Chlorine in PDB 5t88: Prolyl Oligopeptidase From Pyrococcus Furiosus

The structure of Prolyl Oligopeptidase From Pyrococcus Furiosus, PDB code: 5t88 was solved by K.Ellis-Guardiola, J.Lewis, N.Sukumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.09 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.535, 176.757, 57.901, 90.00, 106.03, 90.00
R / Rfree (%)	19.3 / 24.7

The binding sites of Chlorine atom in the Prolyl Oligopeptidase From Pyrococcus Furiosus (pdb code 5t88). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Prolyl Oligopeptidase From Pyrococcus Furiosus, PDB code: 5t88:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Prolyl Oligopeptidase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Prolyl Oligopeptidase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl701 b:67.5 occ:1.00 HH A:TYR555 2.1 24.2 1.0 HH11 A:ARG476 2.5 33.4 1.0 HH12 A:ARG600 2.5 35.7 1.0 HH22 A:ARG600 2.5 29.7 1.0 HD2 A:ARG476 2.7 28.1 1.0 OH A:TYR555 2.9 20.2 1.0 HE2 A:TYR555 3.1 22.4 1.0 HZ2 A:TRP474 3.1 26.8 1.0 NH1 A:ARG600 3.3 29.8 1.0 NH1 A:ARG476 3.3 27.8 1.0 NH2 A:ARG600 3.3 24.7 1.0 HD11 A:LEU607 3.6 21.8 1.0 CD A:ARG476 3.6 23.4 1.0 HH12 A:ARG476 3.6 33.4 1.0 CE2 A:TYR555 3.7 18.6 1.0 HD21 A:LEU604 3.8 31.3 1.0 CZ A:ARG600 3.8 31.6 1.0 CZ A:TYR555 3.8 19.1 1.0 HE1 A:TRP474 3.9 19.8 1.0 HB2 A:ARG476 3.9 28.7 1.0 HH11 A:ARG600 4.0 35.7 1.0 HD3 A:ARG476 4.0 28.1 1.0 HD23 A:LEU604 4.0 31.3 1.0 HH21 A:ARG600 4.0 29.7 1.0 CZ2 A:TRP474 4.0 22.4 1.0 O A:HOH1201 4.2 41.4 1.0 HG3 A:ARG476 4.2 25.3 1.0 CD1 A:LEU607 4.3 18.1 1.0 HD12 A:LEU607 4.3 21.8 1.0 CZ A:ARG476 4.3 23.5 1.0 CD2 A:LEU604 4.3 26.1 1.0 CG A:ARG476 4.4 21.1 1.0 HD13 A:LEU607 4.4 21.8 1.0 NE A:ARG476 4.4 24.2 1.0 NE1 A:TRP474 4.5 16.5 1.0 O A:HOH1062 4.5 37.5 1.0 CB A:ARG476 4.6 23.9 1.0 CE2 A:TRP474 4.7 16.9 1.0 HD22 A:LEU604 4.8 31.3 1.0 HE1 A:TYR501 4.8 25.5 1.0 HB3 A:ARG476 4.9 28.7 1.0 HD1 A:TYR501 5.0 25.2 1.0

Chlorine binding site 2 out of 4 in the Prolyl Oligopeptidase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Prolyl Oligopeptidase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl702 b:46.0 occ:1.00 HH12 A:ARG476 2.2 33.4 1.0 HH22 A:ARG476 2.4 29.7 1.0 OE1 A:GLU603 2.8 25.9 1.0 HE2 A:HIS592 2.9 85.0 1.0 NH1 A:ARG476 3.0 27.8 1.0 HH11 A:ARG600 3.1 35.7 1.0 O A:HOH835 3.1 44.3 1.0 NH2 A:ARG476 3.2 24.7 1.0 HD2 A:HIS592 3.2 82.3 1.0 HH A:TYR501 3.2 25.9 1.0 HD3 A:ARG600 3.3 32.5 1.0 NE2 A:HIS592 3.4 70.8 1.0 OH A:TYR501 3.4 21.6 1.0 NH1 A:ARG600 3.4 29.8 1.0 CD2 A:HIS592 3.6 68.5 1.0 CZ A:ARG476 3.6 23.5 1.0 HH12 A:ARG600 3.7 35.7 1.0 HH11 A:ARG476 3.7 33.4 1.0 CD A:GLU603 3.8 27.9 1.0 CZ A:TYR501 3.9 31.0 1.0 HH21 A:ARG476 3.9 29.7 1.0 HE1 A:TYR501 4.0 25.5 1.0 OE2 A:GLU603 4.0 26.5 1.0 HD2 A:ARG600 4.0 32.5 1.0 CD A:ARG600 4.0 27.1 1.0 HE2 A:MET593 4.0 42.5 0.0 HG2 A:MET593 4.1 59.6 0.0 CZ A:ARG600 4.1 31.6 1.0 CE1 A:TYR501 4.1 21.2 1.0 O A:HOH1085 4.2 50.6 1.0 NE A:ARG600 4.4 28.4 1.0 CE1 A:HIS592 4.5 62.1 1.0 CE2 A:TYR501 4.7 28.2 1.0 CG A:HIS592 4.8 72.1 1.0 O A:HOH1002 4.9 35.8 1.0 NE A:ARG476 4.9 24.2 1.0 HE2 A:TYR501 4.9 33.9 1.0 CE A:MET593 5.0 35.4 0.0 HE1 A:HIS592 5.0 74.5 1.0

