Sodium in PDB 8r30: Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-408

All present enzymatic activity of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-408:
3.5.2.6;

The structure of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-408, PDB code: 8r30 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)	31.72 / 0.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.252, 45.506, 117.416, 90, 90, 90
R / Rfree (%)	12.4 / 13.7

The structure of Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-408 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-408 (pdb code 8r30). 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-408, PDB code: 8r30:
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-408


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-408 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:10.6 occ:1.00 HG1 A:THR181 1.8 5.9 1.0 HB2 A:PHE160 2.6 5.3 1.0 OD2 A:ASP157 2.7 6.4 1.0 OG1 A:THR181 2.7 5.7 1.0 HA A:MET186 2.8 5.5 1.0 HG22 A:THR181 3.0 5.7 1.0 HD2 A:PHE160 3.1 5.8 1.0 HB2 A:MET186 3.2 6.0 1.0 HB1 A:ALA185 3.4 6.6 1.0 CB A:THR181 3.4 5.4 1.0 CA A:MET186 3.4 5.7 1.0 SD A:MET186 3.5 7.0 1.0 N A:MET186 3.5 5.5 1.0 HB A:THR181 3.5 5.3 1.0 CB A:PHE160 3.5 5.5 1.0 CG2 A:THR181 3.6 5.8 1.0 HB3 A:ALA185 3.6 6.6 1.0 CG A:ASP157 3.6 5.6 1.0 C A:ALA185 3.7 5.6 1.0 HG21 A:THR181 3.7 5.7 1.0 CB A:MET186 3.7 5.9 1.0 H A:MET186 3.8 5.6 1.0 H A:PHE160 3.8 5.4 1.0 HG1 A:THR189 3.8 7.0 1.0 HA A:PHE160 3.8 5.5 1.0 OD1 A:ASP157 3.8 5.7 1.0 CB A:ALA185 3.9 6.8 1.0 CD2 A:PHE160 3.9 5.8 1.0 O A:ALA185 3.9 6.1 1.0 HB A:THR189 4.0 6.5 1.0 CA A:PHE160 4.1 5.5 1.0 HB3 A:PHE160 4.1 5.3 1.0 N A:PHE160 4.2 5.5 1.0 HE3 A:MET75 4.2 10.5 0.7 CG A:PHE160 4.2 5.3 1.0 CG A:MET186 4.2 6.8 1.0 HE1 A:MET75 4.2 10.5 0.7 HE2 A:MET75 4.4 10.5 0.7 HB A:THR159 4.4 6.5 1.0 HE2 A:MET186 4.4 9.2 1.0 CA A:ALA185 4.4 6.2 1.0 CE A:MET186 4.4 8.9 1.0 HE1 A:MET186 4.4 9.2 1.0 HG23 A:THR181 4.5 5.7 1.0 CE A:MET75 4.5 9.3 0.7 OG1 A:THR189 4.5 7.0 1.0 H A:SER182 4.5 5.4 1.0 HB3 A:MET186 4.6 6.0 1.0 CB A:THR189 4.7 6.5 1.0 HB2 A:ALA185 4.7 6.6 1.0 HG22 A:THR189 4.7 9.0 1.0 O A:SER182 4.7 5.8 1.0 HG2 A:MET186 4.8 6.7 1.0 C A:MET186 4.8 5.5 1.0 CA A:THR181 4.9 5.4 1.0 HG3 A:MET186 4.9 6.7 1.0 CB A:ASP157 5.0 5.8 1.0

Sodium binding site 2 out of 3 in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-408


