Atomistry » Chlorine » PDB 5dif-5dsx » 5dkj
Atomistry »
  Chlorine »
    PDB 5dif-5dsx »
      5dkj »

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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5dkj:

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

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

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 5dkj

Go back to Chlorine Binding Sites List in 5dkj
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 5dkj

Go back to Chlorine Binding Sites List in 5dkj
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 5dkj

Go back to Chlorine Binding Sites List in 5dkj
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 5dkj

Go back to Chlorine Binding Sites List in 5dkj
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

Reference:

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
Page generated: Sat Dec 12 11:39:06 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy