Chlorine in PDB 5dkj: Yeast 20S Proteasome in Complex with Octreotide-Pi

All present enzymatic activity of Yeast 20S Proteasome in Complex with Octreotide-Pi:
3.4.25.1;

The structure of Yeast 20S Proteasome in Complex with Octreotide-Pi, PDB code: 5dkj was solved by P.Beck, H.Cui, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	136.670, 299.710, 145.430, 90.00, 113.16, 90.00
R / Rfree (%)	19 / 21

The structure of Yeast 20S Proteasome in Complex with Octreotide-Pi also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Chlorine atom in the Yeast 20S Proteasome in Complex with Octreotide-Pi (pdb code 5dkj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Yeast 20S Proteasome in Complex with Octreotide-Pi, PDB code: 5dkj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Yeast 20S Proteasome in Complex with Octreotide-Pi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Yeast 20S Proteasome in Complex with Octreotide-Pi within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl302 b:45.5 occ:1.00 OH H:TYR69 2.7 45.3 1.0 NH1 G:ARG111 3.1 42.8 1.0 OD1 G:ASN114 3.3 46.3 1.0 CZ H:TYR69 3.5 45.9 1.0 CE2 H:TYR69 3.5 46.4 1.0 CD G:ARG111 3.6 42.8 1.0 CB G:ASN114 3.9 43.2 1.0 CG G:ASN114 3.9 44.6 1.0 CZ G:ARG111 4.1 43.1 1.0 NE G:ARG111 4.3 43.1 1.0 CA G:ARG111 4.6 42.7 1.0 CE1 H:TYR69 4.8 46.2 1.0 CD2 H:TYR69 4.9 47.1 1.0 O G:ARG111 4.9 42.3 1.0 CG G:ARG111 4.9 42.5 1.0 OD2 A:ASP87 5.0 57.1 1.0

Chlorine binding site 2 out of 4 in the Yeast 20S Proteasome in Complex with Octreotide-Pi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Yeast 20S Proteasome in Complex with Octreotide-Pi within 5.0Å range: probe atom residue distance (Å) B Occ N:Cl203 b:53.4 occ:1.00 NH2 N:ARG45 3.0 45.7 1.0 NE2 N:GLN53 3.1 38.2 1.0 NH1 N:ARG45 3.4 46.1 1.0 CZ N:ARG45 3.6 45.0 1.0 CG2 N:THR31 3.7 48.5 1.0 C25 N:5BY201 3.9 51.1 1.0 CB N:ALA49 4.0 43.0 1.0 CD N:GLN53 4.2 38.6 1.0 OD1 H:ASP120 4.3 69.2 1.0 CG N:GLN53 4.5 38.6 1.0 O H:THR119 4.5 47.9 1.0 C24 N:5BY201 4.6 48.8 1.0 CB a:TYR228 4.7 46.2 1.0 CA N:ALA49 4.7 43.2 1.0 C23 N:5BY201 4.9 50.2 1.0 OG1 N:THR20 4.9 45.5 1.0 O N:ASP32 4.9 47.5 1.0 NE N:ARG45 5.0 44.3 1.0 O N:ALA49 5.0 41.6 1.0

Chlorine binding site 3 out of 4 in the Yeast 20S Proteasome in Complex with Octreotide-Pi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Yeast 20S Proteasome in Complex with Octreotide-Pi within 5.0Å range: probe atom residue distance (Å) B Occ U:Cl301 b:47.2 occ:1.00 OH V:TYR69 2.9 52.6 1.0 NH1 U:ARG111 3.0 51.2 1.0 OD1 U:ASN114 3.3 49.9 1.0 CB U:ASN114 3.7 46.0 1.0 CD U:ARG111 3.7 47.2 1.0 CE2 V:TYR69 3.8 53.3 1.0 CZ V:TYR69 3.8 53.2 1.0 CG U:ASN114 3.8 48.7 1.0 CZ U:ARG111 4.0 49.5 1.0 NE U:ARG111 4.3 48.8 1.0 CA U:ARG111 4.8 45.0 1.0 O U:ARG111 4.8 48.3 1.0 ND2 U:ASN114 5.0 50.1 1.0 OD2 O:ASP87 5.0 61.9 1.0

Chlorine binding site 4 out of 4 in the Yeast 20S Proteasome in Complex with Octreotide-Pi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Yeast 20S Proteasome in Complex with Octreotide-Pi within 5.0Å range: probe atom residue distance (Å) B Occ b:Cl202 b:65.5 occ:1.00 NE2 b:GLN53 3.0 43.9 1.0 NH2 b:ARG45 3.1 45.0 1.0 NH1 b:ARG45 3.4 46.4 1.0 CZ b:ARG45 3.7 45.3 1.0 CG2 b:THR31 3.7 50.6 1.0 CB b:ALA49 4.0 47.6 1.0 CD b:GLN53 4.1 43.5 1.0 OD1 V:ASP120 4.2 66.9 1.0 C25 b:5BY201 4.2 53.4 1.0 O V:THR119 4.4 46.4 1.0 CG b:GLN53 4.4 43.1 1.0 C24 b:5BY201 4.5 51.8 1.0 CB M:TYR228 4.6 62.6 1.0 CA b:ALA49 4.8 47.8 1.0 O b:ALA49 4.9 45.2 1.0 CD2 M:TYR228 5.0 57.4 1.0 C23 b:5BY201 5.0 52.8 1.0 O b:ASP32 5.0 52.1 1.0 OG1 b:THR20 5.0 50.6 1.0

P.Beck, H.Cui, J.D.Hegemann, M.A.Marahiel, A.Kruger, M.Groll. Targeted Delivery of Proteasome Inhibitors to Somatostatin-Receptor-Expressing Cancer Cells By Octreotide Conjugation. Chemmedchem V. 10 1969 2015.
ISSN: ESSN 1860-7187
PubMed: 26471124
DOI: 10.1002/CMDC.201500449