Sodium in PDB 5oj1: Penicillin Binding Protein 2X (PBP2X) From S.Pneumoniae in Complex with Oxacillin and A Tetrasaccharide

The structure of Penicillin Binding Protein 2X (PBP2X) From S.Pneumoniae in Complex with Oxacillin and A Tetrasaccharide, PDB code: 5oj1 was solved by N.Bernardo-Garcia, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.33 / 2.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.839, 100.839, 189.354, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 22.9

The binding sites of Sodium atom in the Penicillin Binding Protein 2X (PBP2X) From S.Pneumoniae in Complex with Oxacillin and A Tetrasaccharide (pdb code 5oj1). 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 Penicillin Binding Protein 2X (PBP2X) From S.Pneumoniae in Complex with Oxacillin and A Tetrasaccharide, PDB code: 5oj1:

Sodium binding site 1 out of 1 in the Penicillin Binding Protein 2X (PBP2X) From S.Pneumoniae in Complex with Oxacillin and A Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Penicillin Binding Protein 2X (PBP2X) From S.Pneumoniae in Complex with Oxacillin and A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:57.9 occ:1.00 OG A:SER548 3.3 54.1 1.0 CB A:LEU546 3.9 43.6 0.3 CB A:LEU546 3.9 38.5 0.7 CB A:SER548 3.9 53.2 1.0 CG A:LEU546 3.9 44.8 0.3 CD2 A:LEU546 3.9 43.8 0.3 CD2 A:LEU546 3.9 43.0 0.7 O A:THR526 4.2 61.5 1.0 OG1 A:THR536 4.3 67.5 1.0 N A:SER548 4.3 49.3 1.0 CG1 A:VAL518 4.3 52.1 1.0 CG A:LEU546 4.6 38.7 0.7 CA A:SER548 4.8 50.5 1.0 N A:LYS547 4.9 40.5 1.0 CA A:LEU546 5.0 42.3 0.3

N.Bernardo-Garcia, K.V.Mahasenan, M.T.Batuecas, M.Lee, D.Hesek, D.Petrackova, L.Doubravova, P.Branny, S.Mobashery, J.A.Hermoso. Allostery, Recognition of Nascent Peptidoglycan, and Cross-Linking of the Cell Wall By the Essential Penicillin-Binding Protein 2X of Streptococcus Pneumoniae. Acs Chem. Biol. V. 13 694 2018.
ISSN: ESSN 1554-8937
PubMed: 29357220
DOI: 10.1021/ACSCHEMBIO.7B00817