Zinc in PDB 5k0w: Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica

The structure of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica, PDB code: 5k0w was solved by A.Buschiazzo, N.Larrieux, A.J.Vila, M.N.Lisa, J.Moran-Barrio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.33 / 2.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.000, 48.510, 88.940, 90.00, 100.10, 90.00
R / Rfree (%)	19.2 / 24.2

The structure of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica (pdb code 5k0w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica, PDB code: 5k0w:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.2 occ:1.00 O A:HOH429 2.1 29.2 1.0 NE2 A:HIS241 2.1 18.9 1.0 NE2 A:HIS103 2.1 21.5 1.0 OD2 A:ASP102 2.1 37.5 1.0 CE1 A:HIS103 3.0 21.1 1.0 CG A:ASP102 3.1 29.4 1.0 CD2 A:HIS241 3.1 18.8 1.0 CE1 A:HIS241 3.1 18.6 1.0 CD2 A:HIS103 3.1 21.9 1.0 OD1 A:ASP102 3.4 27.5 1.0 ZN A:ZN302 3.5 25.9 1.0 OE1 A:GLN98 3.5 5.3 1.0 NE2 A:GLN98 3.7 12.5 1.0 CD A:GLN98 3.9 22.9 1.0 ND1 A:HIS103 4.2 22.0 1.0 CG A:HIS103 4.2 20.6 1.0 CG A:HIS241 4.2 17.0 1.0 ND1 A:HIS241 4.2 18.8 1.0 CB A:ASP102 4.4 21.4 1.0 O A:HOH428 4.5 23.5 1.0 O A:HOH439 4.5 14.1 1.0 NE2 A:HIS175 4.8 22.0 1.0 CD2 A:LEU52 4.9 20.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:25.9 occ:1.00 OE1 A:GLN98 2.0 5.3 1.0 NE2 A:HIS175 2.1 22.0 1.0 ND1 A:HIS100 2.1 23.1 1.0 O A:HOH429 2.1 29.2 1.0 O A:HOH428 2.2 23.5 1.0 CE1 A:HIS100 2.9 22.1 1.0 CD2 A:HIS175 3.0 21.9 1.0 CD A:GLN98 3.1 22.9 1.0 CE1 A:HIS175 3.2 21.8 1.0 CG A:HIS100 3.2 21.6 1.0 ZN A:ZN301 3.5 25.2 1.0 NE2 A:GLN98 3.6 12.5 1.0 CB A:HIS100 3.6 18.6 1.0 O A:HOH439 3.8 14.1 1.0 NE2 A:HIS100 4.1 22.4 1.0 CG A:HIS175 4.2 20.5 1.0 OD1 A:ASP102 4.2 27.5 1.0 ND1 A:HIS175 4.2 22.5 1.0 CD2 A:HIS100 4.3 23.0 1.0 CG A:GLN98 4.4 18.9 1.0 NE2 A:HIS103 4.4 21.5 1.0 CD2 A:HIS103 4.6 21.9 1.0 OD2 A:ASP102 4.6 37.5 1.0 CG A:ASP102 4.8 29.4 1.0 CB A:GLN98 4.9 16.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:34.8 occ:1.00 NE2 B:HIS175 2.1 21.2 1.0 ND1 B:HIS100 2.1 23.4 1.0 O B:HOH425 2.2 38.0 1.0 OE1 B:GLN98 2.2 25.9 1.0 O B:HOH426 2.3 3.4 1.0 CE1 B:HIS100 2.9 22.5 1.0 CE1 B:HIS175 3.0 20.7 1.0 CD2 B:HIS175 3.1 21.1 1.0 CD B:GLN98 3.2 34.9 1.0 CG B:HIS100 3.3 21.9 1.0 NE2 B:GLN98 3.6 21.9 1.0 CB B:HIS100 3.8 18.8 1.0 ZN B:ZN302 3.8 26.3 1.0 O B:HOH437 3.9 41.7 1.0 ND1 B:HIS175 4.1 20.9 1.0 CG B:HIS175 4.1 19.2 1.0 NE2 B:HIS100 4.1 22.9 1.0 CD2 B:HIS100 4.3 23.3 1.0 OD1 B:ASP102 4.4 23.3 1.0 CG B:GLN98 4.5 26.6 1.0 CD2 B:HIS103 4.8 16.1 1.0 O B:HOH438 4.8 20.6 1.0 OD2 B:ASP102 4.8 31.6 1.0 NE2 B:HIS103 4.9 16.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Metallo-Beta-Lactamase Gob-18 From Elizabethkingia Meningoseptica within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:26.3 occ:1.00 NE2 B:HIS241 2.0 32.8 1.0 OD2 B:ASP102 2.1 31.6 1.0 NE2 B:HIS103 2.2 16.2 1.0 O B:HOH426 2.2 3.4 1.0 CD2 B:HIS103 3.0 16.1 1.0 CE1 B:HIS241 3.0 32.4 1.0 CD2 B:HIS241 3.0 33.0 1.0 CG B:ASP102 3.0 26.1 1.0 CE1 B:HIS103 3.3 16.0 1.0 OD1 B:ASP102 3.5 23.3 1.0 OE1 B:GLN98 3.7 25.9 1.0 NE2 B:GLN98 3.8 21.9 1.0 ZN B:ZN301 3.8 34.8 1.0 CD B:GLN98 4.0 34.9 1.0 CG B:HIS241 4.1 31.0 1.0 ND1 B:HIS241 4.2 32.7 1.0 O B:HOH425 4.2 38.0 1.0 CG B:HIS103 4.2 14.2 1.0 ND1 B:HIS103 4.3 16.4 1.0 CB B:ASP102 4.3 17.5 1.0 CD2 B:LEU52 4.9 20.9 1.0

J.Moran-Barrio, M.N.Lisa, N.Larrieux, S.I.Drusin, A.M.Viale, D.M.Moreno, A.Buschiazzo, A.J.Vila. Crystal Structure of the Metallo-Beta-Lactamase Gob in the Periplasmic Dizinc Form Reveals An Unusual Metal Site. Antimicrob.Agents Chemother. V. 60 6013 2016.
ISSN: ESSN 1098-6596
PubMed: 27458232
DOI: 10.1128/AAC.01067-16