Chlorine in PDB 4y8k: Yeast 20S Proteasome in Complex with H-Apll-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with H-Apll-Ep:
3.4.25.1;

The structure of Yeast 20S Proteasome in Complex with H-Apll-Ep, PDB code: 4y8k was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	136.560, 300.720, 145.430, 90.00, 113.33, 90.00
R / Rfree (%)	20.9 / 23.6

The structure of Yeast 20S Proteasome in Complex with H-Apll-Ep also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Chlorine atom in the Yeast 20S Proteasome in Complex with H-Apll-Ep (pdb code 4y8k). 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 H-Apll-Ep, PDB code: 4y8k:
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 H-Apll-Ep


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 H-Apll-Ep within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl302 b:30.0 occ:1.00 OH H:TYR69 2.6 43.5 1.0 OD1 G:ASN114 3.0 43.4 1.0 NH1 G:ARG111 3.2 39.3 1.0 CZ H:TYR69 3.5 44.1 1.0 CE2 H:TYR69 3.6 44.0 1.0 CB G:ASN114 3.7 42.0 1.0 CG G:ASN114 3.7 42.2 1.0 CD G:ARG111 3.7 37.7 1.0 CZ G:ARG111 4.2 38.6 1.0 NE G:ARG111 4.4 39.3 1.0 CA G:ARG111 4.7 38.6 1.0 CE1 H:TYR69 4.8 44.4 1.0 O G:ARG111 4.8 39.2 1.0 OD2 A:ASP87 4.9 48.6 1.0 ND2 G:ASN114 4.9 43.0 1.0 CD2 H:TYR69 4.9 43.8 1.0 O G:HOH427 5.0 49.1 1.0

Chlorine binding site 2 out of 4 in the Yeast 20S Proteasome in Complex with H-Apll-Ep


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 H-Apll-Ep within 5.0Å range: probe atom residue distance (Å) B Occ N:Cl202 b:43.1 occ:1.00 NH2 N:ARG45 3.0 36.3 1.0 NE2 N:GLN53 3.1 33.7 1.0 NH1 N:ARG45 3.3 34.6 1.0 CG2 N:THR31 3.6 36.0 1.0 CZ N:ARG45 3.6 35.6 1.0 CD1 d:DCL4 4.1 58.5 1.0 CB N:ALA49 4.1 33.9 1.0 CD2 d:DCL4 4.2 57.3 1.0 CD N:GLN53 4.2 34.8 1.0 CG N:GLN53 4.4 35.1 1.0 OD1 H:ASP120 4.6 61.2 1.0 O H:THR119 4.6 44.5 1.0 O N:ASP32 4.7 39.4 1.0 CG d:DCL4 4.7 58.4 1.0 CA N:ALA49 4.7 34.8 1.0 CB a:TYR228 4.7 49.2 1.0 CD2 a:TYR228 4.8 44.7 1.0 O N:ALA49 4.9 35.4 1.0 NE N:ARG45 4.9 36.0 1.0 OG1 N:THR20 5.0 36.0 1.0

Chlorine binding site 3 out of 4 in the Yeast 20S Proteasome in Complex with H-Apll-Ep


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 H-Apll-Ep within 5.0Å range: probe atom residue distance (Å) B Occ U:Cl301 b:30.0 occ:1.00 OH V:TYR69 2.9 45.4 1.0 NH1 U:ARG111 3.0 48.6 1.0 OD1 U:ASN114 3.2 52.8 1.0 CB U:ASN114 3.6 44.0 1.0 CG U:ASN114 3.7 46.0 1.0 CD U:ARG111 3.7 44.5 1.0 CZ V:TYR69 3.8 47.2 1.0 CE2 V:TYR69 3.8 47.6 1.0 CZ U:ARG111 4.1 46.9 1.0 NE U:ARG111 4.3 45.9 1.0 CA U:ARG111 4.8 43.9 1.0 O U:ARG111 4.8 44.8 1.0 ND2 U:ASN114 4.9 44.9 1.0 OD2 O:ASP87 5.0 56.6 1.0

Chlorine binding site 4 out of 4 in the Yeast 20S Proteasome in Complex with H-Apll-Ep


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 H-Apll-Ep within 5.0Å range: probe atom residue distance (Å) B Occ b:Cl201 b:63.7 occ:1.00 NH2 b:ARG45 2.9 38.0 1.0 NH1 b:ARG45 3.0 37.2 1.0 NE2 b:GLN53 3.3 39.9 1.0 CZ b:ARG45 3.4 36.4 1.0 CD1 f:DCL4 3.7 61.7 1.0 CG2 b:THR31 3.7 42.2 1.0 CD2 f:DCL4 3.8 62.4 1.0 CB b:ALA49 4.0 35.2 1.0 CG f:DCL4 4.3 62.4 1.0 CD b:GLN53 4.4 38.5 1.0 CG b:GLN53 4.5 37.4 1.0 CA b:ALA49 4.5 35.1 1.0 O b:ASP32 4.7 41.0 1.0 NE b:ARG45 4.7 36.9 1.0 O b:ALA49 4.8 33.4 1.0 OD1 V:ASP120 4.9 57.2 1.0 O V:THR119 4.9 43.8 1.0 OG1 b:THR20 4.9 36.7 1.0

E.M.Huber, G.De Bruin, W.Heinemeyer, G.Paniagua Soriano, H.S.Overkleeft, M.Groll. Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors. J.Am.Chem.Soc. V. 137 7835 2015.
ISSN: ESSN 1520-5126
PubMed: 26020686
DOI: 10.1021/JACS.5B03688