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-408 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:10.3 occ:1.00 H A:GLN222 2.1 6.2 1.0 HG3 A:GLN222 2.4 8.4 1.0 O A:GLY217 2.7 6.8 1.0 OD2 A:ASP245 2.8 5.9 1.0 HE21 A:GLN222 2.8 9.5 1.0 HB A:ILE221 2.9 6.0 1.0 N A:GLN222 2.9 6.3 1.0 H A:ILE221 3.1 6.0 1.0 CG A:GLN222 3.2 8.3 1.0 OD2 A:ASP233 3.3 6.1 1.0 HA3 A:GLY217 3.3 7.6 1.0 CG A:ASP233 3.3 6.0 1.0 NE2 A:GLN222 3.3 9.2 1.0 HB2 A:GLN222 3.3 7.4 1.0 N A:ILE221 3.3 6.0 1.0 HB2 A:SER220 3.5 6.1 1.0 HG12 A:VAL231 3.5 11.2 1.0 CB A:GLN222 3.6 7.4 1.0 C A:GLY217 3.6 6.6 1.0 OD1 A:ASP233 3.6 7.0 1.0 CD A:GLN222 3.6 9.1 1.0 HB3 A:ASP233 3.7 5.6 1.0 CB A:ILE221 3.7 6.1 1.0 CA A:ILE221 3.8 6.2 1.0 C A:ILE221 3.8 6.3 1.0 CA A:GLN222 3.8 6.9 1.0 CG A:ASP245 3.8 5.3 1.0 CA A:GLY217 3.9 7.6 1.0 CB A:ASP233 3.9 5.9 1.0 HB2 A:ASP233 4.0 5.6 1.0 HG2 A:GLN222 4.0 8.4 1.0 HE22 A:GLN222 4.0 9.5 1.0 H A:SER220 4.0 6.1 1.0 HA2 A:GLY217 4.0 7.6 1.0 C A:SER220 4.0 6.0 1.0 HG22 A:ILE221 4.1 6.3 1.0 HG13 A:VAL231 4.2 11.2 1.0 OD1 A:ASP245 4.2 5.7 1.0 HA A:GLN222 4.2 6.8 1.0 CB A:SER220 4.3 6.2 1.0 CG1 A:VAL231 4.3 10.7 1.0 HB3 A:SER220 4.5 6.1 1.0 CA A:SER220 4.5 6.0 1.0 CG2 A:ILE221 4.5 6.4 1.0 HB3 A:GLN222 4.5 7.4 1.0 N A:SER220 4.6 6.1 1.0 HB1 A:ALA247 4.7 6.6 1.0 HD12 A:ILE221 4.7 5.8 1.0 OE1 A:GLN222 4.7 9.6 1.0 HA A:ILE221 4.7 6.0 1.0 HA A:ALA218 4.7 6.5 1.0 N A:ALA218 4.8 6.4 1.0 H A:ALA223 4.8 6.6 1.0 O A:SER220 4.8 6.5 1.0 HG13 A:ILE221 4.8 5.8 1.0 CG1 A:ILE221 4.8 5.9 1.0 HG11 A:VAL231 4.9 11.2 1.0 HG21 A:ILE221 4.9 6.3 1.0 HG22 A:THR235 4.9 7.1 1.0 HG21 A:THR235 4.9 7.1 1.0 HG21 A:VAL231 5.0 12.0 1.0 O A:ILE221 5.0 6.9 1.0

Sodium binding site 3 out of 3 in the Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-408


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-408 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:10.1 occ:1.00 H A:CYS69 1.9 5.0 1.0 H A:MET68 2.7 5.1 1.0 HB2 A:ALA67 2.7 6.5 1.0 N A:CYS69 2.8 5.0 1.0 O A:LEU169 2.8 6.2 1.0 O A:ASP179 2.8 5.7 1.0 HB3 A:ASP179 2.9 5.6 1.0 HB2 A:ASP179 3.0 5.6 1.0 N A:MET68 3.0 5.2 1.0 HA A:CYS69 3.2 5.1 1.0 HD13 A:LEU169 3.3 7.3 1.0 CB A:ASP179 3.4 5.6 1.0 HA A:ALA67 3.4 5.6 1.0 C A:ALA67 3.5 5.5 1.0 HB2 A:MET68 3.5 5.2 1.0 CA A:CYS69 3.5 5.2 1.0 CB A:ALA67 3.6 6.6 1.0 O A:HOH487 3.6 7.5 1.0 HA A:ASN170 3.6 6.0 1.0 HD11 A:LEU169 3.6 7.3 1.0 CA A:ALA67 3.7 5.7 1.0 C A:MET68 3.7 4.9 1.0 HG A:CYS69 3.8 6.6 1.0 CA A:MET68 3.8 5.1 1.0 C A:ASP179 3.8 5.4 1.0 C A:LEU169 3.9 5.8 1.0 CD1 A:LEU169 3.9 7.3 1.0 HB3 A:ALA67 4.1 6.5 1.0 SG A:CYS69 4.1 6.7 1.0 CB A:MET68 4.2 5.2 1.0 HB1 A:ALA67 4.2 6.5 1.0 CA A:ASP179 4.2 5.5 1.0 HB2 A:LEU169 4.3 5.5 1.0 O A:ALA67 4.4 6.6 1.0 CB A:CYS69 4.5 5.7 1.0 CA A:ASN170 4.5 6.2 1.0 HD12 A:LEU169 4.5 7.3 1.0 CG A:ASP179 4.6 5.7 1.0 O A:CYS69 4.6 5.2 1.0 C A:CYS69 4.6 5.1 1.0 N A:ASN170 4.6 6.1 1.0 HA A:MET68 4.7 5.0 1.0 HA A:ASP179 4.7 5.3 1.0 O A:ARG178 4.8 6.3 1.0 HE2 A:MET68 4.8 6.4 1.0 HB3 A:MET68 4.8 5.2 1.0 HA A:THR180 4.8 5.2 1.0 OD1 A:ASN170 4.9 7.0 1.0 HG3 A:MET68 4.9 5.8 1.0 O A:MET68 4.9 5.1 1.0 CB A:LEU169 4.9 5.6 1.0 HB2 A:ALA172 4.9 7.5 1.0 CA A:LEU169 4.9 5.7 1.0

C.L.Tooke, P.Hinchliffe, J.Spencer. Structure of Ctx-M-15 Complexed with Benzoxaborole Ak-408 To Be Published.