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Chlorine in PDB 5dki: Yeast 20S Proteasome in Complex with Alkyne-Pi

Enzymatic activity of Yeast 20S Proteasome in Complex with Alkyne-Pi

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Alkyne-Pi, PDB code: 5dki 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 (°) 137.160, 298.090, 145.960, 90.00, 113.11, 90.00
R / Rfree (%) 19.9 / 21.9

Other elements in 5dki:

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

Chlorine binding site 1 out of 5 in 5dki

Go back to Chlorine Binding Sites List in 5dki
Chlorine binding site 1 out of 5 in the Yeast 20S Proteasome in Complex with Alkyne-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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:40.2
occ:1.00
 OH H:TYR69 2.8 39.4 1.0
NH1 G:ARG111 3.1 39.2 1.0
OD1 G:ASN114 3.2 43.7 1.0
CZ H:TYR69 3.7 40.1 1.0
CE2 H:TYR69 3.7 41.5 1.0
CD G:ARG111 3.8 39.5 1.0
CB G:ASN114 3.8 39.4 1.0
CG G:ASN114 3.8 41.2 1.0
CZ G:ARG111 4.1 39.3 1.0
NE G:ARG111 4.4 39.6 1.0
CA G:ARG111 4.8 39.7 1.0
O G:ARG111 4.9 40.2 1.0
CE1 H:TYR69 4.9 40.3 1.0
CD2 H:TYR69 5.0 42.1 1.0
OD2 A:ASP87 5.0 54.4 1.0

Chlorine binding site 2 out of 5 in 5dki

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Chlorine binding site 2 out of 5 in the Yeast 20S Proteasome in Complex with Alkyne-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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl303

b:30.0
occ:1.00
 N G:CYS65 3.4 47.7 1.0
NZ G:LYS89 3.7 43.5 1.0
CA G:PHE64 3.9 45.6 1.0
C G:PHE64 4.2 46.3 1.0
CB G:CYS65 4.3 51.4 1.0
CD1 G:PHE64 4.3 46.1 1.0
CA G:CYS65 4.3 48.7 1.0
CB G:PHE64 4.4 45.1 1.0
CE G:LYS89 4.5 41.9 1.0
O G:CYS65 4.5 49.5 1.0
O G:ILE63 4.6 47.3 1.0
CG G:PHE64 4.7 45.7 1.0
C G:CYS65 4.8 48.2 1.0
O N:SER68 4.8 57.0 1.0
SG G:CYS65 4.8 50.2 1.0

Chlorine binding site 3 out of 5 in 5dki

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Chlorine binding site 3 out of 5 in the Yeast 20S Proteasome in Complex with Alkyne-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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl203

b:44.5
occ:1.00
 NH2 N:ARG45 2.9 40.2 1.0
NE2 N:GLN53 3.1 32.7 1.0
NH1 N:ARG45 3.4 41.4 1.0
CZ N:ARG45 3.6 40.0 1.0
CG2 N:THR31 3.7 43.3 1.0
OD1 H:ASP120 4.2 65.3 1.0
CB N:ALA49 4.2 37.8 1.0
CD N:GLN53 4.2 32.9 1.0
C25 N:5BZ201 4.2 46.7 1.0
CG N:GLN53 4.4 33.3 1.0
O H:THR119 4.5 42.8 1.0
CB a:TYR228 4.5 42.0 1.0
C24 N:5BZ201 4.7 44.8 1.0
CD2 a:TYR228 4.8 38.1 1.0
CA N:ALA49 4.9 37.8 1.0
O N:ASP32 4.9 42.4 1.0
NE N:ARG45 4.9 39.1 1.0
CG a:TYR228 5.0 39.0 1.0
O N:ALA49 5.0 37.1 1.0
OG1 N:THR20 5.0 41.1 1.0

Chlorine binding site 4 out of 5 in 5dki

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Chlorine binding site 4 out of 5 in the Yeast 20S Proteasome in Complex with Alkyne-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 Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl301

b:40.0
occ:1.00
 NH1 U:ARG111 3.0 47.1 1.0
OH V:TYR69 3.0 44.5 1.0
OD1 U:ASN114 3.2 48.5 1.0
CD U:ARG111 3.6 43.2 1.0
CB U:ASN114 3.7 42.0 1.0
CG U:ASN114 3.8 45.4 1.0
CE2 V:TYR69 3.9 46.6 1.0
CZ V:TYR69 3.9 46.9 1.0
CZ U:ARG111 4.0 45.5 1.0
NE U:ARG111 4.3 44.8 1.0
CA U:ARG111 4.6 41.2 1.0
O U:ARG111 4.7 42.8 1.0
CG U:ARG111 4.9 41.7 1.0
OD2 O:ASP87 5.0 56.2 1.0
ND2 U:ASN114 5.0 47.1 1.0

Chlorine binding site 5 out of 5 in 5dki

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Chlorine binding site 5 out of 5 in the Yeast 20S Proteasome in Complex with Alkyne-Pi


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Yeast 20S Proteasome in Complex with Alkyne-Pi within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl202

b:56.7
occ:1.00
 NH2 b:ARG45 3.0 39.8 1.0
NE2 b:GLN53 3.0 38.7 1.0
NH1 b:ARG45 3.4 41.6 1.0
CZ b:ARG45 3.7 40.7 1.0
CG2 b:THR31 3.8 45.5 1.0
CB b:ALA49 4.1 42.2 1.0
OD1 V:ASP120 4.1 66.9 1.0
CD b:GLN53 4.1 38.0 1.0
C25 b:5BZ201 4.2 48.4 1.0
O V:THR119 4.3 43.7 1.0
CG b:GLN53 4.4 38.1 1.0
CB M:TYR228 4.5 56.9 1.0
C24 b:5BZ201 4.6 47.3 1.0
CA b:ALA49 4.8 42.6 1.0
CD2 M:TYR228 4.8 52.7 1.0
CG M:TYR228 4.9 54.0 1.0
O b:ALA49 4.9 44.2 1.0
O b:ASP32 4.9 48.2 1.0
NE b:ARG45 5.0 41.0 1.0
OG1 b:THR20 5.0 43.5 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: Fri Jul 26 06:46:41 2024

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