Chlorine in PDB 7oyx: E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y S247D in Complex with Spermidine

The structure of E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y S247D in Complex with Spermidine, PDB code: 7oyx 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)	40.70 / 1.37
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.155, 71.493, 92.661, 90, 90, 90
R / Rfree (%)	16.5 / 19.3

The binding sites of Chlorine atom in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y S247D in Complex with Spermidine (pdb code 7oyx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y S247D in Complex with Spermidine, PDB code: 7oyx:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y 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 Y87S F88Y S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:16.6 occ:0.54 CL A:CL405 0.0 16.6 0.5 CL A:CL405 1.0 18.2 0.5 O A:HOH789 2.5 16.1 0.5 H A:SER87 2.6 13.3 0.4 H A:SER87 2.6 13.3 0.6 H A:PHE277 3.0 17.7 1.0 H A:ALA86 3.1 13.2 1.0 HB2 A:TRP276 3.1 16.3 1.0 HB3 A:SER85 3.1 12.3 1.0 O A:HOH639 3.1 8.6 0.2 HB3 A:ALA86 3.1 14.5 1.0 O A:HOH764 3.2 19.0 0.4 HB3 A:TRP276 3.2 16.3 1.0 O A:HOH639 3.3 13.2 0.8 HA A:TRP276 3.3 15.8 1.0 N A:SER87 3.4 11.1 1.0 HB3 A:SER87 3.4 18.4 0.6 CB A:TRP276 3.5 13.6 1.0 N A:ALA86 3.5 11.0 1.0 HB2 A:SER87 3.6 19.9 0.4 HB3 A:SER87 3.6 19.9 0.4 O A:HOH789 3.7 22.9 0.6 O A:PHE277 3.7 13.8 1.0 N A:PHE277 3.8 14.8 1.0 HG A:SER87 3.8 19.4 0.6 CA A:TRP276 3.8 13.1 1.0 CB A:ALA86 3.9 12.1 1.0 CB A:SER87 4.0 16.6 0.4 CA A:ALA86 4.0 9.8 1.0 CB A:SER85 4.0 10.2 1.0 O A:HOH764 4.0 16.7 0.6 CB A:SER87 4.1 15.4 0.6 HB2 A:ALA86 4.1 14.5 1.0 C A:ALA86 4.1 12.3 1.0 O A:HOH692 4.2 18.3 1.0 CA A:SER87 4.3 12.8 0.4 C A:SER85 4.3 11.2 1.0 CA A:SER87 4.3 12.9 0.6 HB2 A:SER85 4.3 12.3 1.0 C A:TRP276 4.3 16.0 1.0 OG A:SER87 4.4 16.2 0.6 HB3 A:GLN348 4.4 17.2 1.0 HB2 A:PHE277 4.4 17.5 1.0 C A:PHE277 4.6 12.1 1.0 NE2 A:HIS123 4.6 21.9 1.0 CA A:SER85 4.7 9.0 1.0 HB1 A:ALA86 4.7 14.5 1.0 HA A:SER85 4.7 10.8 1.0 HE1 A:HIS123 4.7 27.8 1.0 CA A:PHE277 4.7 11.4 1.0 H A:GLN348 4.7 15.3 1.0 HA A:SER87 4.8 15.4 0.4 CE1 A:HIS123 4.8 23.1 1.0 HA A:SER87 4.8 15.5 0.6 O A:ALA275 4.8 13.3 1.0 H91 A:SPD401 4.8 37.7 1.0 H101 A:SPD401 4.9 28.7 1.0 OG A:SER85 4.9 11.0 1.0 CG A:TRP276 4.9 12.4 1.0 HB2 A:SER87 4.9 18.4 0.6 HA A:ALA86 4.9 11.7 1.0 H A:TYR88 5.0 12.0 1.0

