Zinc in PDB 6knt: Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group P4332)

The structure of Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group P4332), PDB code: 6knt 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 / 2.50
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	202.754, 202.754, 202.754, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.8

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Fold Protein Yhfi From Bacillus Subtilis (Space Group P4332) (pdb code 6knt). 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 P4332), PDB code: 6knt:
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 P4332)


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 P4332) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:38.0 occ:1.00 NE2 A:HIS211 2.1 25.2 1.0 OD2 A:ASP155 2.1 25.7 1.0 NE2 A:HIS64 2.2 22.6 1.0 OD2 A:ASP63 2.7 27.3 1.0 CD2 A:HIS64 2.9 21.9 1.0 CG A:ASP155 3.0 24.8 1.0 CE1 A:HIS211 3.0 25.7 1.0 ZN A:ZN302 3.1 31.8 1.0 CD2 A:HIS211 3.1 25.3 1.0 OD1 A:ASP155 3.2 24.3 1.0 CE1 A:HIS64 3.4 19.8 1.0 CG A:ASP63 3.4 25.9 1.0 OD1 A:ASP63 3.5 23.4 1.0 O A:HOH422 4.0 34.4 1.0 NE2 A:HIS59 4.0 22.0 1.0 CE1 A:HIS59 4.1 20.4 1.0 ND1 A:HIS211 4.2 25.1 1.0 CG A:HIS64 4.2 21.6 1.0 CG A:HIS211 4.2 24.3 1.0 CB A:ASP155 4.3 23.4 1.0 ND1 A:HIS64 4.3 21.9 1.0 CB A:ASP63 4.7 23.6 1.0 CE1 A:HIS189 4.7 24.4 1.0 NE2 A:HIS134 4.8 24.3 1.0 OG A:SER20 4.9 20.3 1.0 N A:GLY11 4.9 24.6 1.0 CB A:HIS61 5.0 23.5 1.0 ND1 A:HIS61 5.0 23.0 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 P4332)


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 P4332) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:31.8 occ:1.00 NE2 A:HIS134 2.1 24.3 1.0 ND1 A:HIS61 2.3 23.0 1.0 NE2 A:HIS59 2.3 22.0 1.0 OD2 A:ASP155 2.5 25.7 1.0 CE1 A:HIS134 3.0 26.6 1.0 ZN A:ZN301 3.1 38.0 1.0 CD2 A:HIS134 3.1 25.5 1.0 CD2 A:HIS59 3.2 22.2 1.0 CE1 A:HIS61 3.2 22.2 1.0 CG A:HIS61 3.3 23.4 1.0 CE1 A:HIS59 3.3 20.4 1.0 CG A:ASP155 3.4 24.8 1.0 CB A:HIS61 3.6 23.5 1.0 CB A:ASP155 3.7 23.4 1.0 ND1 A:HIS134 4.1 24.8 1.0 CG A:HIS134 4.2 23.8 1.0 NE2 A:HIS64 4.2 22.6 1.0 CD2 A:HIS64 4.3 21.9 1.0 NE2 A:HIS61 4.4 22.9 1.0 OD1 A:ASP155 4.4 24.3 1.0 ND1 A:HIS59 4.4 23.4 1.0 CG A:HIS59 4.4 22.2 1.0 CD2 A:HIS61 4.4 21.9 1.0 OD1 A:ASP63 4.4 23.4 1.0 NE2 A:HIS211 4.8 25.2 1.0 CE1 A:HIS189 4.9 24.4 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 P4332)


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 P4332) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:41.5 occ:1.00 OD2 B:ASP155 2.1 29.0 1.0 NE2 B:HIS211 2.1 27.5 1.0 NE2 B:HIS64 2.2 29.3 1.0 OD2 B:ASP63 2.5 32.1 1.0 CE1 B:HIS211 2.9 29.6 1.0 CD2 B:HIS64 3.0 25.4 1.0 ZN B:ZN302 3.0 35.1 1.0 CG B:ASP155 3.0 29.3 1.0 OD1 B:ASP63 3.2 28.1 1.0 CG B:ASP63 3.2 27.8 1.0 OD1 B:ASP155 3.3 30.4 1.0 CD2 B:HIS211 3.3 29.6 1.0 CE1 B:HIS64 3.3 23.7 1.0 NE2 B:HIS59 3.9 26.6 1.0 CE1 B:HIS59 4.1 23.4 1.0 ND1 B:HIS211 4.1 28.9 1.0 CG B:HIS64 4.2 26.4 1.0 CG B:HIS211 4.3 28.0 1.0 ND1 B:HIS64 4.3 27.0 1.0 O B:HOH401 4.3 23.5 1.0 CB B:ASP155 4.4 27.9 1.0 CE1 B:HIS189 4.6 27.7 1.0 CB B:ASP63 4.6 26.4 1.0 NE2 B:HIS134 4.7 28.2 1.0 ND1 B:HIS61 4.8 24.7 1.0 CB B:HIS61 4.9 25.6 1.0 OG B:SER20 4.9 25.4 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 P4332)


