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Chlorine in PDB 4y8j: Yeast 20S Proteasome in Complex with Ac-Lll-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Lll-Ep, PDB code: 4y8j 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.190, 299.330, 144.940, 90.00, 112.97, 90.00
R / Rfree (%) 19.8 / 22.4

Other elements in 4y8j:

The structure of Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep (pdb code 4y8j). 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 Ac-Lll-Ep, PDB code: 4y8j:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4y8j

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Chlorine binding site 1 out of 5 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:30.0
occ:1.00
 OH H:TYR69 2.7 42.7 1.0
OD1 G:ASN114 3.1 47.8 1.0
NH1 G:ARG111 3.1 39.4 1.0
CD G:ARG111 3.5 41.6 1.0
CZ H:TYR69 3.6 45.1 1.0
CE2 H:TYR69 3.6 44.4 1.0
CB G:ASN114 3.7 45.4 1.0
CG G:ASN114 3.8 45.0 1.0
CZ G:ARG111 4.1 39.9 1.0
NE G:ARG111 4.3 41.3 1.0
CA G:ARG111 4.6 43.4 1.0
O G:ARG111 4.8 45.8 1.0
O G:HOH416 4.8 34.8 1.0
CG G:ARG111 4.8 41.5 1.0
CE1 H:TYR69 4.8 46.3 1.0
CB G:ARG111 4.9 42.8 1.0
OD2 A:ASP87 4.9 47.7 1.0
CD2 H:TYR69 5.0 44.9 1.0

Chlorine binding site 2 out of 5 in 4y8j

Go back to Chlorine Binding Sites List in 4y8j
Chlorine binding site 2 out of 5 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl202

b:51.2
occ:1.00
 NH2 N:ARG45 3.0 45.2 1.0
NE2 N:GLN53 3.2 42.8 1.0
NH1 N:ARG45 3.4 42.3 1.0
CG2 N:THR31 3.5 43.8 1.0
CZ N:ARG45 3.7 43.0 1.0
CD2 e:DCL4 4.0 63.4 1.0
CB N:ALA49 4.1 40.8 1.0
CD1 e:DCL4 4.1 61.9 1.0
CD N:GLN53 4.3 40.8 1.0
O H:THR119 4.5 48.2 1.0
CG N:GLN53 4.6 39.6 1.0
CG e:DCL4 4.6 63.6 1.0
OD1 H:ASP120 4.7 69.0 1.0
CA N:ALA49 4.7 41.1 1.0
OG1 N:THR20 4.8 43.5 1.0
O N:ASP32 4.9 47.8 1.0
CB a:TYR228 4.9 53.8 1.0
O N:ALA49 5.0 39.3 1.0
NE N:ARG45 5.0 42.6 1.0

Chlorine binding site 3 out of 5 in 4y8j

Go back to Chlorine Binding Sites List in 4y8j
Chlorine binding site 3 out of 5 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-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 53.0 1.0
OD1 U:ASN114 3.0 50.5 1.0
NH1 U:ARG111 3.2 46.2 1.0
CB U:ASN114 3.5 47.0 1.0
CG U:ASN114 3.6 48.2 1.0
CE2 V:TYR69 3.7 51.1 1.0
CZ V:TYR69 3.8 51.8 1.0
CD U:ARG111 3.8 43.9 1.0
CZ U:ARG111 4.3 47.0 1.0
NE U:ARG111 4.5 47.0 1.0
CA U:ARG111 4.7 44.5 1.0
OD2 O:ASP87 4.8 54.8 1.0
O U:ARG111 4.8 46.2 1.0
ND2 U:ASN114 4.8 49.9 1.0

Chlorine binding site 4 out of 5 in 4y8j

Go back to Chlorine Binding Sites List in 4y8j
Chlorine binding site 4 out of 5 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl201

b:83.1
occ:1.00
 NE2 b:GLN53 3.0 45.0 1.0
NH2 b:ARG45 3.2 42.9 1.0
CG2 b:THR31 3.5 49.5 1.0
NH1 b:ARG45 3.6 43.1 1.0
CZ b:ARG45 3.8 42.4 1.0
O V:THR119 4.2 44.9 1.0
CB b:ALA49 4.2 41.7 1.0
CD b:GLN53 4.2 44.1 1.0
CD2 h:DCL4 4.2 69.7 1.0
CD1 h:DCL4 4.4 69.5 1.0
OD1 V:ASP120 4.4 63.9 1.0
CG b:GLN53 4.5 43.1 1.0
CB M:TYR228 4.6 64.9 1.0
CA b:ALA49 4.8 41.3 1.0
CG h:DCL4 4.9 70.8 1.0
O b:ASP32 4.9 50.8 1.0
OG1 b:THR20 5.0 43.5 1.0

Chlorine binding site 5 out of 5 in 4y8j

Go back to Chlorine Binding Sites List in 4y8j
Chlorine binding site 5 out of 5 in the Yeast 20S Proteasome in Complex with Ac-Lll-Ep


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 Ac-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Cl101

b:30.0
occ:1.00
 OXT e:DCL4 2.8 60.9 1.0
O e:POL5 3.2 60.8 1.0
N N:SER129 3.3 40.5 1.0
CA N:GLY128 3.5 41.5 1.0
N N:GLY47 3.8 38.4 1.0
C N:GLY128 3.9 41.8 1.0
CB N:THR1 3.9 60.6 1.0
C e:DCL4 4.0 62.7 1.0
CB N:SER46 4.0 41.5 1.0
O N:THR1 4.1 55.0 1.0
N N:THR1 4.2 65.0 1.0
CB N:SER129 4.2 40.9 1.0
CA N:SER129 4.3 40.1 1.0
OG N:SER46 4.3 37.1 1.0
C1 e:POL5 4.3 64.2 1.0
OG N:SER129 4.3 42.6 1.0
C2 e:POL5 4.4 65.4 1.0
CA N:GLY47 4.4 37.6 1.0
OG1 N:THR1 4.4 57.3 1.0
CA N:THR1 4.5 61.3 1.0
C N:SER46 4.6 39.8 1.0
N N:GLY128 4.7 41.4 1.0
CA N:SER46 4.7 40.4 1.0
C N:THR1 4.8 58.2 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: Fri Jul 26 03:55:09 2024

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