Sodium in PDB 8r2y: Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29

All present enzymatic activity of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29:
3.5.2.6;

The structure of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29, PDB code: 8r2y was solved by C.L.Tooke, P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.00 / 1.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.43, 45.85, 116.88, 90, 90, 90
R / Rfree (%)	13.4 / 15.4

The structure of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29 (pdb code 8r2y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29, PDB code: 8r2y:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:16.1 occ:1.00 HG1 A:THR181 1.9 12.0 1.0 HB2 A:PHE160 2.5 11.4 1.0 OD2 A:ASP157 2.7 10.6 1.0 OG1 A:THR181 2.7 10.0 1.0 HA A:MET186 2.8 11.5 0.6 HA A:MET186 2.8 11.7 0.4 HG21 A:THR181 3.1 12.1 1.0 HD2 A:PHE160 3.1 11.9 1.0 HB2 A:MET186 3.2 12.1 0.4 HB2 A:MET186 3.3 13.1 0.6 SD A:MET186 3.4 12.7 0.6 HB1 A:ALA185 3.4 13.7 1.0 CB A:THR181 3.5 10.1 1.0 CA A:MET186 3.5 9.8 0.4 CA A:MET186 3.5 9.6 0.6 HB A:THR181 3.5 12.1 1.0 CB A:PHE160 3.5 9.5 1.0 N A:MET186 3.5 9.7 0.6 N A:MET186 3.5 9.9 0.4 SD A:MET186 3.5 9.9 0.4 HB3 A:ALA185 3.6 13.7 1.0 CG2 A:THR181 3.6 10.1 1.0 CG A:ASP157 3.6 10.1 1.0 HG23 A:THR181 3.7 12.1 1.0 CB A:MET186 3.7 10.1 0.4 C A:ALA185 3.7 10.1 1.0 CB A:MET186 3.8 10.9 0.6 H A:PHE160 3.8 11.5 1.0 H A:MET186 3.8 11.6 0.6 H A:MET186 3.8 11.9 0.4 OD1 A:ASP157 3.8 10.0 1.0 HA A:PHE160 3.8 11.2 1.0 HG1 A:THR189 3.9 14.1 1.0 CD2 A:PHE160 3.9 9.9 1.0 CB A:ALA185 3.9 11.4 1.0 O A:ALA185 3.9 10.1 1.0 HB A:THR189 4.0 13.4 1.0 CA A:PHE160 4.1 9.4 1.0 HB3 A:PHE160 4.1 11.4 1.0 HE2 A:MET186 4.1 13.2 0.4 HE2 A:MET75 4.1 17.8 0.7 HE1 A:MET186 4.1 13.2 0.4 N A:PHE160 4.2 9.6 1.0 CE A:MET186 4.2 11.1 0.4 HE1 A:MET75 4.2 17.8 0.7 CG A:PHE160 4.2 9.1 1.0 CG A:MET186 4.2 11.5 0.6 CG A:MET186 4.3 9.8 0.4 HE3 A:MET186 4.3 14.7 0.6 HB A:THR159 4.4 14.1 1.0 HE3 A:MET75 4.4 17.8 0.7 CE A:MET75 4.4 14.8 0.7 CE A:MET186 4.4 12.3 0.6 CA A:ALA185 4.5 10.4 1.0 HG22 A:THR181 4.5 12.1 1.0 OG1 A:THR189 4.5 11.8 1.0 HE1 A:MET186 4.5 14.7 0.6 H A:SER182 4.6 11.8 1.0 HB3 A:MET186 4.6 12.1 0.4 HB3 A:MET186 4.7 13.1 0.6 CB A:THR189 4.7 11.1 1.0 HB2 A:ALA185 4.8 13.7 1.0 O A:SER182 4.8 10.1 1.0 HG2 A:MET186 4.8 13.8 0.6 HG21 A:THR189 4.8 17.2 1.0 HG2 A:MET186 4.8 11.8 0.4 C A:MET186 4.8 9.4 0.6 C A:MET186 4.9 9.9 0.4 CA A:THR181 4.9 9.3 1.0 HG3 A:MET186 4.9 13.8 0.6 HG3 A:MET186 5.0 11.8 0.4 CB A:ASP157 5.0 9.9 1.0

