Zinc in PDB 6kns: Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)

The structure of Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122), PDB code: 6kns was solved by H.W.Na, B.Namgung, W.S.Song, S.I.Yoon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.15
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.378, 106.378, 404.849, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.2

The structure of Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) (pdb code 6kns). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122), PDB code: 6kns:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)


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 Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:29.9 occ:1.00 NE2 A:HIS211 2.1 21.4 1.0 NE2 A:HIS64 2.2 16.7 1.0 OD2 A:ASP155 2.3 17.0 1.0 OD2 A:ASP63 2.5 15.8 1.0 CD2 A:HIS64 2.9 16.3 1.0 CE1 A:HIS211 2.9 19.7 1.0 CG A:ASP155 3.0 20.9 1.0 OD1 A:ASP155 3.1 21.8 1.0 ZN A:ZN304 3.2 24.9 1.0 CD2 A:HIS211 3.2 18.0 1.0 CE1 A:HIS64 3.3 21.0 1.0 CG A:ASP63 3.3 16.7 1.0 OD1 A:ASP63 3.5 15.8 1.0 O A:HOH483 3.5 42.5 1.0 O A:HOH416 3.9 18.8 1.0 NE2 A:HIS59 4.0 16.4 1.0 CE1 A:HIS59 4.0 21.3 1.0 ND1 A:HIS211 4.1 17.4 1.0 CG A:HIS64 4.2 16.9 1.0 CG A:HIS211 4.2 19.3 1.0 ND1 A:HIS64 4.3 16.4 1.0 CB A:ASP155 4.4 21.1 1.0 CE1 A:HIS189 4.6 20.1 1.0 CB A:ASP63 4.7 17.1 1.0 ND1 A:HIS61 4.8 17.5 1.0 N A:GLY11 4.9 19.1 1.0 OG A:SER20 4.9 18.9 1.0 CB A:HIS61 4.9 17.8 1.0 NE2 A:HIS134 5.0 20.8 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)


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 Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:24.9 occ:1.00 ND1 A:HIS61 2.1 17.5 1.0 NE2 A:HIS134 2.3 20.8 1.0 NE2 A:HIS59 2.3 16.4 1.0 OD2 A:ASP155 2.4 17.0 1.0 CE1 A:HIS61 3.0 18.9 1.0 ZN A:ZN303 3.2 29.9 1.0 CG A:HIS61 3.2 18.3 1.0 CD2 A:HIS59 3.2 19.9 1.0 CE1 A:HIS134 3.2 17.2 1.0 CD2 A:HIS134 3.2 21.5 1.0 CE1 A:HIS59 3.3 21.3 1.0 CG A:ASP155 3.4 20.9 1.0 O A:HOH483 3.5 42.5 1.0 CB A:HIS61 3.6 17.8 1.0 CB A:ASP155 3.8 21.1 1.0 NE2 A:HIS61 4.2 19.3 1.0 CD2 A:HIS61 4.3 19.0 1.0 NE2 A:HIS64 4.3 16.7 1.0 ND1 A:HIS134 4.3 20.2 1.0 CG A:HIS134 4.3 22.1 1.0 ND1 A:HIS59 4.3 18.1 1.0 CG A:HIS59 4.4 20.7 1.0 OD1 A:ASP155 4.4 21.8 1.0 CD2 A:HIS64 4.4 16.3 1.0 OD1 A:ASP63 4.6 15.8 1.0 CE1 A:HIS189 4.7 20.1 1.0 NE2 A:HIS211 5.0 21.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)


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 Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:32.3 occ:1.00 NE2 B:HIS211 2.1 21.6 1.0 NE2 B:HIS64 2.1 18.8 1.0 OD2 B:ASP155 2.3 22.6 1.0 OD2 B:ASP63 2.4 18.4 1.0 CD2 B:HIS64 2.9 19.2 1.0 CG B:ASP155 3.0 23.8 1.0 CE1 B:HIS211 3.1 20.0 1.0 CD2 B:HIS211 3.1 18.8 1.0 OD1 B:ASP155 3.2 25.1 1.0 CE1 B:HIS64 3.2 17.6 1.0 ZN B:ZN303 3.3 25.9 1.0 CG B:ASP63 3.3 19.5 1.0 OD1 B:ASP63 3.4 20.6 1.0 O B:HOH402 3.9 19.6 1.0 NE2 B:HIS59 4.0 19.4 1.0 CE1 B:HIS59 4.1 20.4 1.0 CG B:HIS64 4.1 18.2 1.0 ND1 B:HIS211 4.2 23.0 1.0 CG B:HIS211 4.2 22.1 1.0 ND1 B:HIS64 4.3 17.8 1.0 CB B:ASP155 4.5 22.6 1.0 CE1 B:HIS189 4.6 26.3 1.0 CB B:ASP63 4.7 19.9 1.0 OG B:SER20 4.7 19.9 1.0 N B:GLY11 4.9 20.4 1.0 ND1 B:HIS61 4.9 17.7 1.0 NE2 B:HIS134 4.9 19.1 1.0 CB B:HIS61 5.0 20.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)