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 P4332) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:35.1 occ:1.00 NE2 B:HIS134 2.2 28.2 1.0 NE2 B:HIS59 2.3 26.6 1.0 ND1 B:HIS61 2.3 24.7 1.0 OD2 B:ASP155 2.5 29.0 1.0 ZN B:ZN301 3.0 41.5 1.0 CE1 B:HIS134 3.1 31.8 1.0 CD2 B:HIS134 3.1 29.8 1.0 CD2 B:HIS59 3.2 25.9 1.0 CE1 B:HIS61 3.2 25.9 1.0 CG B:HIS61 3.3 25.1 1.0 CE1 B:HIS59 3.3 23.4 1.0 CG B:ASP155 3.4 29.3 1.0 CB B:HIS61 3.6 25.6 1.0 CB B:ASP155 3.8 27.9 1.0 NE2 B:HIS64 4.1 29.3 1.0 ND1 B:HIS134 4.2 30.5 1.0 CG B:HIS134 4.3 29.7 1.0 CD2 B:HIS64 4.3 25.4 1.0 OD1 B:ASP63 4.3 28.1 1.0 NE2 B:HIS61 4.4 27.8 1.0 CG B:HIS59 4.4 26.2 1.0 ND1 B:HIS59 4.4 27.4 1.0 CD2 B:HIS61 4.4 26.0 1.0 OD1 B:ASP155 4.5 30.4 1.0 NE2 B:HIS211 4.8 27.5 1.0 CE1 B:HIS189 4.9 27.7 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 P4332)


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 P4332) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:55.3 occ:1.00 OD2 C:ASP155 2.0 44.0 1.0 NE2 C:HIS211 2.2 49.5 1.0 OD2 C:ASP63 2.4 43.2 1.0 NE2 C:HIS64 2.4 40.9 1.0 CE1 C:HIS211 2.9 49.0 1.0 ZN C:ZN302 2.9 46.7 1.0 CD2 C:HIS64 3.1 37.1 1.0 CG C:ASP155 3.1 47.0 1.0 CG C:ASP63 3.1 40.6 1.0 OD1 C:ASP63 3.2 40.5 1.0 CD2 C:HIS211 3.3 50.2 1.0 OD1 C:ASP155 3.5 51.0 1.0 CE1 C:HIS64 3.6 41.8 1.0 NE2 C:HIS59 3.9 41.5 1.0 CE1 C:HIS59 4.0 40.1 1.0 ND1 C:HIS211 4.1 49.7 1.0 CG C:HIS211 4.3 50.3 1.0 CG C:HIS64 4.3 40.4 1.0 CB C:ASP155 4.4 47.1 1.0 ND1 C:HIS64 4.5 41.7 1.0 CE1 C:HIS189 4.6 48.7 1.0 CB C:ASP63 4.6 39.5 1.0 ND1 C:HIS61 4.7 38.3 1.0 NE2 C:HIS134 4.7 42.3 1.0 CB C:HIS61 4.8 37.3 1.0 OG C:SER20 4.8 45.2 1.0 CE1 C:HIS134 4.9 46.9 1.0 N C:GLY11 5.0 43.0 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 P4332)


