Sodium in PDB 2y2h: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA2)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA2):
2.4.1.129;

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA2), PDB code: 2y2h 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)	48.00 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.992, 100.484, 143.969, 90.00, 90.00, 90.00
R / Rfree (%)	21.168 / 25.398

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA2) also contains other interesting chemical elements:

Chlorine

(Cl)

20 atoms

The binding sites of Sodium atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA2) (pdb code 2y2h). 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 (ZA2), PDB code: 2y2h:
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 (ZA2)


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 (ZA2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1300 b:31.0 occ:1.00 O A:HOH2047 3.0 57.9 1.0 OG1 A:THR652 3.1 23.2 1.0 O2 A:ZA21000 3.1 49.9 1.0 OG1 A:THR654 3.2 43.5 1.0 O A:HOH2110 3.6 34.1 1.0 CB A:THR652 3.6 25.6 1.0 O A:THR652 3.7 26.7 1.0 C A:THR652 3.7 31.0 1.0 N A:GLY653 3.7 30.8 1.0 CA A:GLY653 3.7 31.8 1.0 C A:GLY653 3.8 30.2 1.0 N A:THR654 3.9 33.1 1.0 CB A:THR654 3.9 35.5 1.0 O1 A:ZA21000 3.9 42.2 1.0 OG A:SER516 4.0 24.4 1.0 B A:ZA21000 4.1 42.2 1.0 CB A:SER516 4.3 26.9 1.0 CB A:THR629 4.3 26.0 1.0 O A:GLY653 4.4 32.6 1.0 CA A:THR652 4.4 31.6 1.0 CG2 A:THR629 4.4 21.1 1.0 O A:HOH2121 4.5 33.3 1.0 NZ A:LYS651 4.5 32.2 1.0 CB A:SER460 4.5 28.3 1.0 O A:HOH2122 4.5 37.6 1.0 CA A:THR654 4.5 32.6 1.0 OG1 A:THR629 4.8 23.8 1.0 OH A:TYR498 4.8 56.1 1.0 OG A:SER460 4.8 37.0 1.0 CG2 A:THR652 4.9 23.1 1.0

Sodium binding site 2 out of 2 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (ZA2)


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 (ZA2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1300 b:26.9 occ:1.00 O B:HOH2068 2.9 37.5 1.0 O2 B:ZA21000 3.0 45.1 1.0 OG1 B:THR652 3.0 22.1 1.0 OG1 B:THR654 3.4 39.1 1.0 O B:THR652 3.6 25.1 1.0 O B:HOH2141 3.6 37.4 1.0 N B:THR654 3.6 27.0 1.0 CB B:THR652 3.7 26.8 1.0 C B:THR652 3.7 27.4 1.0 C B:GLY653 3.7 28.3 1.0 CA B:GLY653 3.7 22.6 1.0 N B:GLY653 3.8 20.7 1.0 O1 B:ZA21000 3.9 31.6 1.0 CB B:THR654 4.0 29.3 1.0 B B:ZA21000 4.0 47.5 1.0 OG B:SER516 4.1 28.9 1.0 CB B:SER516 4.3 28.9 1.0 NZ B:LYS651 4.3 23.5 1.0 O B:HOH2152 4.3 35.5 1.0 CA B:THR652 4.4 29.1 1.0 O B:GLY653 4.4 23.1 1.0 CB B:THR629 4.4 24.2 1.0 CA B:THR654 4.4 32.8 1.0 CB B:SER460 4.6 26.8 1.0 O B:HOH2153 4.6 30.5 1.0 CG2 B:THR629 4.7 20.1 1.0 OG B:SER460 4.7 36.6 1.0 OG1 B:THR629 4.7 23.5 1.0 OH B:TYR498 4.9 64.5 1.0 CG2 B:THR652 5.0 24.6 1.0 O B:HOH2151 5.0 29.1 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