Sodium in PDB 1j9m: K38H Mutant of Streptomyces K15 Dd-Transpeptidase

All present enzymatic activity of K38H Mutant of Streptomyces K15 Dd-Transpeptidase:
3.4.16.4;

The structure of K38H Mutant of Streptomyces K15 Dd-Transpeptidase, PDB code: 1j9m was solved by E.Fonze, N.Rhazi, M.Nguyen-Disteche, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.596, 53.638, 104.690, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.6

The structure of K38H Mutant of Streptomyces K15 Dd-Transpeptidase also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the K38H Mutant of Streptomyces K15 Dd-Transpeptidase (pdb code 1j9m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the K38H Mutant of Streptomyces K15 Dd-Transpeptidase, PDB code: 1j9m:

Sodium binding site 1 out of 1 in the K38H Mutant of Streptomyces K15 Dd-Transpeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of K38H Mutant of Streptomyces K15 Dd-Transpeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na600 b:24.5 occ:1.00 CL A:CL601 2.8 33.2 1.0 OG1 A:THR214 2.9 10.3 1.0 OG A:SER96 3.1 10.2 1.0 O A:HOH332 3.1 21.9 1.0 OG A:SER35 3.4 20.2 1.0 NZ A:LYS213 3.5 8.7 1.0 CB A:SER96 3.5 10.6 1.0 C A:THR214 3.6 11.4 1.0 N A:GLY215 3.6 10.5 1.0 O A:THR214 3.7 12.5 1.0 CA A:GLY215 3.7 10.9 1.0 CB A:SER35 3.8 18.4 1.0 CB A:THR214 3.8 11.4 1.0 C A:GLY215 4.2 10.4 1.0 OG1 A:THR199 4.3 11.4 1.0 CA A:THR214 4.4 10.7 1.0 N A:SER216 4.4 13.3 1.0 O A:HOH303 4.6 8.8 1.0 OG A:SER216 4.7 18.7 1.0 CE A:LYS213 4.9 9.7 1.0 CB A:THR199 4.9 11.4 1.0 O A:GLY215 5.0 11.4 1.0 CA A:SER96 5.0 10.7 1.0

N.Rhazi, P.Charlier, D.Dehareng, D.Engher, M.Vermeire, J.M.Frere, M.Nguyen-Disteche, E.Fonze. Catalytic Mechanism of the Streptomyces K15 Dd-Transpeptidase/Penicillin-Binding Protein Probed By Site-Directed Mutagenesis and Structural Analysis. Biochemistry V. 42 2895 2003.
ISSN: ISSN 0006-2960
PubMed: 12627955
DOI: 10.1021/BI027256X