Atomistry » Chlorine » PDB 4y0c-4y89 » 4y6z
Atomistry »
  Chlorine »
    PDB 4y0c-4y89 »
      4y6z »

Chlorine in PDB 4y6z: Yeast 20S Proteasome in Complex with Ac-Pal-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Pal-Ep

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Pal-Ep, PDB code: 4y6z was solved by M.Groll, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.580, 301.570, 146.350, 90.00, 113.25, 90.00
R / Rfree (%) 19.1 / 21.6

Other elements in 4y6z:

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

Magnesium (Mg) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Yeast 20S Proteasome in Complex with Ac-Pal-Ep (pdb code 4y6z). 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 Ac-Pal-Ep, PDB code: 4y6z:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4y6z

Go back to Chlorine Binding Sites List in 4y6z
Chlorine binding site 1 out of 4 in the Yeast 20S Proteasome in Complex with Ac-Pal-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 Ac-Pal-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 43.3 1.0
OD1 G:ASN114 2.9 47.6 1.0
NH1 G:ARG111 3.1 41.3 1.0
CB G:ASN114 3.6 44.1 1.0
CD G:ARG111 3.6 40.2 1.0
CG G:ASN114 3.6 43.8 1.0
CZ H:TYR69 3.8 45.6 1.0
CE2 H:TYR69 3.8 45.2 1.0
CZ G:ARG111 4.2 40.8 1.0
NE G:ARG111 4.3 40.7 1.0
CA G:ARG111 4.6 42.4 1.0
O G:ARG111 4.8 44.9 1.0
O G:HOH422 4.8 45.7 1.0
CG G:ARG111 4.9 40.1 1.0
ND2 G:ASN114 4.9 42.7 1.0
OD2 A:ASP87 4.9 51.1 1.0

Chlorine binding site 2 out of 4 in 4y6z

Go back to Chlorine Binding Sites List in 4y6z
Chlorine binding site 2 out of 4 in the Yeast 20S Proteasome in Complex with Ac-Pal-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 Ac-Pal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl202

b:30.0
occ:1.00
NH2 N:ARG45 2.9 42.8 1.0
NE2 N:GLN53 3.1 39.0 1.0
NH1 N:ARG45 3.1 42.1 1.0
CZ N:ARG45 3.5 41.5 1.0
CG2 N:THR31 3.8 41.8 1.0
CB N:ALA49 4.0 40.6 1.0
CD1 e:DCL4 4.1 72.0 1.0
CD2 e:DCL4 4.2 72.6 1.0
CD N:GLN53 4.2 38.2 1.0
CG N:GLN53 4.4 37.9 1.0
CA N:ALA49 4.6 40.6 1.0
CG e:DCL4 4.6 73.5 1.0
O H:THR119 4.6 44.9 1.0
O N:ALA49 4.7 40.4 1.0
NE N:ARG45 4.8 40.1 1.0
CB a:TYR228 4.9 44.9 1.0
O N:ASP32 5.0 40.9 1.0
OD1 H:ASP120 5.0 65.0 1.0

Chlorine binding site 3 out of 4 in 4y6z

Go back to Chlorine Binding Sites List in 4y6z
Chlorine binding site 3 out of 4 in the Yeast 20S Proteasome in Complex with Ac-Pal-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 Ac-Pal-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 48.1 1.0
OD1 U:ASN114 2.9 50.6 1.0
NH1 U:ARG111 3.2 50.6 1.0
CB U:ASN114 3.5 48.4 1.0
CG U:ASN114 3.6 48.3 1.0
CD U:ARG111 3.7 46.0 1.0
CZ V:TYR69 3.8 51.6 1.0
CE2 V:TYR69 3.8 51.3 1.0
CZ U:ARG111 4.2 49.2 1.0
NE U:ARG111 4.4 49.4 1.0
CA U:ARG111 4.6 45.9 1.0
O U:ARG111 4.7 49.6 1.0
ND2 U:ASN114 4.8 49.6 1.0
OD2 O:ASP87 4.9 60.8 1.0
CG U:ARG111 4.9 44.5 1.0

Chlorine binding site 4 out of 4 in 4y6z

Go back to Chlorine Binding Sites List in 4y6z
Chlorine binding site 4 out of 4 in the Yeast 20S Proteasome in Complex with Ac-Pal-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 Ac-Pal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl201

b:30.0
occ:1.00
NH2 b:ARG45 2.9 41.9 1.0
NH1 b:ARG45 3.0 44.1 1.0
NE2 b:GLN53 3.1 43.6 1.0
CZ b:ARG45 3.4 42.2 1.0
CD1 h:DCL4 3.8 80.7 1.0
CG2 b:THR31 3.9 47.1 1.0
CD2 h:DCL4 3.9 81.1 1.0
CB b:ALA49 4.0 41.6 1.0
CD b:GLN53 4.2 43.1 1.0
CG b:GLN53 4.4 42.7 1.0
CG h:DCL4 4.4 81.3 1.0
CA b:ALA49 4.5 41.8 1.0
O b:ALA49 4.6 42.9 1.0
NE b:ARG45 4.7 41.3 1.0
O V:THR119 4.8 45.1 1.0
C b:ALA49 5.0 41.8 1.0
CB M:TYR228 5.0 50.2 1.0
O b:ASP32 5.0 46.8 1.0

Reference:

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
Page generated: Sat Dec 12 11:22:24 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