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 Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:25.9 occ:1.00 NE2 B:HIS134 2.2 19.1 1.0 ND1 B:HIS61 2.2 17.7 1.0 NE2 B:HIS59 2.2 19.4 1.0 OD2 B:ASP155 2.3 22.6 1.0 CD2 B:HIS59 3.1 18.6 1.0 CE1 B:HIS61 3.1 20.7 1.0 CE1 B:HIS134 3.1 22.0 1.0 CD2 B:HIS134 3.2 22.0 1.0 CG B:HIS61 3.2 20.4 1.0 ZN B:ZN302 3.3 32.3 1.0 CE1 B:HIS59 3.3 20.4 1.0 CG B:ASP155 3.3 23.8 1.0 CB B:HIS61 3.6 20.5 1.0 CB B:ASP155 3.8 22.6 1.0 ND1 B:HIS134 4.2 23.4 1.0 NE2 B:HIS61 4.3 20.2 1.0 CG B:HIS134 4.3 23.9 1.0 CG B:HIS59 4.3 20.6 1.0 NE2 B:HIS64 4.3 18.8 1.0 CD2 B:HIS61 4.3 20.5 1.0 ND1 B:HIS59 4.3 20.1 1.0 OD1 B:ASP155 4.4 25.1 1.0 CD2 B:HIS64 4.5 19.2 1.0 OD1 B:ASP63 4.6 20.6 1.0 CE1 B:HIS189 4.8 26.3 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:31.3 occ:1.00 NE2 C:HIS211 2.0 19.1 1.0 NE2 C:HIS64 2.1 16.2 1.0 OD2 C:ASP155 2.3 16.6 1.0 OD2 C:ASP63 2.6 17.9 1.0 CE1 C:HIS211 2.8 18.2 1.0 CD2 C:HIS64 2.9 15.7 1.0 CG C:ASP155 3.0 18.7 1.0 CD2 C:HIS211 3.1 18.3 1.0 CE1 C:HIS64 3.2 16.0 1.0 OD1 C:ASP155 3.2 19.1 1.0 ZN C:ZN302 3.3 23.3 1.0 CG C:ASP63 3.4 16.4 1.0 OD1 C:ASP63 3.5 16.6 1.0 CE1 C:HIS59 4.0 15.9 1.0 NE2 C:HIS59 4.0 16.4 1.0 ND1 C:HIS211 4.0 17.4 1.0 O C:HOH411 4.0 15.4 1.0 CG C:HIS64 4.1 15.1 1.0 CG C:HIS211 4.1 18.0 1.0 ND1 C:HIS64 4.2 15.2 1.0 CE1 C:HIS189 4.4 20.2 1.0 CB C:ASP155 4.4 17.7 1.0 CB C:ASP63 4.7 15.6 1.0 OG C:SER20 4.8 16.1 1.0 N C:GLY11 4.9 17.6 1.0 ND1 C:HIS61 4.9 14.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:23.3 occ:1.00 NE2 C:HIS59 2.2 16.4 1.0 ND1 C:HIS61 2.2 14.6 1.0 NE2 C:HIS134 2.2 19.1 1.0 OD2 C:ASP155 2.4 16.6 1.0 CE1 C:HIS61 3.1 16.1 1.0 CE1 C:HIS134 3.1 15.8 1.0 CD2 C:HIS59 3.1 16.1 1.0 CE1 C:HIS59 3.1 15.9 1.0 CG C:HIS61 3.3 15.5 1.0 ZN C:ZN301 3.3 31.3 1.0 CD2 C:HIS134 3.3 18.9 1.0 CG C:ASP155 3.4 18.7 1.0 CB C:HIS61 3.6 14.8 1.0 CB C:ASP155 3.8 17.7 1.0 ND1 C:HIS59 4.2 18.7 1.0 NE2 C:HIS64 4.2 16.2 1.0 ND1 C:HIS134 4.2 18.5 1.0 CG C:HIS59 4.2 17.3 1.0 NE2 C:HIS61 4.2 17.2 1.0 CD2 C:HIS61 4.4 16.5 1.0 CG C:HIS134 4.4 19.4 1.0 CD2 C:HIS64 4.4 15.7 1.0 OD1 C:ASP155 4.4 19.1 1.0 OD1 C:ASP63 4.6 16.6 1.0 CE1 C:HIS189 4.7 20.2 1.0 NE2 C:HIS211 5.0 19.