Sodium binding site 2 out of 3 in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na312 b:15.6 occ:1.00 H A:GLN222 2.1 13.1 0.9 H A:GLN222 2.1 13.5 0.1 HG3 A:GLN222 2.3 16.4 0.9 O A:GLY217 2.7 11.5 1.0 OD2 A:ASP245 2.8 9.9 1.0 HB2 A:GLN222 2.8 15.2 0.1 HE21 A:GLN222 2.8 17.6 0.9 HB A:ILE221 2.9 12.7 1.0 N A:GLN222 2.9 10.9 0.9 N A:GLN222 2.9 11.2 0.1 H A:ILE221 3.0 12.5 1.0 CG A:GLN222 3.1 13.7 0.9 CG A:ASP233 3.3 10.0 1.0 OD2 A:ASP233 3.3 10.0 1.0 N A:ILE221 3.3 10.4 1.0 HB2 A:GLN222 3.3 15.5 0.9 HA3 A:GLY217 3.4 16.0 1.0 HB2 A:SER220 3.4 12.6 1.0 NE2 A:GLN222 3.4 14.7 0.9 HG11 A:VAL231 3.5 18.4 1.0 HB3 A:ASP233 3.5 12.4 1.0 CB A:GLN222 3.5 12.7 0.1 CB A:GLN222 3.6 12.9 0.9 HB3 A:GLN222 3.6 15.2 0.1 OD1 A:ASP233 3.6 11.6 1.0 C A:GLY217 3.6 11.6 1.0 CB A:ILE221 3.7 10.6 1.0 CD A:GLN222 3.7 14.8 0.9 CA A:ILE221 3.7 10.4 1.0 C A:ILE221 3.8 10.6 1.0 CB A:ASP233 3.8 10.3 1.0 CA A:GLN222 3.8 11.3 0.9 CA A:GLN222 3.8 11.9 0.1 CG A:ASP245 3.8 9.5 1.0 HB2 A:ASP233 3.8 12.4 1.0 HE21 A:GLN222 3.9 18.1 0.1 HG2 A:GLN222 3.9 16.4 0.9 CA A:GLY217 3.9 13.4 1.0 H A:SER220 4.0 13.0 1.0 C A:SER220 4.0 10.8 1.0 HE22 A:GLN222 4.1 17.6 0.9 HG22 A:ILE221 4.1 12.5 1.0 HA2 A:GLY217 4.1 16.0 1.0 OD1 A:ASP245 4.2 10.0 1.0 HG12 A:VAL231 4.2 18.4 1.0 HA A:GLN222 4.2 13.5 0.9 CB A:SER220 4.2 10.5 1.0 HA A:GLN222 4.2 14.3 0.1 CG1 A:VAL231 4.3 15.3 1.0 CA A:SER220 4.5 10.4 1.0 HB3 A:SER220 4.5 12.6 1.0 CG2 A:ILE221 4.5 10.4 1.0 HB3 A:GLN222 4.5 15.5 0.9 NE2 A:GLN222 4.6 15.1 0.1 N A:SER220 4.6 10.8 1.0 HB2 A:ALA247 4.6 12.7 1.0 HA A:ALA218 4.7 13.9 1.0 HA A:ILE221 4.7 12.4 1.0 HG13 A:ILE221 4.7 12.8 1.0 H A:ALA223 4.7 14.1 1.0 HD12 A:ILE221 4.7 12.7 1.0 O A:SER220 4.8 10.8 1.0 N A:ALA218 4.8 11.6 1.0 CG1 A:ILE221 4.8 10.7 1.0 OE1 A:GLN222 4.8 16.3 0.9 HG13 A:VAL231 4.8 18.4 1.0 CG A:GLN222 4.9 13.1 0.1 HG21 A:ILE221 4.9 12.5 1.0 O A:ILE221 5.0 11.4 1.0

