Chlorine in PDB 6cd7: Crystal Structure of Aph(2")-Iva in Complex with Plazomicin

The structure of Crystal Structure of Aph(2")-Iva in Complex with Plazomicin, PDB code: 6cd7 was solved by P.J.Stogios, E.Evdokimova, A.Dong, R.Di Leo, A.Savchenko, K.J.Satchell, J.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.60 / 1.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.455, 101.813, 72.921, 90.00, 98.47, 90.00
R / Rfree (%)	17.1 / 20.8

The binding sites of Chlorine atom in the Crystal Structure of Aph(2")-Iva in Complex with Plazomicin (pdb code 6cd7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Aph(2")-Iva in Complex with Plazomicin, PDB code: 6cd7:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Aph(2")-Iva in Complex with Plazomicin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Aph(2")-Iva in Complex with Plazomicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:18.0 occ:0.79 O A:HOH605 3.0 19.3 1.0 O A:HOH552 3.1 20.1 1.0 N A:VAL78 3.3 14.0 1.0 CA A:GLU77 3.8 15.1 1.0 O A:LEU64 3.9 17.8 1.0 CB A:HIS68 3.9 22.1 1.0 CG2 A:VAL78 4.0 16.2 1.0 C A:GLU77 4.0 15.6 1.0 C A:LEU64 4.1 19.5 1.0 CB A:VAL78 4.1 16.5 1.0 CG A:LYS65 4.1 24.5 1.0 CA A:LYS65 4.2 20.6 1.0 CA A:VAL78 4.2 15.2 1.0 N A:LYS65 4.2 18.3 1.0 CB A:LEU64 4.3 14.4 1.0 O A:PRO76 4.3 14.8 1.0 CB A:GLU77 4.4 22.6 1.0 O A:VAL78 4.5 17.7 1.0 CG A:HIS68 4.7 24.5 1.0 CB A:LYS65 4.8 23.0 1.0 CG A:GLU77 4.8 26.3 1.0 CA A:LEU64 4.8 18.7 1.0 C A:VAL78 4.8 18.3 1.0 N A:GLU77 4.9 15.7 1.0 O A:HOH677 5.0 26.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Aph(2")-Iva in Complex with Plazomicin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Aph(2")-Iva in Complex with Plazomicin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:20.3 occ:0.97 O B:HOH987 3.1 18.9 1.0 O B:HOH667 3.3 24.8 1.0 N B:ASP19 3.3 17.0 1.0 CA B:TYR17 3.5 13.0 1.0 C B:TYR17 3.5 14.1 1.0 N B:PRO18 3.6 15.7 1.0 CD B:PRO18 3.6 17.4 1.0 CB B:ASP19 3.6 19.1 1.0 OD2 B:ASP19 3.9 19.4 1.0 CG B:ASP19 3.9 22.1 1.0 CA B:ASP19 4.0 20.0 1.0 CB B:TYR17 4.1 14.0 1.0 CG B:PRO18 4.1 17.6 1.0 O B:TYR17 4.1 16.0 1.0 C B:PRO18 4.3 17.9 1.0 CD2 B:TYR17 4.3 15.0 1.0 CA B:PRO18 4.4 18.0 1.0 N B:PHE20 4.4 17.3 1.0 C B:ASP19 4.5 22.9 1.0 O B:LEU16 4.7 18.5 1.0 CG B:TYR17 4.7 14.7 1.0 OD1 B:ASP19 4.7 22.6 1.0 N B:TYR17 4.7 14.4 1.0 O A:HOH829 4.8 29.4 1.0 CB B:PRO18 4.9 18.9 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Aph(2")-Iva in Complex with Plazomicin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Aph(2")-Iva in Complex with Plazomicin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:37.3 occ:1.00 O B:HOH813 3.5 21.8 1.0 O B:HOH981 3.6 31.4 1.0 NE B:ARG66 3.6 15.5 1.0 O B:HOH679 3.7 36.3 1.0 O B:HOH989 3.7 55.6 1.0 NH2 B:ARG66 3.7 16.6 1.0 O B:HOH1000 3.8 49.9 1.0 O B:HOH669 3.9 21.4 1.0 O B:HOH701 3.9 22.2 1.0 CE2 B:PHE138 4.0 17.9 1.0 CZ B:ARG66 4.1 17.7 1.0 CB B:ARG66 4.4 18.2 1.0 CD2 B:PHE138 4.6 15.1 1.0 CG B:ARG66 4.7 14.7 1.0 CD B:ARG66 4.7 16.8 1.0 O B:HOH933 4.8 40.3 1.0 O B:HOH1056 4.8 36.4 1.0 CZ B:PHE138 4.8 18.2 1.0 O B:ARG66 4.9 18.0 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Aph(2")-Iva in Complex with Plazomicin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Aph(2")-Iva in Complex with Plazomicin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl404 b:68.9 occ:0.99 OE2 B:GLU290 2.6 79.1 1.0 O B:HOH759 2.6 38.5 1.0 NZ B:LYS275 3.0 49.0 1.0 CD B:LYS275 3.1 48.5 1.0 O B:HOH513 3.4 60.2 1.0 O B:HOH517 3.4 58.7 1.0 CB B:GLU290 3.6 65.2 1.0 CE B:LYS275 3.6 49.1 1.0 CD B:GLU290 3.7 80.0 1.0 OE2 B:GLU294 4.0 53.6 1.0 CG B:GLU290 4.1 75.7 1.0 CD1 B:TRP287 4.4 68.9 1.0 NE1 B:TRP287 4.4 71.1 1.0 CG B:LYS275 4.5 42.4 1.0 OE1 B:GLU290 4.8 83.7 1.0 O B:HOH691 4.8 73.3 1.0 CA B:GLU290 4.9 57.4 1.0

G.Cox, L.Ejim, P.J.Stogios, K.Koteva, E.Bordeleau, E.Evdokimova, A.O.Sieron, A.Savchenko, A.W.Serio, K.M.Krause, G.D.Wright. Plazomicin Retains Antibiotic Activity Against Most Aminoglycoside Modifying Enzymes. Acs Infect Dis V. 4 980 2018.
ISSN: ESSN 2373-8227
PubMed: 29634241
DOI: 10.1021/ACSINFECDIS.8B00001