Sodium in PDB 7kz5: Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Plp External Aldimine Adduct with Kanosamine-6-Phosphate

All present enzymatic activity of Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Plp External Aldimine Adduct with Kanosamine-6-Phosphate:
2.6.1.1;

The structure of Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Plp External Aldimine Adduct with Kanosamine-6-Phosphate, PDB code: 7kz5 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)	46.75 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.67, 66.6, 111.78, 77.35, 81.06, 87.91
R / Rfree (%)	17.5 / 21.5

The binding sites of Sodium atom in the Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Plp External Aldimine Adduct with Kanosamine-6-Phosphate (pdb code 7kz5). 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 Plp External Aldimine Adduct with Kanosamine-6-Phosphate, PDB code: 7kz5:
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 Plp External Aldimine Adduct with Kanosamine-6-Phosphate


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 Plp External Aldimine Adduct with Kanosamine-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:46.4 occ:1.00 OD2 B:ASP134 2.4 30.8 1.0 O A:HOH682 2.5 36.6 1.0 O A:HOH826 2.6 39.5 1.0 O B:HOH628 2.7 33.4 1.0 OD1 A:ASP134 2.8 33.3 1.0 OD2 A:ASP134 2.8 30.2 1.0 OD1 B:ASP134 3.0 30.4 1.0 CG A:ASP134 3.1 22.7 1.0 CG B:ASP134 3.1 27.0 1.0 O A:HOH743 3.7 22.0 1.0 OG B:SER300 3.9 21.4 1.0 O A:HOH784 4.0 25.6 1.0 OG A:SER130 4.1 17.9 1.0 OG B:SER130 4.1 18.4 1.0 OG A:SER300 4.2 18.1 1.0 CB A:ASP134 4.5 12.9 1.0 O B:ASN299 4.6 14.3 1.0 O A:ASN299 4.6 15.5 1.0 CB B:ASP134 4.6 19.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Plp External Aldimine Adduct with Kanosamine-6-Phosphate


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 Plp External Aldimine Adduct with Kanosamine-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:45.5 occ:1.00 O C:HOH644 2.4 32.7 1.0 OD2 C:ASP134 2.5 28.7 1.0 O C:HOH653 2.6 36.8 1.0 O D:HOH615 2.6 30.0 1.0 OD1 D:ASP134 2.7 37.2 1.0 OD2 D:ASP134 2.9 33.1 1.0 OD1 C:ASP134 3.1 28.0 1.0 CG D:ASP134 3.1 29.6 1.0 CG C:ASP134 3.2 25.4 1.0 OG D:SER130 3.9 19.0 1.0 OG D:SER300 3.9 22.2 1.0 O C:HOH782 3.9 22.2 1.0 O D:HOH746 4.0 23.3 1.0 OG C:SER130 4.1 17.8 1.0 OG C:SER300 4.3 19.7 1.0 CB D:ASP134 4.5 15.4 1.0 O D:ASN299 4.5 14.5 1.0 O C:ASN299 4.5 13.8 1.0 CB C:ASP134 4.7 15.3 1.0 CB D:SER130 4.9 16.5 1.0 O D:HOH699 4.9 26.4 1.0 O C:HOH861 5.0 25.6 1.0 CB D:SER300 5.0 17.2 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