Chlorine in PDB 4y8h: Yeast 20S Proteasome in Complex with N3-Apal-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with N3-Apal-Ep:
3.4.25.1;

The structure of Yeast 20S Proteasome in Complex with N3-Apal-Ep, PDB code: 4y8h 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 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	136.320, 300.790, 145.460, 90.00, 113.64, 90.00
R / Rfree (%)	20.1 / 21.4

The structure of Yeast 20S Proteasome in Complex with N3-Apal-Ep also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Chlorine atom in the Yeast 20S Proteasome in Complex with N3-Apal-Ep (pdb code 4y8h). 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 N3-Apal-Ep, PDB code: 4y8h:
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 N3-Apal-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 N3-Apal-Ep within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl302 b:30.0 occ:1.00 OH H:TYR69 2.9 37.0 1.0 NH1 G:ARG111 3.0 36.0 1.0 OD1 G:ASN114 3.2 40.0 1.0 CD G:ARG111 3.6 33.9 1.0 CE2 H:TYR69 3.7 34.5 1.0 CZ H:TYR69 3.8 34.9 1.0 CB G:ASN114 3.9 36.8 1.0 CG G:ASN114 4.0 38.0 1.0 CZ G:ARG111 4.1 36.0 1.0 NE G:ARG111 4.3 34.7 1.0 CA G:ARG111 4.8 33.5 1.0 O G:ARG111 4.9 34.4 1.0 OD2 A:ASP87 4.9 43.4 1.0 CG G:ARG111 4.9 32.6 1.0 O G:HOH428 5.0 37.5 1.0

Chlorine binding site 2 out of 4 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range: probe atom residue distance (Å) B Occ N:Cl203 b:30.0 occ:1.00 NH2 N:ARG45 3.1 32.4 1.0 NH1 N:ARG45 3.1 30.9 1.0 NE2 N:GLN53 3.2 34.7 1.0 CZ N:ARG45 3.5 30.9 1.0 CG2 N:THR31 3.6 35.1 1.0 C28 e:05W6 3.9 42.5 1.0 CB N:ALA49 4.0 26.4 1.0 C27 e:05W6 4.0 39.9 1.0 CD N:GLN53 4.2 32.4 1.0 CG N:GLN53 4.4 30.3 1.0 C26 e:05W6 4.5 40.5 1.0 CA N:ALA49 4.5 29.0 1.0 O N:ALA49 4.7 30.9 1.0 OG1 N:THR20 4.7 35.1 1.0 OD1 H:ASP120 4.7 52.4 1.0 O H:THR119 4.8 35.5 1.0 NE N:ARG45 4.9 29.7 1.0 O N:HOH319 5.0 42.7 1.0 O N:ASP32 5.0 36.5 1.0

Chlorine binding site 3 out of 4 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range: probe atom residue distance (Å) B Occ U:Cl301 b:30.0 occ:1.00 OH V:TYR69 2.8 43.2 1.0 OD1 U:ASN114 3.0 42.6 1.0 NH1 U:ARG111 3.1 46.8 1.0 CB U:ASN114 3.6 40.6 1.0 CG U:ASN114 3.7 40.8 1.0 CZ V:TYR69 3.7 41.0 1.0 CE2 V:TYR69 3.7 40.0 1.0 CD U:ARG111 3.8 37.8 1.0 CZ U:ARG111 4.2 43.5 1.0 NE U:ARG111 4.4 41.5 1.0 CA U:ARG111 4.8 36.7 1.0 O U:ARG111 4.8 38.7 1.0 OD2 O:ASP87 4.8 51.8 1.0 ND2 U:ASN114 4.9 40.9 1.0 CE1 V:TYR69 5.0 41.0 1.0

Chlorine binding site 4 out of 4 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range: probe atom residue distance (Å) B Occ b:Cl201 b:30.0 occ:1.00 NH2 b:ARG45 3.0 32.6 1.0 NE2 b:GLN53 3.0 36.8 1.0 O b:HOH314 3.0 42.5 1.0 NH1 b:ARG45 3.1 33.3 1.0 CZ b:ARG45 3.5 32.9 1.0 CG2 b:THR31 3.7 35.3 1.0 C27 h:05W6 4.0 46.9 1.0 CB b:ALA49 4.0 37.3 1.0 CD b:GLN53 4.1 34.4 1.0 C28 h:05W6 4.1 48.9 1.0 CG b:GLN53 4.3 32.3 1.0 CA b:ALA49 4.6 38.0 1.0 C26 h:05W6 4.7 46.7 1.0 O b:ALA49 4.7 40.2 1.0 O V:THR119 4.8 38.3 1.0 NE b:ARG45 4.8 32.1 1.0 OG1 b:THR20 4.9 34.2 1.0 CB M:TYR228 4.9 40.7 1.0 OD1 V:ASP120 4.9 56.6 1.0 O b:ASP32 4.9 38.7 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