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Sodium in PDB 2y2p: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z10)

Enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z10)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z10):
2.4.1.129;

Protein crystallography data

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z10), PDB code: 2y2p 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) 44.39 / 1.62
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.670, 149.506, 98.688, 90.00, 90.00, 90.00
R / Rfree (%) 21.676 / 25.051

Other elements in 2y2p:

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z10) also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 20 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z10) (pdb code 2y2p). 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 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z10), PDB code: 2y2p:

Sodium binding site 1 out of 1 in 2y2p

Go back to Sodium Binding Sites List in 2y2p
Sodium binding site 1 out of 1 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (Z10)


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 (Z10) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1300

b:35.0
occ:1.00
 O2 A:Z101000 3.1 53.5 1.0
OG1 A:THR652 3.1 26.4 1.0
C18 A:Z101000 3.2 72.4 1.0
OG1 A:THR654 3.4 50.3 1.0
O A:HOH2198 3.5 38.1 1.0
O A:THR652 3.7 21.9 1.0
CB A:THR652 3.7 26.2 1.0
CA A:GLY653 3.7 19.8 1.0
C A:THR652 3.7 24.2 1.0
N A:GLY653 3.7 26.1 1.0
N A:THR654 3.8 26.9 1.0
C A:GLY653 3.8 27.6 1.0
O1 A:Z101000 3.8 32.8 1.0
C17 A:Z101000 3.8 74.4 1.0
B A:Z101000 4.1 52.3 1.0
OG A:SER516 4.1 27.7 1.0
CB A:THR654 4.1 41.9 1.0
C19 A:Z101000 4.2 82.3 1.0
CB A:SER516 4.3 26.0 1.0
CA A:THR652 4.4 20.7 1.0
CB A:THR629 4.4 21.3 1.0
O A:GLY653 4.5 23.6 1.0
CB A:SER460 4.6 23.9 1.0
NZ A:LYS651 4.6 24.3 1.0
CA A:THR654 4.6 32.0 1.0
O A:HOH2209 4.7 35.9 1.0
CG2 A:THR629 4.7 23.7 1.0
OG A:SER460 4.8 30.3 1.0
OG1 A:THR629 4.8 22.5 1.0
CG2 A:THR652 5.0 26.8 1.0

Reference:

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
Page generated: Sun Aug 17 12:22:10 2025

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