Cadmium in PDB 6q9n: Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone

The structure of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone, PDB code: 6q9n was solved by S.Martinez-Caballero, M.T.Batuecas, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.55 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.170, 102.876, 187.367, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 28.6

The structure of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Cadmium atom in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone (pdb code 6q9n). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone, PDB code: 6q9n:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd705 b:73.2 occ:1.00 O A:GLY135 2.1 63.3 1.0 OD2 B:ASP209 2.2 79.8 1.0 NE2 A:HIS311 2.3 65.7 1.0 CL A:CL703 2.4 74.8 1.0 OD1 B:ASP209 2.5 73.2 1.0 CG B:ASP209 2.7 77.6 1.0 C A:GLY135 3.2 61.0 1.0 CD2 A:HIS311 3.2 66.1 1.0 CE1 A:HIS311 3.3 65.7 1.0 CA A:GLY135 3.5 59.3 1.0 CB B:ASP209 4.2 78.0 1.0 N A:MET136 4.4 62.6 1.0 CG A:HIS311 4.4 65.4 1.0 NE2 A:GLN137 4.4 66.0 1.0 ND1 A:HIS311 4.4 64.4 1.0 CG A:GLN137 4.5 68.9 1.0 CD A:GLN137 4.7 67.6 1.0 N A:GLY135 4.9 58.1 1.0 CA A:MET136 4.9 66.8 1.0 CB B:GLN207 5.0 92.9 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd706 b:58.6 occ:1.00 OE1 A:GLU145 2.1 57.6 1.0 OE1 B:GLU145 2.2 59.5 1.0 O B:HOH807 2.3 45.6 1.0 ND1 A:HIS143 2.3 65.7 1.0 CL A:CL704 2.4 50.9 1.0 OE2 B:GLU145 2.8 50.4 1.0 CD B:GLU145 2.8 58.6 1.0 CD A:GLU145 3.0 64.3 1.0 CG A:HIS143 3.3 63.6 1.0 CE1 A:HIS143 3.3 65.8 1.0 CB A:HIS143 3.5 61.5 1.0 CG A:GLU145 3.7 66.3 1.0 CD B:CD703 3.9 59.0 1.0 OE2 A:GLU145 4.0 64.5 1.0 OD1 A:ASN307 4.0 89.0 1.0 ND1 B:HIS143 4.2 62.0 1.0 CG B:GLU145 4.3 59.1 1.0 CG2 A:VAL302 4.4 73.1 1.0 CD2 A:HIS143 4.4 64.5 1.0 NE2 A:HIS143 4.5 63.9 1.0 CE1 B:HIS143 4.7 62.7 1.0 OG1 A:THR300 4.7 61.9 1.0 CG B:HIS143 4.8 58.3 1.0 CA A:HIS143 4.9 62.3 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd703 b:59.0 occ:1.00 OE2 B:GLU145 1.8 50.4 1.0 ND1 B:HIS143 2.2 62.0 1.0 OE2 A:GLU145 2.3 64.5 1.0 CL B:CL702 2.5 51.0 1.0 OE1 A:GLU145 2.7 57.6 1.0 CD A:GLU145 2.8 64.3 1.0 CD B:GLU145 2.9 58.6 1.0 CE1 B:HIS143 3.1 62.7 1.0 CG B:HIS143 3.2 58.3 1.0 CB B:HIS143 3.6 54.1 1.0 CG B:GLU145 3.7 59.1 1.0 OE1 B:GLU145 3.9 59.5 1.0 CD A:CD706 3.9 58.6 1.0 NE2 B:HIS143 4.2 62.6 1.0 CD2 B:HIS143 4.3 60.7 1.0 CG2 B:VAL302 4.3 56.2 1.0 CG A:GLU145 4.4 66.3 1.0 ND1 A:HIS143 4.4 65.7 1.0 O A:ILE144 4.8 68.7 1.0 CG A:HIS143 4.8 63.6 1.0 OG1 B:THR300 4.8 55.0 1.0 CE1 A:HIS143 4.9 65.8 1.0 OD1 B:ASN307 4.9 85.3 1.0 CB A:HIS143 5.0 61.5 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of PBP2A From Mrsa in Complex with Piperacillin and Quinazolinone within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd704 b:60.5 occ:1.00 OD2 A:ASP209 2.2 51.2 1.0 OD1 A:ASP209 2.2 60.0 1.0 O B:GLY135 2.3 50.5 1.0 NE2 B:HIS311 2.3 49.8 1.0 CL B:CL701 2.4 54.1 1.0 CG A:ASP209 2.5 57.1 1.0 CD2 B:HIS311 3.2 49.4 1.0 CE1 B:HIS311 3.3 48.4 1.0 NE2 B:GLN137 3.3 65.6 1.0 C B:GLY135 3.3 51.9 1.0 CA B:GLY135 3.7 50.0 1.0 CB A:ASP209 4.0 59.0 1.0 CD B:GLN137 4.2 64.6 1.0 ND1 B:HIS311 4.4 45.5 1.0 CG B:HIS311 4.4 48.0 1.0 N B:MET136 4.5 52.9 1.0 CG B:GLN137 4.5 61.3 1.0 CA A:ASP209 4.9 62.3 1.0 CB A:GLN207 5.0 69.7 1.0

J.Janardhanan, R.Bouley, S.Martinez-Caballero, Z.Peng, M.Batuecas-Mordillo, J.E.Meisel, D.Ding, V.A.Schroeder, W.R.Wolter, K.V.Mahasenan, J.A.Hermoso, S.Mobashery, M.Chang. The Quinazolinone Allosteric Inhibitor of Pbp 2A Synergizes with Piperacillin and Tazobactam Against Methicillin-Resistant Staphylococcus Aureus. Antimicrob.Agents Chemother. V. 63 2019.
ISSN: ESSN 1098-6596
PubMed: 30858202
DOI: 10.1128/AAC.02637-18