Chlorine in PDB 7oyw: E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine

The structure of E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine, PDB code: 7oyw was solved by S.Shanmugaratnam, P.Kroeger, B.Hocker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.39 / 1.28
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.881, 71.285, 92.417, 90, 90, 90
R / Rfree (%)	13.2 / 16.1

The binding sites of Chlorine atom in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine (pdb code 7oyw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine, PDB code: 7oyw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:30.8 occ:0.43 CL A:CL406 0.0 30.8 0.4 CL A:CL406 0.3 18.1 0.6 H A:TYR87 2.6 21.7 1.0 O A:HOH705 2.8 26.7 1.0 HD2 A:TYR87 2.9 21.9 1.0 H A:PHE277 2.9 13.5 1.0 HB3 A:ALA86 2.9 20.0 1.0 HB3 A:TYR87 3.0 24.0 1.0 O A:HOH677 3.1 13.9 1.0 HA A:TRP276 3.2 13.2 1.0 HB2 A:TRP276 3.3 14.5 1.0 N A:TYR87 3.3 18.1 1.0 HB3 A:TRP276 3.4 14.5 1.0 H A:ALA86 3.4 17.0 1.0 HB3 A:SER85 3.6 15.8 0.7 CB A:TRP276 3.6 12.1 1.0 N A:PHE277 3.7 11.2 1.0 CD2 A:TYR87 3.8 18.2 1.0 HB2 A:SER85 3.8 18.0 0.3 CA A:TRP276 3.8 11.0 1.0 N A:ALA86 3.8 14.2 1.0 O A:PHE277 3.8 12.8 1.0 CB A:ALA86 3.8 16.7 1.0 CB A:TYR87 3.9 20.0 1.0 HG23 A:THR347 4.0 24.2 1.0 CA A:ALA86 4.1 14.3 1.0 C A:ALA86 4.1 15.8 1.0 CA A:TYR87 4.2 19.6 1.0 C A:TRP276 4.3 11.2 1.0 CG A:TYR87 4.3 19.2 1.0 HB2 A:PHE277 4.3 15.9 1.0 NE2 A:HIS123 4.3 19.5 1.0 HB1 A:ALA86 4.4 20.0 1.0 HB2 A:ALA86 4.4 20.0 1.0 HE1 A:HIS123 4.4 23.8 1.0 CE1 A:HIS123 4.5 19.8 1.0 O A:HOH535 4.5 19.1 1.0 HB3 A:GLN348 4.5 16.6 1.0 CB A:SER85 4.5 13.2 0.7 HA A:TYR87 4.6 23.5 1.0 HB2 A:TYR87 4.6 24.0 1.0 H A:GLN348 4.6 16.4 1.0 O A:ALA275 4.7 12.7 1.0 HD2 A:PHE277 4.7 20.4 1.0 C A:PHE277 4.7 10.9 1.0 CA A:PHE277 4.7 11.1 1.0 C A:SER85 4.7 14.7 1.0 CB A:SER85 4.7 15.0 0.3 O A:HOH555 4.7 22.3 1.0 CE2 A:TYR87 4.8 19.4 1.0 HE2 A:TYR87 4.9 23.2 1.0 CG2 A:THR347 4.9 20.1 1.0 HB2 A:SER85 4.9 15.8 0.7 CD2 A:HIS123 5.0 18.1 1.0 HG21 A:THR347 5.0 24.2 1.0