Chlorine binding site 3 out of 4 in the Prolyl Oligopeptidase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Prolyl Oligopeptidase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl701 b:19.8 occ:1.00 HH12 B:ARG600 2.3 28.1 1.0 HH B:TYR555 2.4 22.9 1.0 HH22 B:ARG600 2.5 36.3 1.0 HH11 B:ARG476 2.6 27.4 1.0 HD2 B:ARG476 2.8 34.0 1.0 NH1 B:ARG600 3.1 23.5 1.0 HZ2 B:TRP474 3.1 24.9 1.0 OH B:TYR555 3.2 19.1 1.0 HE2 B:TYR555 3.2 20.2 1.0 NH2 B:ARG600 3.2 30.2 1.0 NH1 B:ARG476 3.4 22.9 1.0 HD21 B:LEU604 3.5 25.2 1.0 CZ B:ARG600 3.6 29.1 1.0 HD11 B:LEU607 3.6 28.9 1.0 HD23 B:LEU604 3.7 25.2 1.0 HH11 B:ARG600 3.7 28.1 1.0 CD B:ARG476 3.8 28.3 1.0 HH12 B:ARG476 3.8 27.4 1.0 CE2 B:TYR555 3.9 16.9 1.0 HH21 B:ARG600 3.9 36.3 1.0 CZ2 B:TRP474 4.0 20.7 1.0 CZ B:TYR555 4.0 16.7 1.0 HD3 B:ARG476 4.0 34.0 1.0 CD2 B:LEU604 4.1 21.0 1.0 HE1 B:TRP474 4.1 26.2 1.0 HB2 B:ARG476 4.2 22.3 1.0 HD12 B:LEU607 4.3 28.9 1.0 CD1 B:LEU607 4.3 24.1 1.0 HG3 B:ARG476 4.4 36.1 1.0 O B:HOH1097 4.4 44.8 1.0 CZ B:ARG476 4.4 28.6 1.0 HD22 B:LEU604 4.5 25.2 1.0 CG B:ARG476 4.6 30.1 1.0 NE B:ARG476 4.6 21.5 1.0 HD13 B:LEU607 4.6 28.9 1.0 NE1 B:TRP474 4.7 21.8 1.0 CE2 B:TRP474 4.7 24.5 1.0 CB B:ARG476 4.8 18.6 1.0 HE1 B:TYR501 4.8 23.9 1.0 HH2 B:TRP474 4.9 30.4 1.0 NE B:ARG600 4.9 20.4 1.0 CH2 B:TRP474 5.0 25.3 1.0 HD1 B:TYR501 5.0 30.0 1.0

Chlorine binding site 4 out of 4 in the Prolyl Oligopeptidase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Prolyl Oligopeptidase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl702 b:45.4 occ:1.00 HH12 B:ARG476 2.1 27.4 1.0 HH22 B:ARG476 2.7 33.6 1.0 O B:HOH1068 2.7 39.4 1.0 HG2 B:MET593 2.8 72.2 1.0 OE1 B:GLU603 2.9 24.4 1.0 NH1 B:ARG476 3.0 22.9 1.0 HH B:TYR501 3.0 24.3 1.0 HH11 B:ARG600 3.1 28.1 1.0 HD3 B:ARG600 3.2 26.5 1.0 OH B:TYR501 3.3 20.2 1.0 NH2 B:ARG476 3.4 28.0 1.0 NH1 B:ARG600 3.4 23.5 1.0 HH11 B:ARG476 3.6 27.4 1.0 HE1 B:TYR501 3.6 23.9 1.0 CZ B:ARG476 3.6 28.6 1.0 HE3 B:MET593 3.7 62.1 1.0 CZ B:TYR501 3.7 24.1 1.0 HH12 B:ARG600 3.7 28.1 1.0 CG B:MET593 3.8 60.1 1.0 CE1 B:TYR501 3.8 19.9 1.0 CD B:GLU603 3.8 24.1 1.0 CD B:ARG600 3.9 22.1 1.0 HD2 B:ARG600 4.0 26.5 1.0 CZ B:ARG600 4.0 29.1 1.0 OE2 B:GLU603 4.0 19.1 1.0 NE B:ARG600 4.2 20.4 1.0 HH21 B:ARG476 4.2 33.6 1.0 HG3 B:MET593 4.3 72.2 1.0 HB3 B:MET593 4.4 61.3 1.0 HB2 B:MET593 4.4 61.3 1.0 CE B:MET593 4.5 51.8 1.0 CB B:MET593 4.5 51.1 1.0 CE2 B:TYR501 4.6 25.1 1.0 SD B:MET593 4.7 69.4 1.0 HE B:ARG600 4.8 24.5 1.0 CD1 B:TYR501 4.8 25.0 1.0 HE2 B:MET593 4.8 62.1 1.0 O B:HOH1149 4.8 46.4 1.0 HE2 B:TYR501 4.9 30.1 1.0 NH2 B:ARG600 4.9 30.2 1.0 NE B:ARG476 5.0 21.5 1.0

K.Ellis-Guardiola, H.Rui, R.L.Beckner, P.Srivastava, N.Sukumar, B.Roux, J.C.Lewis. Crystal Structure and Conformational Dynamics of Pyrococcus Furiosus Prolyl Oligopeptidase. Biochemistry V. 58 1616 2019.
ISSN: ISSN 1520-4995
PubMed: 30786206
DOI: 10.1021/ACS.BIOCHEM.9B00031