Sodium binding site 3 out of 3 in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na313 b:27.2 occ:0.91 S A:SO4314 0.9 15.0 0.1 O1 A:SO4314 1.0 15.1 0.1 O3 A:SO4314 1.5 16.8 0.1 O4 A:SO4314 1.8 17.1 0.1 HG1 A:THR235 2.1 15.8 1.0 O2 A:SO4314 2.3 16.2 0.1 O1 A:6M9301 2.7 12.5 0.9 OG1 A:THR235 2.8 13.1 1.0 HA2 A:GLY236 2.9 12.4 1.0 H5 A:6M9301 3.0 15.6 0.9 HB A:THR235 3.2 13.1 1.0 C7 A:6M9301 3.3 13.0 0.9 HB2 A:SER70 3.5 12.2 1.0 C A:THR235 3.5 9.8 1.0 CB A:THR235 3.5 10.9 1.0 O A:THR235 3.5 10.4 1.0 CA A:GLY236 3.5 10.3 1.0 N A:GLY236 3.6 10.2 1.0 H7 A:6M9301 3.7 15.6 0.9 H A:SER237 3.7 13.9 0.2 H A:SER237 3.7 13.3 0.6 H A:SER237 3.8 13.8 0.2 C A:GLY236 3.8 11.2 1.0 O A:HOH441 3.8 32.4 1.0 HZ3 A:LYS234 3.8 14.0 1.0 N A:SER237 3.8 11.6 0.2 OG A:SER130 3.8 10.9 1.0 B1 A:6M9301 3.8 11.6 0.9 N A:SER237 3.9 11.1 0.6 N A:SER237 3.9 11.5 0.2 HZ1 A:LYS234 3.9 14.0 1.0 O2 A:6M9301 3.9 10.9 0.9 HB3 A:SER237 3.9 16.4 0.2 HB2 A:SER237 4.0 16.5 0.2 HB2 A:SER130 4.0 13.5 1.0 H A:GLY236 4.1 12.2 1.0 HB2 A:SER237 4.1 16.4 0.2 OG A:SER237 4.1 14.2 0.2 OG A:SER237 4.1 16.9 0.6 CA A:THR235 4.1 9.8 1.0 NZ A:LYS234 4.2 11.7 1.0 O A:HOH583 4.2 38.7 1.0 HZ2 A:LYS234 4.2 14.0 1.0 HG A:SER130 4.2 13.1 1.0 HG1 A:THR216 4.2 16.6 1.0 HB3 A:SER237 4.2 18.7 0.6 CB A:SER70 4.3 10.2 1.0 HG A:SER237 4.3 20.2 0.6 CB A:SER130 4.3 11.2 1.0 HG A:SER237 4.4 17.0 0.2 HB3 A:SER130 4.4 13.5 1.0 CB A:SER237 4.4 13.7 0.2 HA3 A:GLY236 4.4 12.4 1.0 O A:GLY236 4.5 11.9 1.0 CB A:SER237 4.5 13.7 0.2 HB3 A:SER70 4.5 12.2 1.0 OG A:SER70 4.5 11.7 1.0 HB A:THR216 4.5 15.7 1.0 CB A:SER237 4.6 15.6 0.6 C6 A:6M9301 4.6 12.7 0.9 H6 A:6M9301 4.7 13.1 0.9 H A:THR235 4.7 10.9 1.0 CA A:SER237 4.8 12.2 0.2 CA A:SER237 4.8 12.2 0.2 CG2 A:THR235 4.8 12.3 1.0 HG21 A:THR235 4.8 14.7 1.0 OG1 A:THR216 4.8 13.8 1.0 CA A:SER237 4.9 12.4 0.6 HA A:THR235 4.9 11.7 1.0 C1 A:6M9301 4.9 11.7 0.9 N A:THR235 4.9 9.1 1.0 HG21 A:THR216 5.0 18.5 1.0

C.L.Tooke, P.Hinchliffe, J.Spencer. Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-29 To Be Published.