Chlorine binding site 2 out of 6 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:18.1 occ:0.57 CL A:CL406 0.0 18.1 0.6 CL A:CL406 0.3 30.8 0.4 H A:TYR87 2.7 21.7 1.0 H A:PHE277 2.7 13.5 1.0 O A:HOH705 2.8 26.7 1.0 HB3 A:ALA86 2.8 20.0 1.0 HD2 A:TYR87 3.0 21.9 1.0 HA A:TRP276 3.1 13.2 1.0 HB2 A:TRP276 3.2 14.5 1.0 H A:ALA86 3.2 17.0 1.0 HB3 A:TYR87 3.2 24.0 1.0 O A:HOH677 3.3 13.9 1.0 N A:TYR87 3.4 18.1 1.0 HB3 A:TRP276 3.4 14.5 1.0 HB3 A:SER85 3.5 15.8 0.7 N A:PHE277 3.5 11.2 1.0 CB A:TRP276 3.6 12.1 1.0 O A:PHE277 3.6 12.8 1.0 N A:ALA86 3.7 14.2 1.0 HB2 A:SER85 3.7 18.0 0.3 CA A:TRP276 3.7 11.0 1.0 CB A:ALA86 3.7 16.7 1.0 CD2 A:TYR87 3.9 18.2 1.0 CA A:ALA86 4.0 14.3 1.0 CB A:TYR87 4.0 20.0 1.0 C A:ALA86 4.1 15.8 1.0 HB2 A:PHE277 4.1 15.9 1.0 C A:TRP276 4.1 11.2 1.0 HB2 A:ALA86 4.2 20.0 1.0 HG23 A:THR347 4.3 24.2 1.0 HB1 A:ALA86 4.3 20.0 1.0 CA A:TYR87 4.3 19.6 1.0 NE2 A:HIS123 4.4 19.5 1.0 C A:PHE277 4.4 10.9 1.0 CB A:SER85 4.4 13.2 0.7 CA A:PHE277 4.5 11.1 1.0 CG A:TYR87 4.5 19.2 1.0 HD2 A:PHE277 4.5 20.4 1.0 C A:SER85 4.6 14.7 1.0 CE1 A:HIS123 4.6 19.8 1.0 O A:HOH535 4.6 19.1 1.0 CB A:SER85 4.6 15.0 0.3 HE1 A:HIS123 4.6 23.8 1.0 HA A:TYR87 4.7 23.5 1.0 O A:ALA275 4.7 12.7 1.0 HB3 A:GLN348 4.8 16.6 1.0 O A:HOH555 4.8 22.3 1.0 CB A:PHE277 4.8 13.3 1.0 HB2 A:TYR87 4.8 24.0 1.0 HB2 A:SER85 4.8 15.8 0.7 H A:GLN348 4.9 16.4 1.0 CE2 A:TYR87 4.9 19.4 1.0 HA A:ALA86 4.9 17.2 1.0 HE2 A:TYR87 4.9 23.2 1.0 CA A:SER85 5.0 14.2 0.7 HA A:SER85 5.0 17.6 1.0 CA A:SER85 5.0 14.7 0.3 CD2 A:HIS123 5.0 18.1 1.0 N A:TRP276 5.0 11.4 1.0 H21 A:SPD401 5.0 18.5 0.4

Chlorine binding site 3 out of 6 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:44.9 occ:1.00 O A:HOH614 2.6 18.6 0.4 HE3 A:LYS146 2.9 27.7 1.0 O A:HOH943 3.1 18.1 1.0 O A:HOH715 3.1 18.1 1.0 HA3 A:GLY236 3.3 19.5 1.0 HZ1 A:LYS146 3.6 30.8 1.0 CE A:LYS146 3.7 23.1 1.0 O A:HOH809 3.7 48.0 1.0 HE2 A:LYS146 3.8 27.7 1.0 HG22 A:VAL262 4.0 19.8 1.0 NZ A:LYS146 4.0 25.6 1.0 HZ2 A:LYS146 4.2 30.8 1.0 O A:GLY236 4.2 18.4 1.0 CA A:GLY236 4.2 16.2 1.0 O A:HOH614 4.3 32.8 0.6 HA2 A:GLY236 4.5 19.5 1.0 O A:ASN235 4.6 18.1 1.0 C A:GLY236 4.7 16.5 1.0 O A:HOH913 4.7 17.8 1.0 HD21 A:ASN143 4.7 17.9 1.0 HG21 A:VAL262 4.8 19.8 1.0 CG2 A:VAL262 4.8 16.5 1.0 HZ3 A:LYS146 4.8 30.8 1.0 CD A:LYS146 5.0 19.7 1.0

