Sodium in PDB 2y2g: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01):
2.4.1.129;

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01), PDB code: 2y2g was solved by C.Contreras-Martel, A.Amoroso, E.C.Woon, A.Zervosen, S.Inglis, A.Martins, O.Verlaine, A.Rydzik, V.Job, A.Luxen, B.Joris, C.J.Schofield, A.Dessen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.74 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.526, 97.526, 149.356, 90.00, 90.00, 90.00
R / Rfree (%)	22.221 / 25.97

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) also contains other interesting chemical elements:

Chlorine

(Cl)

30 atoms

The binding sites of Sodium atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) (pdb code 2y2g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01), PDB code: 2y2g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


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 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1300 b:40.1 occ:1.00 O2 A:A011000 2.6 42.0 1.0 OG1 A:THR652 3.1 33.3 1.0 OG1 A:THR654 3.3 40.0 1.0 O A:HOH2227 3.3 42.2 1.0 O9 A:A011000 3.6 0.7 1.0 CB A:THR652 3.6 33.0 1.0 N A:GLY653 3.7 26.6 1.0 CA A:GLY653 3.7 26.8 1.0 C A:GLY653 3.8 31.0 1.0 C A:THR652 3.8 28.7 1.0 N A:THR654 3.8 33.2 1.0 C10 A:A011000 3.8 58.5 1.0 B A:A011000 3.9 53.0 1.0 O A:THR652 4.0 31.1 1.0 CB A:THR654 4.1 38.4 1.0 O1 A:A011000 4.1 35.2 1.0 OG A:SER516 4.3 33.0 1.0 CB A:THR629 4.3 28.1 1.0 N4 A:A011000 4.3 64.7 1.0 O A:GLY653 4.3 37.7 1.0 O A:HOH2243 4.3 45.0 1.0 O A:HOH2242 4.4 47.2 1.0 CB A:SER516 4.4 30.5 1.0 CA A:THR652 4.4 25.0 1.0 C8 A:A011000 4.5 84.0 1.0 CG2 A:THR629 4.6 27.9 1.0 CA A:THR654 4.6 34.4 1.0 OG1 A:THR629 4.6 25.4 1.0 NZ A:LYS651 4.7 35.3 1.0 C3 A:A011000 4.7 39.5 1.0 CB A:SER460 4.8 30.7 1.0 CG2 A:THR652 4.9 30.5 1.0

Sodium binding site 2 out of 2 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1300 b:37.9 occ:1.00 O2 B:A011000 2.4 43.6 1.0 OG1 B:THR654 3.0 37.5 1.0 O B:HOH2216 3.2 41.6 1.0 OG1 B:THR652 3.2 33.1 1.0 CB B:THR652 3.7 30.6 1.0 N B:GLY653 3.7 26.1 1.0 C B:THR652 3.8 27.8 1.0 CA B:GLY653 3.8 28.6 1.0 C B:GLY653 3.8 33.9 1.0 O B:THR652 3.8 27.1 1.0 N B:THR654 3.8 31.9 1.0 B B:A011000 3.8 57.6 1.0 C10 B:A011000 3.9 66.3 1.0 O9 B:A011000 3.9 82.0 1.0 CB B:THR654 4.0 41.1 1.0 O1 B:A011000 4.2 47.1 1.0 O B:HOH2230 4.2 32.5 1.0 CB B:THR629 4.3 31.5 1.0 OG B:SER516 4.3 30.8 1.0 N4 B:A011000 4.3 0.1 1.0 O B:GLY653 4.4 28.7 1.0 CA B:THR652 4.4 26.5 1.0 O B:HOH2231 4.5 55.5 1.0 CB B:SER516 4.5 34.1 1.0 CA B:THR654 4.6 39.5 1.0 CG2 B:THR629 4.6 28.3 1.0 OG1 B:THR629 4.7 28.2 1.0 C3 B:A011000 4.7 52.0 1.0 C8 B:A011000 4.8 70.5 1.0 CB B:SER460 4.8 42.4 1.0 NZ B:LYS651 4.9 25.8 1.0 CG2 B:THR652 4.9 25.0 1.0

C.Contreras-Martel, A.Amoroso, E.C.Woon, A.Zervosen, S.Inglis, A.Martins, O.Verlaine, A.Rydzik, V.Job, A.Luxen, B.Joris, C.J.Schofield, A.Dessen. Structure-Guided Design of Cell Wall Biosynthesis Inhibitors That Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa). Acs Chem.Biol. V. 6 943 2011.
ISSN: ISSN 1554-8929
PubMed: 21732689
DOI: 10.1021/CB2001846