Zinc in PDB 4h9u: Structure of Geobacillus Kaustophilus Lactonase, Wild-Type with ZN2+

The structure of Structure of Geobacillus Kaustophilus Lactonase, Wild-Type with ZN2+, PDB code: 4h9u was solved by B.Xue, J.Y.Chow, W.S.Yew, R.C.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.340, 157.122, 49.936, 90.00, 116.18, 90.00
R / Rfree (%)	17.2 / 21.7

The structure of Structure of Geobacillus Kaustophilus Lactonase, Wild-Type with ZN2+ also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Structure of Geobacillus Kaustophilus Lactonase, Wild-Type with ZN2+ (pdb code 4h9u). 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, Wild-Type with ZN2+, PDB code: 4h9u:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Wild-Type with ZN2+


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, Wild-Type with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:20.4 occ:1.00 ND1 A:HIS178 2.2 15.1 1.0 NE2 A:HIS206 2.2 17.8 1.0 OQ2 A:KCX145 2.2 14.9 1.0 O A:OH403 2.4 20.3 1.0 CG A:HIS178 3.1 14.9 1.0 CD2 A:HIS206 3.1 15.0 1.0 CE1 A:HIS178 3.2 8.3 1.0 CX A:KCX145 3.2 36.5 1.0 CE1 A:HIS206 3.2 23.9 1.0 CB A:HIS178 3.3 8.8 1.0 OQ1 A:KCX145 3.5 26.4 1.0 FE A:FE401 3.6 14.4 1.0 NH2 A:ARG230 3.8 31.5 1.0 CA A:HIS178 4.0 16.3 1.0 CD2 A:HIS178 4.2 16.6 1.0 NE2 A:HIS23 4.2 6.7 1.0 CG A:HIS206 4.3 14.2 1.0 NE2 A:HIS178 4.3 16.6 1.0 OD2 A:ASP266 4.3 20.9 1.0 CE1 A:HIS23 4.3 8.9 1.0 ND1 A:HIS206 4.3 15.6 1.0 CE1 A:TYR99 4.4 19.4 1.0 NZ A:KCX145 4.4 18.2 1.0 O A:HOH612 4.5 29.6 1.0 OH A:TYR99 4.6 22.0 1.0 CZ A:ARG230 4.6 39.5 1.0 CE A:KCX145 4.7 14.5 1.0 CZ A:TYR99 5.0 22.0 1.0 NE A:ARG230 5.0 34.2 1.0

Zinc binding site 2 out of 2 in the Structure of Geobacillus Kaustophilus Lactonase, Wild-Type with ZN2+


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, Wild-Type with ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:20.9 occ:1.00 NE2 B:HIS206 2.2 18.3 1.0 OQ2 B:KCX145 2.2 12.0 1.0 ND1 B:HIS178 2.2 22.6 1.0 O B:OH403 2.3 14.6 1.0 CD2 B:HIS206 3.1 15.6 1.0 CX B:KCX145 3.2 12.3 1.0 CG B:HIS178 3.2 12.0 1.0 CE1 B:HIS206 3.2 23.8 1.0 CE1 B:HIS178 3.2 12.0 1.0 CB B:HIS178 3.4 12.2 1.0 OQ1 B:KCX145 3.4 23.4 1.0 FE B:FE401 3.4 12.8 1.0 NH2 B:ARG230 3.7 31.4 1.0 OD2 B:ASP266 4.1 24.8 1.0 CA B:HIS178 4.1 14.3 1.0 NE2 B:HIS23 4.1 13.2 1.0 CE1 B:HIS23 4.2 15.3 1.0 CG B:HIS206 4.3 20.6 1.0 ND1 B:HIS206 4.3 17.9 1.0 CD2 B:HIS178 4.3 18.7 1.0 NE2 B:HIS178 4.3 26.2 1.0 NZ B:KCX145 4.3 24.6 1.0 CE1 B:TYR99 4.3 16.6 1.0 O B:HOH618 4.4 29.7 1.0 OH B:TYR99 4.5 25.3 1.0 CZ B:ARG230 4.5 40.7 1.0 CE B:KCX145 4.6 16.3 1.0 NE B:ARG230 4.9 37.1 1.0 CZ B:TYR99 4.9 24.7 1.0 CG B:ASP266 4.9 24.2 1.0 OD1 B:ASP266 4.9 29.2 1.0

B.Xue, J.Y.Chow, A.Baldansuren, L.L.Yap, Y.H.Gan, S.A.Dikanov, R.C.Robinson, W.S.Yew. Structural Evidence of A Productive Active Site Architecture For An Evolved Quorum-Quenching Gkl Lactonase. Biochemistry V. 52 2359 2013.
ISSN: ISSN 0006-2960
PubMed: 23461395
DOI: 10.1021/BI4000904