Sodium in PDB 2y2q: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06):
2.4.1.129;

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06), PDB code: 2y2q 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)	45.64 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.152, 101.806, 145.370, 90.00, 90.00, 90.00
R / Rfree (%)	20.286 / 26.193

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06) also contains other interesting chemical elements:

Chlorine

(Cl)

25 atoms

The binding sites of Sodium atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06) (pdb code 2y2q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06), PDB code: 2y2q:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06)


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 (Z06) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1300 b:40.0 occ:1.00 OG1 A:THR652 2.9 41.5 1.0 OG1 A:THR654 3.1 49.1 1.0 O16 A:Z061000 3.2 53.8 1.0 O A:HOH2173 3.5 38.8 1.0 CB A:THR652 3.5 32.8 1.0 C A:THR652 3.6 31.9 1.0 N A:THR654 3.7 46.2 1.0 CA A:GLY653 3.7 32.9 1.0 O A:THR652 3.7 41.3 1.0 C A:GLY653 3.7 33.7 1.0 O A:HOH2171 3.7 58.6 1.0 N A:GLY653 3.7 29.9 1.0 O15 A:Z061000 3.8 51.5 1.0 OG A:SER516 4.0 42.5 1.0 CB A:THR654 4.0 52.1 1.0 B14 A:Z061000 4.0 73.7 1.0 CA A:THR652 4.2 39.5 1.0 CB A:SER516 4.3 43.2 1.0 O A:GLY653 4.3 44.4 1.0 NZ A:LYS651 4.4 33.5 1.0 CA A:THR654 4.5 39.4 1.0 CB A:THR629 4.5 38.8 1.0 CB A:SER460 4.5 24.7 1.0 O A:HOH2170 4.6 43.2 1.0 OG A:SER460 4.7 51.1 1.0 CG2 A:THR629 4.7 29.7 1.0 CG2 A:THR652 4.8 30.0 1.0 O A:HOH2172 4.8 44.1 1.0 OG1 A:THR629 4.8 35.1 1.0

Sodium binding site 2 out of 3 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06)


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 (Z06) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1300 b:35.7 occ:1.00 O B:HOH2098 2.9 53.2 1.0 O16 B:Z061000 3.2 53.4 1.0 OG1 B:THR652 3.3 34.6 1.0 OG1 B:THR654 3.4 48.4 1.0 O B:HOH2179 3.7 39.2 1.0 CB B:THR652 3.8 30.6 1.0 C B:THR652 3.8 37.3 1.0 O15 B:Z061000 3.8 46.9 1.0 O B:THR652 3.8 32.3 1.0 N B:THR654 3.8 43.1 1.0 C B:GLY653 3.9 44.5 1.0 CA B:GLY653 3.9 35.4 1.0 N B:GLY653 3.9 30.5 1.0 B14 B:Z061000 4.0 64.0 1.0 OG B:SER516 4.1 43.5 1.0 CB B:THR654 4.2 48.4 1.0 CB B:SER516 4.2 32.7 1.0 CB B:THR629 4.3 29.1 1.0 CG2 B:THR629 4.4 21.7 1.0 CA B:THR652 4.4 34.1 1.0 CB B:SER460 4.5 29.7 1.0 NZ B:LYS651 4.5 28.2 1.0 O B:GLY653 4.5 37.7 1.0 OG B:SER460 4.6 45.0 1.0 O B:HOH2189 4.6 43.8 1.0 OG1 B:THR629 4.6 41.1 1.0 CA B:THR654 4.6 45.9 1.0 O B:HOH2190 4.7 50.0 1.0 O B:HOH2188 5.0 35.9 1.0

Sodium binding site 3 out of 3 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z06) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1301 b:58.8 occ:1.00 OD2 B:ASP414 2.8 47.9 1.0 CB B:ASP414 3.4 41.0 1.0 CG B:ASP414 3.5 48.5 1.0 CB B:TYR411 3.8 36.5 1.0 O B:TYR411 4.2 47.9 1.0 CA B:TYR411 4.2 43.7 1.0 C B:TYR411 4.7 38.6 1.0 OD1 B:ASP414 4.7 42.7 1.0 CG B:TYR411 4.9 46.4 1.0 CA B:ASP414 4.9 44.3 1.0 CD2 B:TYR411 4.9 33.8 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