Sodium in PDB 8c4d: N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome

The structure of N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome, PDB code: 8c4d was solved by A.C.Papageorgiou, G.E.Premetis, N.E.Labrou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.73 / 1.97
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.713, 74.713, 133.272, 90, 90, 90
R / Rfree (%)	17.3 / 19.5

The structure of N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome (pdb code 8c4d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome, PDB code: 8c4d:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:45.2 occ:1.00 CE A:MET45 2.7 33.3 1.0 O A:GLY53 2.8 26.7 1.0 O A:HOH534 3.0 50.2 1.0 O A:GLN49 3.3 25.3 1.0 N A:GLY53 3.4 27.1 1.0 CB A:ALA52 3.5 29.4 1.0 O A:HOH581 3.6 50.1 1.0 SD A:MET45 3.7 40.5 1.0 C A:ALA52 3.7 27.4 1.0 C A:GLY53 3.8 24.6 1.0 CA A:ALA52 4.0 27.1 1.0 O A:LEU50 4.1 27.2 1.0 CA A:LEU50 4.1 26.6 1.0 CA A:GLY53 4.1 23.7 1.0 N A:ALA52 4.1 24.1 1.0 O A:HOH582 4.2 38.3 1.0 C A:GLN49 4.2 28.5 1.0 C A:LEU50 4.2 26.4 1.0 O A:ALA52 4.4 28.4 1.0 NH1 A:ARG41 4.6 42.3 1.0 CD2 A:LEU42 4.6 24.3 1.0 N A:LEU50 4.6 24.8 1.0 NH2 A:ARG41 4.7 45.9 1.0 N A:PHE54 5.0 22.5 1.0 CD2 A:LEU50 5.0 27.4 1.0

Sodium binding site 2 out of 3 in the N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:62.7 occ:1.00 O A:HOH581 3.1 50.1 1.0 OH A:TYR58 3.1 29.5 1.0 OE1 A:GLU90 3.3 37.2 1.0 O A:HOH599 3.3 60.1 1.0 NA A:NA409 3.5 73.2 1.0 CD A:GLU90 3.9 34.7 1.0 CZ A:TYR58 4.0 26.8 1.0 CE2 A:TYR58 4.1 23.9 1.0 CA A:PHE54 4.3 22.1 1.0 CG A:GLU90 4.3 28.0 1.0 O A:GLY53 4.6 26.7 1.0 N A:PHE54 4.6 22.5 1.0 C A:GLY53 4.7 24.6 1.0 N A:ALA55 4.7 21.5 1.0 CL A:CL403 4.7 60.4 1.0 C A:PHE54 4.7 22.6 1.0 OE2 A:GLU90 4.8 31.8 1.0

Sodium binding site 3 out of 3 in the N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of N-Acetylmuramoyl-L-Alanine Amidase From Enterococcus Faecium Prophage Genome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:73.2 occ:1.00 NA A:NA408 3.5 62.7 1.0 O A:THR29 3.7 30.9 1.0 CB A:THR29 4.2 28.6 1.0 CA A:THR29 4.3 30.2 1.0 OE2 A:GLU38 4.3 48.3 1.0 OE1 A:GLU38 4.4 45.2 1.0 O A:HOH581 4.4 50.1 1.0 C A:THR29 4.4 32.0 1.0 CG2 A:THR31 4.5 34.5 1.0 CG2 A:THR29 4.7 27.8 1.0 CD A:GLU38 4.7 41.1 1.0 NH1 A:ARG41 4.8 42.3 1.0 O A:HOH513 4.8 38.2 1.0 OE1 A:GLU90 5.0 37.2 1.0

G.E.Premetis, A.Stathi, A.C.Papageorgiou, N.E.Labrou. Structural and Functional Features of A Broad-Spectrum Prophage-Encoded Enzybiotic From Enterococcus Faecium. Sci Rep V. 13 7450 2023.
ISSN: ESSN 2045-2322
PubMed: 37156923
DOI: 10.1038/S41598-023-34309-2