Chlorine binding site 4 out of 6 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:59.3 occ:1.00 H A:ALA327 2.3 24.8 1.0 HA A:SER326 2.9 22.4 1.0 N A:ALA327 3.1 20.7 1.0 O A:HOH795 3.4 29.6 1.0 HB2 A:SER326 3.4 25.4 1.0 HB3 A:ALA327 3.6 29.9 1.0 HB2 A:ALA327 3.6 29.9 1.0 O A:HOH910 3.6 56.0 1.0 CA A:SER326 3.6 18.7 1.0 C A:SER326 3.9 18.0 1.0 CB A:ALA327 3.9 24.9 1.0 CB A:SER326 4.0 21.1 1.0 CA A:ALA327 4.1 21.6 1.0 O A:HOH759 4.2 43.4 1.0 HH21 A:ARG330 4.3 41.8 1.0 HB3 A:SER326 4.4 25.4 1.0 H A:GLU328 4.4 24.7 1.0 O A:HOH551 4.7 38.2 1.0 HA A:ALA327 4.7 25.9 1.0 HH22 A:ARG330 4.8 41.8 1.0 HB1 A:ALA327 4.9 29.9 1.0 N A:SER326 4.9 16.7 1.0 NH2 A:ARG330 4.9 34.9 1.0 O A:VAL325 4.9 17.8 1.0

Chlorine binding site 5 out of 6 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl405 b:13.4 occ:0.46 CL B:CL405 0.0 13.4 0.5 CL B:CL405 0.1 36.5 0.5 H B:TYR87 2.6 21.6 1.0 H B:PHE277 2.8 15.6 1.0 HB3 B:ALA86 2.8 21.0 1.0 HD2 B:TYR87 2.9 22.3 1.0 O B:HOH705 2.9 26.3 1.0 HA B:TRP276 3.1 15.4 1.0 HB2 B:TRP276 3.2 15.6 1.0 HB3 B:TYR87 3.2 23.9 1.0 O B:HOH645 3.2 15.2 1.0 H B:ALA86 3.3 18.3 1.0 HB3 B:TRP276 3.3 15.6 1.0 N B:TYR87 3.4 18.0 1.0 HB3 B:SER85 3.5 18.2 0.8 N B:PHE277 3.5 13.0 1.0 CB B:TRP276 3.5 13.0 1.0 HB2 B:SER85 3.6 18.5 0.2 CA B:TRP276 3.7 12.8 1.0 O B:PHE277 3.7 15.0 1.0 N B:ALA86 3.7 15.3 1.0 CB B:ALA86 3.7 17.5 1.0 CD2 B:TYR87 3.8 18.6 1.0 CB B:TYR87 4.0 19.9 1.0 CA B:ALA86 4.0 14.8 1.0 C B:ALA86 4.1 16.6 1.0 HG23 B:THR347 4.1 27.6 1.0 C B:TRP276 4.2 12.8 1.0 HB2 B:PHE277 4.2 21.1 1.0 CA B:TYR87 4.3 18.8 1.0 HB2 B:ALA86 4.3 21.0 1.0 HB1 B:ALA86 4.3 21.0 1.0 CG B:TYR87 4.4 18.8 1.0 NE2 B:HIS123 4.4 21.7 1.0 CB B:SER85 4.4 15.2 0.8 C B:PHE277 4.5 13.5 1.0 CB B:SER85 4.5 15.4 0.2 HE1 B:HIS123 4.5 26.2 1.0 CA B:PHE277 4.5 13.7 1.0 CE1 B:HIS123 4.5 21.8 1.0 C B:SER85 4.6 15.2 1.0 O B:HOH525 4.6 21.4 1.0 HD2 B:PHE277 4.6 25.0 1.0 O B:ALA275 4.7 14.4 1.0 HB3 B:GLN348 4.7 18.6 1.0 HA B:TYR87 4.7 22.6 1.0 HB2 B:TYR87 4.7 23.9 1.0 H B:GLN348 4.8 18.9 1.0 O B:HOH562 4.8 29.3 1.0 HB2 B:SER85 4.8 18.2 0.8 CE2 B:TYR87 4.9 18.8 1.0 CB B:PHE277 4.9 17.6 1.0 HE2 B:TYR87 4.9 22.6 1.0 N B:TRP276 5.0 13.4 1.0 HA B:SER85 5.0 18.4 1.0 CA B:SER85 5.0 15.3 0.8 CA B:SER85 5.0 15.4 0.2 H21 B:SPD401 5.0 17.9 0.3 CG B:TRP276 5.0 12.9 1.0 HA B:ALA86 5.0 17.8 1.0

