Cadmium in PDB 5m19: Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand

The structure of Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand, PDB code: 5m19 was solved by R.Molina, 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)	46.42 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.499, 102.190, 185.682, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 24.7

The binding sites of Cadmium atom in the Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand (pdb code 5m19). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand, PDB code: 5m19:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand


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 the Presence of Oxacillin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd701 b:31.6 occ:1.00 O A:HOH998 2.3 27.3 1.0 ND1 A:HIS143 2.4 23.7 1.0 OE2 A:GLU145 2.5 33.9 1.0 OE1 B:GLU145 2.5 30.4 1.0 O A:HOH1078 2.6 21.3 1.0 OE2 B:GLU145 2.6 32.8 1.0 CD B:GLU145 2.9 36.2 1.0 CD A:GLU145 3.2 36.2 1.0 CG A:HIS143 3.3 27.8 1.0 CE1 A:HIS143 3.4 29.1 1.0 CB A:HIS143 3.6 25.4 1.0 CD A:CD704 3.7 32.1 1.0 CG A:GLU145 3.8 30.5 1.0 OE1 A:GLU145 4.0 26.8 1.0 O A:HOH1069 4.2 52.2 1.0 CG2 A:VAL302 4.3 31.7 1.0 ND1 B:HIS143 4.4 23.4 1.0 OD1 A:ASN307 4.4 33.1 1.0 CG B:GLU145 4.4 34.4 1.0 NE2 A:HIS143 4.5 25.2 1.0 CD2 A:HIS143 4.5 25.9 1.0 OG1 A:THR300 4.7 29.7 1.0 O B:ILE144 4.7 27.8 1.0 CG B:HIS143 4.8 30.7 1.0 CE1 B:HIS143 4.9 31.9 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand


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 the Presence of Oxacillin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd702 b:40.0 occ:1.00 NE2 A:HIS311 2.4 32.4 1.0 O A:HOH876 2.5 32.1 1.0 O A:HOH1101 2.5 26.1 1.0 OD1 B:ASP209 2.5 32.5 1.0 O A:GLY135 2.6 33.2 1.0 OD2 B:ASP209 2.6 37.3 1.0 CG B:ASP209 2.9 36.0 1.0 CD2 A:HIS311 3.3 33.6 1.0 CE1 A:HIS311 3.4 34.8 1.0 C A:GLY135 3.5 37.8 1.0 CA A:GLY135 3.7 38.8 1.0 O B:HOH837 4.1 36.8 1.0 NE2 A:GLN137 4.2 52.8 1.0 O B:HOH1044 4.3 49.1 1.0 CG A:GLN137 4.3 50.6 1.0 CB B:ASP209 4.4 39.1 1.0 CG A:HIS311 4.5 36.2 1.0 ND1 A:HIS311 4.5 36.2 1.0 CD A:GLN137 4.7 51.8 1.0 N A:MET136 4.7 38.6 1.0 CB B:GLN207 4.8 44.0 1.0 CG B:GLN207 5.0 47.0 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand


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 the Presence of Oxacillin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd704 b:32.1 occ:1.00 O B:HOH1024 2.2 24.3 1.0 OE2 B:GLU145 2.3 32.8 1.0 ND1 B:HIS143 2.4 23.4 1.0 O B:HOH1031 2.5 20.9 1.0 OE1 A:GLU145 2.5 26.8 1.0 OE2 A:GLU145 2.6 33.9 1.0 CD A:GLU145 2.9 36.2 1.0 CD B:GLU145 3.1 36.2 1.0 CG B:HIS143 3.4 30.7 1.0 CE1 B:HIS143 3.4 31.9 1.0 CB B:HIS143 3.6 27.4 1.0 CD A:CD701 3.7 31.6 1.0 CG B:GLU145 3.8 34.4 1.0 OE1 B:GLU145 3.9 30.4 1.0 O B:HOH984 4.2 43.4 1.0 CG2 B:VAL302 4.3 31.5 1.0 ND1 A:HIS143 4.4 23.7 1.0 CG A:GLU145 4.4 30.5 1.0 NE2 B:HIS143 4.5 27.9 1.0 CD2 B:HIS143 4.5 27.8 1.0 OD1 B:ASN307 4.6 32.7 1.0 OG1 B:THR300 4.6 36.3 1.0 CG A:HIS143 4.8 27.8 1.0 O A:ILE144 4.9 32.4 1.0 CE1 A:HIS143 4.9 29.1 1.0 O B:HOH855 4.9 45.3 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand


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 the Presence of Oxacillin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd705 b:34.4 occ:1.00 NE2 B:HIS311 2.4 27.9 1.0 O B:HOH1071 2.5 25.2 1.0 OD1 A:ASP209 2.5 30.0 1.0 O B:GLY135 2.5 29.9 1.0 O B:HOH810 2.5 38.9 1.0 OD2 A:ASP209 2.5 38.6 1.0 CG A:ASP209 2.9 38.2 1.0 CD2 B:HIS311 3.3 28.6 1.0 CE1 B:HIS311 3.4 34.3 1.0 C B:GLY135 3.5 30.2 1.0 CA B:GLY135 3.7 31.8 1.0 NE2 B:GLN137 3.9 46.5 1.0 CG B:GLN137 4.0 49.8 1.0 O A:HOH842 4.1 36.4 1.0 CD B:GLN137 4.3 51.0 1.0 CB A:ASP209 4.4 38.0 1.0 CG B:HIS311 4.5 30.6 1.0 ND1 B:HIS311 4.5 29.8 1.0 N B:MET136 4.7 26.9 1.0 CB A:GLN207 4.9 35.8 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd701 b:0.3 occ:1.00 ND1 B:HIS583 2.7 57.5 1.0 OD1 B:ASP573 2.7 58.6 1.0 O B:HOH1076 2.9 51.0 1.0 OD2 B:ASP573 2.9 76.5 1.0 CG B:ASP573 3.1 63.5 1.0 CE1 B:HIS583 3.6 51.3 1.0 CG B:HIS583 3.6 54.7 1.0 CB B:HIS583 3.8 56.1 1.0 NZ B:LYS456 3.8 74.8 1.0 CE B:LYS456 4.2 72.4 1.0 CG B:GLN577 4.3 60.4 1.0 CB B:ASP573 4.6 54.6 1.0 NE2 B:GLN577 4.6 64.3 1.0 O B:HOH817 4.7 39.1 1.0 CA B:HIS583 4.7 58.2 1.0 CD B:GLN577 4.7 61.8 1.0 NE2 B:HIS583 4.7 55.8 1.0 CD2 B:HIS583 4.8 56.2 1.0 O B:HOH1028 5.0 62.3 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of PBP2A From Mrsa in the Presence of Oxacillin Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd702 b:0.3 occ:1.00 O B:HOH1102 2.7 67.8 1.0 O B:HOH1096 2.8 53.2 1.0 O B:HOH1094 2.8 60.5 1.0 OE1 B:GLU447 3.1 94.9 1.0 OE2 B:GLU447 3.5 95.7 1.0 CD B:GLU447 3.7 91.7 1.0 O B:HOH1009 4.5 59.7 1.0

K.V.Mahasenan, R.Molina, R.Bouley, M.T.Batuecas, J.F.Fisher, J.A.Hermoso, M.Chang, S.Mobashery. Conformational Dynamics in Penicillin-Binding Protein 2A of Methicillin-Resistant Staphylococcus Aureus, Allosteric Communication Network and Enablement of Catalysis. J. Am. Chem. Soc. V. 139 2102 2017.
ISSN: ESSN 1520-5126
PubMed: 28099001
DOI: 10.1021/JACS.6B12565