Chlorine binding site 2 out of 5 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y 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 Y87S F88Y S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:18.2 occ:0.46 CL A:CL405 0.0 18.2 0.5 CL A:CL405 1.0 16.6 0.5 O A:HOH764 2.3 19.0 0.4 H A:SER87 2.3 13.3 0.6 H A:SER87 2.3 13.3 0.4 HB3 A:SER87 2.8 18.4 0.6 HB3 A:SER87 2.8 19.9 0.4 HG A:SER87 2.9 19.4 0.6 HB2 A:SER87 2.9 19.9 0.4 HB3 A:SER85 2.9 12.3 1.0 O A:HOH639 3.0 13.2 0.8 O A:HOH639 3.1 8.6 0.2 O A:HOH764 3.1 16.7 0.6 N A:SER87 3.2 11.1 1.0 CB A:SER87 3.2 16.6 0.4 HB3 A:TRP276 3.4 16.3 1.0 CB A:SER87 3.4 15.4 0.6 O A:HOH789 3.5 16.1 0.5 HB2 A:TRP276 3.5 16.3 1.0 OG A:SER87 3.5 16.2 0.6 H A:ALA86 3.6 13.2 1.0 O A:HOH692 3.6 18.3 1.0 HB3 A:GLN348 3.6 17.2 1.0 HB3 A:ALA86 3.8 14.5 1.0 CA A:SER87 3.8 12.8 0.4 CB A:SER85 3.8 10.2 1.0 CB A:TRP276 3.8 13.6 1.0 N A:ALA86 3.8 11.0 1.0 CA A:SER87 3.9 12.9 0.6 HB2 A:SER85 3.9 12.3 1.0 H A:PHE277 4.0 17.7 1.0 HA A:TRP276 4.0 15.8 1.0 C A:ALA86 4.2 12.3 1.0 HB2 A:SER87 4.3 18.4 0.6 H101 A:SPD401 4.3 28.7 1.0 CA A:ALA86 4.4 9.8 1.0 C A:SER85 4.4 11.2 1.0 H A:GLN348 4.4 15.3 1.0 HA A:SER87 4.4 15.4 0.4 O A:HOH789 4.4 22.9 0.6 O A:PHE277 4.4 13.8 1.0 CA A:TRP276 4.4 13.1 1.0 H A:TYR88 4.5 12.0 1.0 HA A:SER87 4.5 15.5 0.6 OG A:SER87 4.5 16.9 0.4 CB A:ALA86 4.5 12.1 1.0 CB A:GLN348 4.5 14.3 1.0 H91 A:SPD401 4.6 37.7 1.0 HB2 A:GLN348 4.6 17.2 1.0 CA A:SER85 4.7 9.0 1.0 N A:PHE277 4.7 14.8 1.0 OG A:SER85 4.7 11.0 1.0 HE1 A:HIS123 4.8 27.8 1.0 HB2 A:ALA86 4.9 14.5 1.0 HD2 A:TYR88 4.9 13.7 1.0 HA A:SER85 4.9 10.8 1.0 HG2 A:GLN348 4.9 18.1 1.0 C A:SER87 4.9 10.7 1.0 HG A:SER85 5.0 13.2 1.0 CE1 A:HIS123 5.0 23.1 1.0 HG A:SER87 5.0 20.3 0.4

Chlorine binding site 3 out of 5 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y 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 Y87S F88Y S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:59.0 occ:1.00 H A:ALA327 2.5 23.7 1.0 HA A:SER326 3.1 20.4 1.0 N A:ALA327 3.3 19.8 1.0 O A:HOH708 3.6 27.8 1.0 HB2 A:SER326 3.6 22.8 1.0 HB2 A:ALA327 3.6 32.5 1.0 HB3 A:ALA327 3.6 32.5 1.0 CA A:SER326 3.8 17.0 1.0 CB A:ALA327 4.0 27.1 1.0 C A:SER326 4.1 21.3 1.0 CB A:SER326 4.2 19.0 1.0 O A:HOH713 4.3 39.6 1.0 CA A:ALA327 4.3 23.5 1.0 HB3 A:SER326 4.4 22.8 1.0 H A:GLU328 4.6 23.6 1.0 O A:HOH548 4.6 34.0 1.0 HH21 A:ARG330 4.6 45.6 1.0 HA A:ALA327 4.9 28.1 1.0 HB1 A:ALA327 4.9 32.5 1.0

Chlorine binding site 4 out of 5 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y 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 Y87S F88Y S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl408 b:18.7 occ:0.52 CL B:CL408 0.0 18.7 0.5 CL B:CL408 1.2 16.6 0.5 H B:SER87 2.3 18.0 0.6 H B:SER87 2.3 18.0 0.5 HB3 B:SER87 2.5 20.6 0.5 HB3 B:SER87 2.9 20.2 0.6 O B:HOH750 2.9 22.6 1.0 HB2 B:SER87 2.9 20.2 0.6 HB3 B:SER85 2.9 15.9 1.0 O B:HOH759 3.0 7.5 0.3 O B:HOH558 3.0 21.1 1.0 HG B:SER87 3.1 19.5 0.5 N B:SER87 3.2 15.0 1.0 CB B:SER87 3.3 16.8 0.6 CB B:SER87 3.3 17.2 0.5 HB3 B:TRP276 3.4 17.8 1.0 HB2 B:TRP276 3.4 17.8 1.0 O B:HOH726 3.5 22.9 1.0 H B:ALA86 3.5 16.5 1.0 OG B:SER87 3.6 16.2 0.5 HB3 B:GLN348 3.6 20.9 1.0 HB3 B:ALA86 3.8 17.1 1.0 CA B:SER87 3.8 14.5 0.6 CB B:SER85 3.8 13.3 1.0 CB B:TRP276 3.8 14.8 1.0 O B:HOH759 3.8 18.6 0.4 N B:ALA86 3.8 13.8 1.0 CA B:SER87 3.8 14.6 0.5 HB2 B:SER85 3.9 15.9 1.0 HA B:TRP276 3.9 18.8 1.0 H B:PHE277 3.9 17.8 1.0 HB2 B:SER87 4.1 20.6 0.5 C B:ALA86 4.2 13.5 1.0 CA B:ALA86 4.4 12.0 1.0 C B:SER85 4.4 14.2 1.0 HA B:SER87 4.4 17.4 0.6 H B:GLN348 4.4 19.6 1.0 CA B:TRP276 4.4 15.7 1.0 O B:PHE277 4.5 18.4 1.0 HA B:SER87 4.5 17.5 0.5 H B:TYR88 4.5 16.1 1.0 CB B:GLN348 4.5 17.4 1.0 HB2 B:GLN348 4.5 20.9 1.0 CB B:ALA86 4.5 14.3 1.0 OG B:SER87 4.6 16.8 0.6 O B:HOH759 4.6 18.2 0.4 H91 B:SPD401 4.6 25.5 1.0 N B:PHE277 4.7 14.8 1.0 H92 B:SPD401 4.7 25.5 1.0 CA B:SER85 4.7 12.5 1.0 OG B:SER85 4.7 13.9 1.0 HE1 B:HIS123 4.8 27.8 1.0 H101 B:SPD401 4.8 30.5 1.0 HG B:SER85 4.9 16.7 1.0 HD2 B:TYR88 4.9 16.2 1.0 HG2 B:GLN348 4.9 19.7 1.0 CE1 B:HIS123 4.9 23.1 1.0 C B:SER87 5.0 15.0 1.0 HA B:SER85 5.0 15.0 1.0 HG B:SER87 5.0 20.2 0.6 H102 B:SPD401 5.0 30.5 1.0 NE2 B:HIS123 5.0 23.3 1.0

