Chlorine in PDB 6yed: E.Coli'S Putrescine Receptor Potf in Its Open Apo State

The structure of E.Coli'S Putrescine Receptor Potf in Its Open Apo State, PDB code: 6yed 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)	45.90 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.22, 53.45, 88.13, 90, 111.59, 90
R / Rfree (%)	22.8 / 27.3

The binding sites of Chlorine atom in the E.Coli'S Putrescine Receptor Potf in Its Open Apo State (pdb code 6yed). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the E.Coli'S Putrescine Receptor Potf in Its Open Apo State, PDB code: 6yed:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the E.Coli'S Putrescine Receptor Potf in Its Open Apo State


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 Potf in Its Open Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl415 b:53.0 occ:1.00 O A:HOH507 3.1 26.9 1.0 CE2 A:TRP37 3.4 30.4 1.0 CD2 A:TRP37 3.5 30.3 1.0 NE1 A:TRP37 3.7 29.8 1.0 OD2 A:ASP278 3.7 28.4 1.0 CG A:TRP37 3.8 27.3 1.0 CZ2 A:TRP37 3.9 32.1 1.0 CD1 A:TRP37 3.9 27.9 1.0 O3 A:PGE401 3.9 52.3 1.0 CE3 A:TRP37 3.9 32.3 1.0 C3 A:PGE401 4.1 53.5 1.0 O A:HOH669 4.2 52.8 1.0 CH2 A:TRP37 4.3 32.5 1.0 CZ3 A:TRP37 4.3 32.4 1.0 CZ A:TYR40 4.6 22.8 1.0 CB A:TRP37 4.6 25.0 1.0 CE2 A:TYR40 4.6 21.0 1.0 C4 A:PGE401 4.7 52.5 1.0 CG A:ASP278 4.7 27.7 1.0 CE1 A:TYR40 4.8 23.4 1.0 OH A:TYR40 4.8 23.4 1.0 C5 A:PGE401 4.9 52.2 1.0 OD1 A:ASP278 4.9 29.1 1.0 C6 A:PGE401 4.9 51.9 1.0 CD2 A:TYR40 5.0 23.6 1.0

Chlorine binding site 2 out of 3 in the E.Coli'S Putrescine Receptor Potf in Its Open Apo State


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 Potf in Its Open Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl416 b:84.9 occ:1.00 OE2 A:GLU185 3.4 28.0 1.0 NE1 A:TRP244 3.8 22.6 1.0 CG A:PHE276 3.9 26.3 1.0 CD2 A:PHE276 3.9 26.2 1.0 O A:HOH588 4.1 60.9 1.0 O1 A:EDO407 4.2 42.9 1.0 CD1 A:PHE276 4.2 26.0 1.0 CB A:PHE276 4.3 24.6 1.0 O A:HOH506 4.3 44.0 1.0 CD1 A:TRP244 4.3 20.8 1.0 CE2 A:PHE276 4.3 26.9 1.0 CE2 A:TRP244 4.3 22.4 1.0 CE A:MET274 4.3 34.4 1.0 CD A:GLU185 4.4 27.7 1.0 CE1 A:PHE276 4.5 27.1 1.0 CZ A:PHE276 4.6 28.4 1.0 OE1 A:GLU185 4.6 26.9 1.0 CZ2 A:TRP244 4.7 22.2 1.0 O A:HOH678 4.7 58.8 1.0 C1 A:EDO407 4.9 40.8 1.0

Chlorine binding site 3 out of 3 in the E.Coli'S Putrescine Receptor Potf in Its Open Apo State


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 Potf in Its Open Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl409 b:105.4 occ:1.00 O1 B:EDO408 3.3 67.1 1.0 OD2 B:ASP278 3.6 43.9 1.0 CE2 B:TRP37 3.7 58.2 1.0 CD2 B:TRP37 3.8 56.2 1.0 C1 B:EDO408 3.8 66.3 1.0 C1 B:PEG401 3.8 69.0 1.0 O2 B:PEG401 3.8 68.7 1.0 NE1 B:TRP37 4.0 58.0 1.0 CZ2 B:TRP37 4.1 58.6 1.0 CG B:TRP37 4.1 54.0 1.0 CD1 B:TRP37 4.2 55.9 1.0 C2 B:PEG401 4.2 69.1 1.0 CE3 B:TRP37 4.2 57.4 1.0 CH2 B:TRP37 4.5 58.9 1.0 CG B:ASP278 4.5 43.8 1.0 CZ3 B:TRP37 4.5 58.8 1.0 C3 B:PEG401 4.6 68.3 1.0 CZ B:TYR40 4.6 38.8 1.0 OD1 B:ASP278 4.7 43.4 1.0 C4 B:PEG401 4.7 67.9 1.0 OH B:TYR40 4.8 39.0 1.0 CE1 B:TYR40 4.8 38.2 1.0 CE2 B:TYR40 4.8 38.8 1.0 O1 B:PEG401 4.9 68.0 1.0 CB B:TRP37 4.9 50.8 1.0

P.Kroger, S.Shanmugaratnam, N.Ferruz, K.Schweimer, B.Hocker. A Comprehensive Binding Study Illustrates Ligand Recognition in the Periplasmic Binding Protein Potf. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 33406388
DOI: 10.1016/J.STR.2020.12.005