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 P4332) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:46.7 occ:1.00 NE2 C:HIS134 2.0 42.3 1.0 ND1 C:HIS61 2.2 38.3 1.0 NE2 C:HIS59 2.3 41.5 1.0 OD2 C:ASP155 2.6 44.0 1.0 CE1 C:HIS134 2.8 46.9 1.0 ZN C:ZN301 2.9 55.3 1.0 CE1 C:HIS61 3.1 37.9 1.0 CG C:HIS61 3.2 37.6 1.0 CD2 C:HIS134 3.2 42.7 1.0 CD2 C:HIS59 3.2 40.7 1.0 CE1 C:HIS59 3.3 40.1 1.0 CB C:HIS61 3.5 37.3 1.0 CG C:ASP155 3.6 47.0 1.0 CB C:ASP155 3.9 47.1 1.0 ND1 C:HIS134 4.0 48.3 1.0 NE2 C:HIS64 4.2 40.9 1.0 CG C:HIS134 4.2 45.3 1.0 NE2 C:HIS61 4.3 38.1 1.0 OD1 C:ASP63 4.3 40.5 1.0 CD2 C:HIS61 4.3 37.7 1.0 CD2 C:HIS64 4.4 37.1 1.0 ND1 C:HIS59 4.4 41.8 1.0 CG C:HIS59 4.4 39.7 1.0 OD1 C:ASP155 4.6 51.0 1.0 CE1 C:HIS189 4.8 48.7 1.0 OD2 C:ASP63 4.8 43.2 1.0 NE2 C:HIS211 4.9 49.5 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 P4332)


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 P4332) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:51.7 occ:1.00 OD2 D:ASP155 1.9 37.9 1.0 NE2 D:HIS211 2.1 43.6 1.0 NE2 D:HIS64 2.4 36.9 1.0 OD2 D:ASP63 2.5 38.7 1.0 CE1 D:HIS211 2.8 44.5 1.0 CG D:ASP155 2.9 40.8 1.0 CD2 D:HIS64 3.1 33.2 1.0 ZN D:ZN302 3.1 42.6 1.0 CG D:ASP63 3.2 37.3 1.0 OD1 D:ASP155 3.2 43.8 1.0 CD2 D:HIS211 3.3 44.8 1.0 OD1 D:ASP63 3.3 34.7 1.0 CE1 D:HIS64 3.6 36.8 1.0 NE2 D:HIS59 4.0 35.0 1.0 ND1 D:HIS211 4.0 45.3 1.0 O D:HOH405 4.0 31.5 1.0 CE1 D:HIS59 4.1 34.1 1.0 CG D:HIS211 4.2 45.4 1.0 CB D:ASP155 4.3 40.2 1.0 CG D:HIS64 4.3 35.6 1.0 ND1 D:HIS64 4.5 38.2 1.0 CE1 D:HIS189 4.6 41.8 1.0 CB D:ASP63 4.6 36.8 1.0 ND1 D:HIS61 4.7 33.5 1.0 NE2 D:HIS134 4.8 39.1 1.0 OG D:SER20 4.9 39.6 1.0 CB D:HIS61 4.9 33.8 1.0 N D:GLY11 4.9 41.2 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 P4332)


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 P4332) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:42.6 occ:1.00 NE2 D:HIS134 2.2 39.1 1.0 ND1 D:HIS61 2.2 33.5 1.0 NE2 D:HIS59 2.3 35.0 1.0 OD2 D:ASP155 2.4 37.9 1.0 ZN D:ZN301 3.1 51.7 1.0 CE1 D:HIS61 3.1 34.0 1.0 CD2 D:HIS59 3.2 34.9 1.0 CD2 D:HIS134 3.2 38.4 1.0 CE1 D:HIS134 3.2 41.1 1.0 CG D:HIS61 3.3 33.2 1.0 CE1 D:HIS59 3.4 34.1 1.0 CG D:ASP155 3.4 40.8 1.0 CB D:HIS61 3.6 33.8 1.0 CB D:ASP155 3.8 40.2 1.0 NE2 D:HIS61 4.3 34.5 1.0 ND1 D:HIS134 4.3 40.6 1.0 CG D:HIS134 4.3 38.4 1.0 CD2 D:HIS61 4.4 32.3 1.0 NE2 D:HIS64 4.4 36.9 1.0 CG D:HIS59 4.4 33.9 1.0 ND1 D:HIS59 4.4 34.5 1.0 OD1 D:ASP63 4.5 34.7 1.0 OD1 D:ASP155 4.5 43.8 1.0 CD2 D:HIS64 4.5 33.2 1.0 CE1 D:HIS189 4.7 41.8 1.0 NE2 D:HIS211 5.0 43.6 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