIS23 4.1 21.9 1.0 NH2 A:ARG230 4.1 30.3 1.0 CE1 A:HIS23 4.1 17.4 1.0 NZ A:KCX145 4.2 21.6 1.0 ND1 A:HIS206 4.2 19.9 1.0 NE2 A:HIS178 4.2 23.2 1.0 CD2 A:HIS178 4.2 24.7 1.0 CG A:HIS206 4.2 19.0 1.0 CA A:HIS178 4.3 18.7 1.0 CE A:KCX145 4.5 22.4 1.0 O A:HOH685 4.7 46.6 1.0 ND2 A:ASN266 4.7 27.5 1.0 CZ A:ARG230 4.8 39.6 1.0 OD1 A:ASN266 4.8 21.7 1.0

Zinc binding site 2 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Y99C/D266N Double 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, Y99C/D266N Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:21.0 occ:0.77 O B:OH403 2.0 22.3 1.0 OQ2 B:KCX145 2.0 25.4 1.0 NE2 B:HIS206 2.1 25.4 1.0 ND1 B:HIS178 2.1 22.0 1.0 CX B:KCX145 3.0 27.1 1.0 CE1 B:HIS178 3.0 25.3 1.0 CD2 B:HIS206 3.1 21.7 1.0 CE1 B:HIS206 3.1 26.0 1.0 CG B:HIS178 3.1 20.8 1.0 OQ1 B:KCX145 3.3 23.6 1.0 FE B:FE401 3.4 18.4 1.0 CB B:HIS178 3.4 23.0 1.0 O B:HOH667 3.7 42.9 1.0 NH2 B:ARG230 3.9 34.8 1.0 CE1 B:HIS23 4.0 21.4 1.0 NE2 B:HIS23 4.1 21.1 1.0 NE2 B:HIS178 4.2 26.0 1.0 NZ B:KCX145 4.2 24.1 1.0 ND1 B:HIS206 4.2 23.1 1.0 CG B:HIS206 4.2 22.2 1.0 CD2 B:HIS178 4.2 22.9 1.0 CA B:HIS178 4.3 18.5 1.0 CE B:KCX145 4.5 23.9 1.0 O B:HOH692 4.5 45.4 1.0 ND2 B:ASN266 4.6 27.2 1.0 OD1 B:ASN266 4.7 19.6 1.0 CZ B:ARG230 4.7 48.4 1.0 O B:HOH720 4.7 53.1 1.0 NE B:ARG230 4.9 37.8 1.0 CG B:ASN266 5.0 29.5 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