Chlorine binding site 5 out of 5 in the E.Coli'S Putrescine Receptor Variant Potf/D (4JDF) with Mutations E39D Y87S F88Y 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 Y87S F88Y S247D in Complex with Spermidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl408 b:16.6 occ:0.48 CL B:CL408 0.0 16.6 0.5 CL B:CL408 1.2 18.7 0.5 O B:HOH759 1.8 7.5 0.3 H B:SER87 2.6 18.0 0.6 H B:SER87 2.6 18.0 0.5 O B:HOH759 2.8 18.6 0.4 H B:PHE277 2.9 17.8 1.0 HB3 B:ALA86 2.9 17.1 1.0 H B:ALA86 3.1 16.5 1.0 HB2 B:TRP276 3.1 17.8 1.0 HA B:TRP276 3.1 18.8 1.0 O B:HOH558 3.2 21.1 1.0 HB3 B:SER85 3.2 15.9 1.0 HB3 B:SER87 3.3 20.6 0.5 HB3 B:TRP276 3.3 17.8 1.0 N B:SER87 3.4 15.0 1.0 CB B:TRP276 3.5 14.8 1.0 N B:ALA86 3.5 13.8 1.0 HB2 B:SER87 3.6 20.2 0.6 N B:PHE277 3.7 14.8 1.0 CA B:TRP276 3.7 15.7 1.0 O B:PHE277 3.7 18.4 1.0 O B:HOH759 3.7 18.2 0.4 CB B:ALA86 3.8 14.3 1.0 HB3 B:SER87 3.8 20.2 0.6 CA B:ALA86 4.0 12.0 1.0 O B:HOH750 4.0 22.6 1.0 CB B:SER87 4.1 16.8 0.6 CB B:SER87 4.1 17.2 0.5 C B:ALA86 4.1 13.5 1.0 CB B:SER85 4.2 13.3 1.0 HG B:SER87 4.2 19.5 0.5 C B:TRP276 4.3 14.6 1.0 HB2 B:ALA86 4.3 17.1 1.0 O B:HOH726 4.3 22.9 1.0 CA B:SER87 4.3 14.5 0.6 CA B:SER87 4.3 14.6 0.5 C B:SER85 4.4 14.2 1.0 NE2 B:HIS123 4.4 23.3 1.0 HB2 B:PHE277 4.4 20.8 1.0 HB1 B:ALA86 4.4 17.1 1.0 HB2 B:SER85 4.5 15.9 1.0 HB3 B:GLN348 4.5 20.9 1.0 C B:PHE277 4.6 14.0 1.0 OG B:SER87 4.6 16.2 0.5 CE1 B:HIS123 4.6 23.1 1.0 HE1 B:HIS123 4.6 27.8 1.0 CA B:PHE277 4.7 13.2 1.0 O B:ALA275 4.7 17.7 1.0 HA B:SER87 4.7 17.4 0.6 H B:GLN348 4.8 19.6 1.0 CA B:SER85 4.8 12.5 1.0 HB2 B:SER87 4.8 20.6 0.5 HA B:SER85 4.8 15.0 1.0 HA B:SER87 4.8 17.5 0.5 HD2 B:PHE277 4.9 35.9 1.0 HA B:ALA86 4.9 14.4 1.0 CG B:TRP276 5.0 16.1 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