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:38.9 occ:1.00 OD2 D:ASP155 2.0 25.9 1.0 NE2 D:HIS64 2.1 27.6 1.0 NE2 D:HIS211 2.1 29.4 1.0 OD2 D:ASP63 2.4 29.2 1.0 CD2 D:HIS64 3.0 26.5 1.0 CG D:ASP155 3.0 29.6 1.0 CE1 D:HIS211 3.1 29.9 1.0 CD2 D:HIS211 3.1 29.4 1.0 ZN D:ZN303 3.2 30.2 1.0 CE1 D:HIS64 3.2 26.7 1.0 OD1 D:ASP155 3.2 30.6 1.0 CG D:ASP63 3.3 26.2 1.0 OD1 D:ASP63 3.4 25.5 1.0 O D:HOH404 3.9 24.5 1.0 NE2 D:HIS59 4.0 24.6 1.0 CE1 D:HIS59 4.1 24.8 1.0 CG D:HIS64 4.2 25.5 1.0 ND1 D:HIS211 4.2 30.8 1.0 CG D:HIS211 4.2 32.5 1.0 ND1 D:HIS64 4.3 23.5 1.0 CB D:ASP155 4.3 29.0 1.0 CE1 D:HIS189 4.5 31.6 1.0 CB D:ASP63 4.7 25.3 1.0 NE2 D:HIS134 4.8 24.0 1.0 OG D:SER20 4.9 28.7 1.0 N D:GLY11 4.9 29.7 1.0 CB D:HIS61 5.0 24.2 1.0 ND1 D:HIS61 5.0 23.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group I4122) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:30.2 occ:1.00 NE2 D:HIS134 2.1 24.0 1.0 ND1 D:HIS61 2.2 23.6 1.0 NE2 D:HIS59 2.3 24.6 1.0 OD2 D:ASP155 2.6 25.9 1.0 CE1 D:HIS134 3.0 26.6 1.0 CE1 D:HIS61 3.1 24.3 1.0 CD2 D:HIS59 3.2 23.1 1.0 CD2 D:HIS134 3.2 28.3 1.0 ZN D:ZN302 3.2 38.9 1.0 CG D:HIS61 3.2 24.7 1.0 CE1 D:HIS59 3.3 24.8 1.0 CG D:ASP155 3.5 29.6 1.0 CB D:HIS61 3.5 24.2 1.0 CB D:ASP155 3.9 29.0 1.0 ND1 D:HIS134 4.2 27.9 1.0 NE2 D:HIS64 4.2 27.6 1.0 CG D:HIS134 4.3 28.3 1.0 NE2 D:HIS61 4.3 26.7 1.0 CD2 D:HIS61 4.3 25.5 1.0 CG D:HIS59 4.3 24.5 1.0 ND1 D:HIS59 4.4 25.3 1.0 OD1 D:ASP63 4.4 25.5 1.0 CD2 D:HIS64 4.4 26.5 1.0 OD1 D:ASP155 4.5 30.6 1.0 CE1 D:HIS189 4.8 31.6 1.0 OD2 D:ASP63 4.9 29.2 1.0 NE2 D:HIS211 5.0 29.4 1.0 CA D:HIS61 5.0 24.3 1.0

H.W.Na, B.Namgung, W.S.Song, S.I.Yoon. Structural and Biochemical Analyses of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis. Biochem.Biophys.Res.Commun. V. 519 35 2019.
ISSN: ESSN 1090-2104
PubMed: 31481231
DOI: 10.1016/J.BBRC.2019.08.106