Calcium 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:

Zinc

(Zn)

8 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca301 b:37.2 occ:1.00 O B:HOH404 2.4 28.1 1.0 OE1 A:GLU232 2.5 36.5 1.0 OE1 B:GLU232 2.5 39.6 1.0 O A:HOH435 2.5 34.1 1.0 OE2 A:GLU232 2.6 34.2 1.0 OE2 B:GLU232 2.6 35.3 1.0 CD A:GLU232 2.9 32.3 1.0 CD B:GLU232 2.9 37.5 1.0 OE2 B:GLU206 4.1 33.1 1.0 OE1 A:GLU206 4.2 32.4 1.0 OE2 A:GLU206 4.2 28.5 1.0 OE1 B:GLU206 4.3 38.0 1.0 CG B:GLU232 4.4 35.3 1.0 CD B:GLU206 4.4 35.0 1.0 CG A:GLU232 4.4 31.3 1.0 O A:HOH469 4.4 36.8 1.0 CD A:GLU206 4.6 30.2 1.0 O A:HOH501 4.8 43.1 1.0 ND2 A:ASN234 4.9 26.9 1.0 ND2 B:ASN234 4.9 29.1 1.0

Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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:Ca302 b:63.0 occ:1.00 O A:HOH405 2.5 35.2 1.0 OD2 A:ASP53 2.6 26.5 1.0 O A:LYS51 2.7 28.2 1.0 O A:ASP28 2.8 29.9 1.0 OD1 A:ASP53 3.1 28.3 1.0 CG A:ASP53 3.2 27.6 1.0 C A:LYS51 3.6 28.1 1.0 C A:ASP28 4.0 31.6 1.0 CA A:LYS51 4.0 30.2 1.0 CB A:LYS51 4.3 31.1 1.0 N A:SER30 4.6 26.4 1.0 CB A:ASP53 4.6 25.7 1.0 CA A:TYR29 4.7 29.6 1.0 N A:ASP53 4.7 23.9 1.0 N A:LEU52 4.7 26.2 1.0 N A:TYR29 4.8 30.8 1.0 CG A:LYS51 4.8 34.3 1.0 OG A:SER30 4.8 31.4 1.0 CB A:ASP28 4.9 35.1 1.0 CB A:SER30 4.9 26.0 1.0 CA A:ASP28 5.0 33.5 1.0 C A:LEU52 5.0 24.5 1.0 C A:TYR29 5.0 28.0 1.0

Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca 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:Ca301 b:44.1 occ:1.00 O B:LYS51 2.4 26.9 1.0 OD2 B:ASP53 2.5 24.3 1.0 O B:HOH420 2.5 36.2 1.0 O B:ASP28 2.5 30.2 1.0 O B:HOH500 2.6 39.4 1.0 CG B:ASP53 3.3 26.4 1.0 C B:LYS51 3.5 27.3 1.0 OD1 B:ASP53 3.5 27.9 1.0 C B:ASP28 3.7 30.6 1.0 CA B:LYS51 4.0 29.2 1.0 CB B:LYS51 4.1 29.7 1.0 N B:SER30 4.3 25.8 1.0 OG B:SER30 4.4 31.1 1.0 CA B:TYR29 4.5 28.3 1.0 N B:TYR29 4.6 29.3 1.0 CB B:SER30 4.6 25.7 1.0 N B:LEU52 4.7 25.4 1.0 CB B:ASP53 4.7 25.0 1.0 CA B:ASP28 4.7 32.1 1.0 CB B:ASP28 4.7 34.0 1.0 C B:TYR29 4.8 26.8 1.0 N B:ASP53 4.8 23.5 1.0 CG B:LYS51 4.9 30.7 1.0 C B:LEU52 5.0 24.0 1.0

Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca 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 D:Ca301 b:39.6 occ:1.00 OD2 D:ASP53 2.4 33.6 1.0 O D:HOH406 2.5 30.9 1.0 O D:ASP28 2.5 39.6 1.0 O D:LYS51 2.5 34.2 1.0 O D:HOH414 2.7 28.6 1.0 CG D:ASP53 3.3 33.2 1.0 OD1 D:ASP53 3.4 30.3 1.0 C D:LYS51 3.6 34.0 1.0 C D:ASP28 3.7 41.0 1.0 CA D:LYS51 4.1 36.3 1.0 N D:SER30 4.2 35.8 1.0 CB D:LYS51 4.3 37.6 1.0 CA D:TYR29 4.3 38.2 1.0 CB D:SER30 4.4 34.5 1.0 OG D:SER30 4.4 40.9 1.0 N D:TYR29 4.4 39.9 1.0 C D:TYR29 4.6 37.1 1.0 CB D:ASP53 4.6 31.2 1.0 N D:ASP53 4.6 30.2 1.0 N D:LEU52 4.7 32.1 1.0 CA D:ASP28 4.7 43.9 1.0 CB D:ASP28 4.8 44.5 1.0 CG D:LYS51 4.8 39.4 1.0 C D:LEU52 4.9 30.4 1.0 CA D:SER30 5.0 35.1 1.0 CA D:LEU52 5.0 31.0 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