Sodium in PDB 7kz3: Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine

All present enzymatic activity of Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine:
2.6.1.1;

The structure of Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine, PDB code: 7kz3 was solved by T.Prasertanan, D.R.J.Palmer, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.24 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.46, 66.68, 111.83, 81.08, 77.41, 88.05
R / Rfree (%)	15 / 18.1

The binding sites of Sodium atom in the Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine (pdb code 7kz3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine, PDB code: 7kz3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na522 b:28.5 occ:1.00 O D:ASP56 2.3 30.8 1.0 OD2 D:ASP62 2.3 29.6 1.0 O D:HOH742 2.3 34.7 1.0 O C:HOH845 2.4 31.5 1.0 O D:HOH910 2.4 44.8 1.0 CG D:ASP62 3.2 27.1 1.0 OD1 D:ASP62 3.4 42.1 1.0 C D:ASP56 3.5 24.9 1.0 N D:ASP58 3.9 23.2 1.0 ND2 C:ASN65 4.0 33.8 1.0 CB D:ASP56 4.2 27.3 1.0 CB D:ASP58 4.3 24.8 1.0 CA D:ILE57 4.3 23.0 1.0 N D:ILE57 4.3 24.1 1.0 C D:ILE57 4.4 25.0 1.0 OD2 D:ASP56 4.4 40.7 1.0 CA D:ASP56 4.4 26.4 1.0 CG D:ASP56 4.5 30.9 1.0 O D:HOH957 4.6 28.7 1.0 CB D:ASP62 4.6 22.2 1.0 CA D:ASP58 4.7 23.8 1.0 O C:HOH889 4.9 45.6 1.0 O D:HOH624 5.0 38.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na523 b:32.1 occ:1.00 O D:THR197 2.3 16.8 1.0 O D:HOH852 2.5 31.8 1.0 O D:HOH756 2.5 24.9 1.0 O D:HOH946 2.6 41.8 1.0 C D:THR197 3.5 15.1 1.0 CD2 D:LEU224 3.8 25.3 1.0 O D:GLN195 4.2 22.8 1.0 CA D:LYS198 4.4 16.6 1.0 N D:LYS198 4.4 15.4 1.0 O D:HOH875 4.4 32.9 1.0 N D:THR197 4.5 15.7 1.0 CA D:THR197 4.5 15.2 1.0 CD D:LYS198 4.6 43.0 1.0 CB D:THR197 4.8 15.3 1.0 O D:THR194 4.8 19.3 1.0 CG D:LYS198 4.9 32.2 1.0 C D:LYS196 4.9 17.3 1.0 C D:GLN195 4.9 18.0 1.0

T.Prasertanan, D.R.J.Palmer, D.A.R.Sanders. Snapshots Along the Catalytic Path of Kaba, A Plp-Dependent Aminotransferase Required For Kanosamine Biosynthesis in Bacillus Cereus UW85. J.Struct.Biol. 07744 2021.
ISSN: ESSN 1095-8657
PubMed: 33984505
DOI: 10.1016/J.JSB.2021.107744