Sodium in PDB 8f3t: Crystal Structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium

The structure of Crystal Structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium, PDB code: 8f3t was solved by E.D.D'andrea, M.S.Choy, M.V.Schoenle, R.Page, W.Peti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.78 / 2.56
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	192.777, 192.777, 155.427, 90, 90, 120
R / Rfree (%)	19.2 / 21.4

The binding sites of Sodium atom in the Crystal Structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium (pdb code 8f3t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium, PDB code: 8f3t:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium


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 Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na720 b:66.1 occ:1.00 O A:HOH888 2.6 51.3 1.0 O A:HOH904 2.8 55.6 1.0 OE1 A:GLU542 2.8 53.9 1.0 O A:HOH1047 2.9 51.4 1.0 O A:HOH813 3.1 60.4 1.0 OE2 A:GLU542 3.2 53.2 1.0 CD A:GLU542 3.4 64.1 1.0 CD2 A:LEU532 3.8 55.5 1.0 CB A:ASN523 4.0 51.1 1.0 N A:GLU524 4.3 51.7 1.0 N A:ASN523 4.4 45.5 1.0 O A:PHE527 4.4 51.9 1.0 O A:SER526 4.4 56.6 1.0 CG A:GLU524 4.5 55.1 1.0 ND2 A:ASN523 4.6 49.2 1.0 CG A:ASN523 4.6 47.0 1.0 CA A:ASN523 4.7 46.3 1.0 CB A:GLU524 4.7 44.6 1.0 CB A:SER522 4.8 52.8 1.0 CG A:GLU542 4.8 37.1 1.0 O A:HOH840 4.9 46.1 1.0 C A:ASN523 4.9 50.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium


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 Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na721 b:63.6 occ:1.00 O A:HOH973 2.5 50.9 1.0 CB A:ASN517 3.4 57.5 1.0 O A:HOH868 3.5 52.4 1.0 ND2 A:ASN517 3.7 60.4 1.0 O A:HOH847 3.8 50.6 1.0 CG A:ASN517 4.1 55.3 1.0 CA A:GLY417 4.2 46.8 1.0 N A:GLY417 4.3 49.0 1.0 CA A:ASN517 4.6 46.8 1.0 CD1 A:LEU544 4.6 45.1 1.0 O A:ASN517 4.7 51.0 1.0 CB A:LEU544 4.7 47.3 1.0 O A:PRO518 4.7 54.0 1.0 C A:ASN517 4.8 57.6 1.0 N A:ASN517 4.9 46.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Penicillin Binding Protein 5 (PBP5) T485M T499I V629E Variant Apo Form From Enterococcus Faecium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na722 b:66.0 occ:1.00 OG1 A:THR618 2.7 52.5 1.0 OG A:SER480 3.0 65.4 1.0 N A:GLY619 3.4 43.3 1.0 CB A:SER480 3.5 48.1 1.0 CA A:GLY619 3.6 42.1 1.0 C A:THR618 3.6 48.5 1.0 O A:HOH845 3.6 62.3 1.0 O A:HOH1007 3.7 77.5 1.0 CB A:THR618 3.7 52.7 1.0 O A:THR618 3.8 51.1 1.0 O A:HOH972 3.9 65.9 1.0 C A:GLY619 3.9 44.1 1.0 OG A:SER422 4.0 52.0 1.0 N A:THR620 4.3 40.7 1.0 CA A:THR618 4.3 41.2 1.0 CG2 A:THR620 4.4 48.2 1.0 O A:GLY619 4.5 44.9 1.0 O A:HOH986 4.6 70.9 1.0 CG2 A:THR603 4.6 45.4 1.0 NZ A:LYS617 4.6 43.9 1.0 OG1 A:THR603 4.7 55.5 1.0 CB A:THR603 4.7 43.3 1.0 O A:HOH858 4.7 48.9 1.0 OG1 A:THR620 4.9 73.4 1.0

Y.Hunashal, G.S.Kumar, M.S.Choy, A.Da Silva Santiago, E.D.D'andrea, M.V.Schoenle, M.Arthur, L.B.Rice, R.Page, W.Peti. The Molecular Basis For Resistance of E. Faecium PBP5 to Beta-Lactam Antibiotics Nat Commun 2023.
ISSN: ESSN 2041-1723