Chlorine binding site 6 out of 6 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D F88L S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl405 b:36.5 occ:0.54 CL B:CL405 0.0 36.5 0.5 CL B:CL405 0.1 13.4 0.5 H B:TYR87 2.6 21.6 1.0 H B:PHE277 2.7 15.6 1.0 HB3 B:ALA86 2.8 21.0 1.0 O B:HOH705 2.9 26.3 1.0 HD2 B:TYR87 3.0 22.3 1.0 HA B:TRP276 3.1 15.4 1.0 HB2 B:TRP276 3.2 15.6 1.0 HB3 B:TYR87 3.2 23.9 1.0 H B:ALA86 3.2 18.3 1.0 O B:HOH645 3.3 15.2 1.0 N B:TYR87 3.3 18.0 1.0 HB3 B:TRP276 3.4 15.6 1.0 HB3 B:SER85 3.5 18.2 0.8 N B:PHE277 3.5 13.0 1.0 CB B:TRP276 3.6 13.0 1.0 HB2 B:SER85 3.6 18.5 0.2 O B:PHE277 3.6 15.0 1.0 N B:ALA86 3.7 15.3 1.0 CA B:TRP276 3.7 12.8 1.0 CB B:ALA86 3.7 17.5 1.0 CD2 B:TYR87 3.9 18.6 1.0 CA B:ALA86 4.0 14.8 1.0 CB B:TYR87 4.0 19.9 1.0 C B:ALA86 4.1 16.6 1.0 HB2 B:PHE277 4.1 21.1 1.0 C B:TRP276 4.1 12.8 1.0 HG23 B:THR347 4.2 27.6 1.0 HB2 B:ALA86 4.2 21.0 1.0 HB1 B:ALA86 4.2 21.0 1.0 CA B:TYR87 4.3 18.8 1.0 NE2 B:HIS123 4.4 21.7 1.0 CB B:SER85 4.4 15.2 0.8 CG B:TYR87 4.4 18.8 1.0 C B:PHE277 4.5 13.5 1.0 CA B:PHE277 4.5 13.7 1.0 CB B:SER85 4.5 15.4 0.2 HE1 B:HIS123 4.5 26.2 1.0 CE1 B:HIS123 4.6 21.8 1.0 C B:SER85 4.6 15.2 1.0 HD2 B:PHE277 4.6 25.0 1.0 O B:HOH525 4.7 21.4 1.0 O B:ALA275 4.7 14.4 1.0 HA B:TYR87 4.7 22.6 1.0 HB3 B:GLN348 4.7 18.6 1.0 HB2 B:TYR87 4.8 23.9 1.0 CB B:PHE277 4.8 17.6 1.0 O B:HOH562 4.8 29.3 1.0 H B:GLN348 4.8 18.9 1.0 HB2 B:SER85 4.8 18.2 0.8 CE2 B:TYR87 4.9 18.8 1.0 HE2 B:TYR87 4.9 22.6 1.0 HA B:SER85 4.9 18.4 1.0 HA B:ALA86 4.9 17.8 1.0 CA B:SER85 4.9 15.3 0.8 CA B:SER85 4.9 15.4 0.2 N B:TRP276 5.0 13.4 1.0 HB3 B:SER85 5.0 18.5 0.2 CD2 B:HIS123 5.0 19.5 1.0

P.Kroger, S.Shanmugaratnam, U.Scheib, B.Hocker. Fine-Tuning Spermidine Binding Modes in the Putrescine Binding Protein Potf. J.Biol.Chem. 01419 2021.
ISSN: ESSN 1083-351X
PubMed: 34801550
DOI: 10.1016/J.JBC.2021.101419