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Chlorine in PDB 4y8l: Yeast 20S Proteasome in Complex with Ac-Apll-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Apll-Ep, PDB code: 4y8l 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 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.610, 299.760, 144.950, 90.00, 113.06, 90.00
R / Rfree (%) 20.8 / 22.4

Other elements in 4y8l:

The structure of Yeast 20S Proteasome in Complex with Ac-Apll-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-Apll-Ep (pdb code 4y8l). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep, PDB code: 4y8l:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4y8l

Go back to Chlorine Binding Sites List in 4y8l
Chlorine binding site 1 out of 6 in the Yeast 20S Proteasome in Complex with Ac-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 Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:30.0
occ:1.00
 OH H:TYR69 2.8 45.1 1.0
OD1 G:ASN114 3.0 42.4 1.0
NH1 G:ARG111 3.2 37.4 1.0
CZ H:TYR69 3.6 45.2 1.0
CE2 H:TYR69 3.7 45.8 1.0
CG G:ASN114 3.7 40.2 1.0
CB G:ASN114 3.7 38.9 1.0
CD G:ARG111 3.8 35.7 1.0
CZ G:ARG111 4.2 37.2 1.0
NE G:ARG111 4.5 36.6 1.0
O G:HOH439 4.6 49.1 1.0
CA G:ARG111 4.8 36.5 1.0
ND2 G:ASN114 4.9 40.7 1.0
OD2 A:ASP87 4.9 45.7 1.0
CE1 H:TYR69 4.9 45.7 1.0
O G:ARG111 4.9 37.0 1.0
CD2 H:TYR69 5.0 46.5 1.0

Chlorine binding site 2 out of 6 in 4y8l

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Chlorine binding site 2 out of 6 in the Yeast 20S Proteasome in Complex with Ac-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 Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl202

b:51.3
occ:1.00
 NH2 N:ARG45 2.9 37.3 1.0
O N:HOH1108 3.0 38.7 1.0
NH1 N:ARG45 3.1 36.6 1.0
NE2 N:GLN53 3.1 35.1 1.0
O H:HOH317 3.2 43.6 1.0
CZ N:ARG45 3.4 36.5 1.0
CG2 N:THR31 3.7 36.8 1.0
C27 d:05W5 3.9 63.0 1.0
C28 d:05W5 4.0 61.7 1.0
CB N:ALA49 4.1 34.0 1.0
CD N:GLN53 4.2 34.4 1.0
CG N:GLN53 4.4 33.2 1.0
C26 d:05W5 4.4 62.1 1.0
CA N:ALA49 4.6 34.2 1.0
NE N:ARG45 4.8 35.5 1.0
O N:ALA49 4.8 35.7 1.0
O H:THR119 4.8 42.3 1.0
O N:ASP32 4.8 40.3 1.0
OG1 N:THR20 4.8 37.5 1.0
OD1 H:ASP120 4.9 54.9 1.0
CB a:TYR228 4.9 49.3 1.0

Chlorine binding site 3 out of 6 in 4y8l

Go back to Chlorine Binding Sites List in 4y8l
Chlorine binding site 3 out of 6 in the Yeast 20S Proteasome in Complex with Ac-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 Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl301

b:30.0
occ:1.00
 OH V:TYR69 3.0 45.7 1.0
OD1 U:ASN114 3.0 49.6 1.0
NH1 U:ARG111 3.1 43.6 1.0
CB U:ASN114 3.7 41.6 1.0
CG U:ASN114 3.7 43.5 1.0
CD U:ARG111 3.7 39.4 1.0
CE2 V:TYR69 3.8 46.5 1.0
CZ V:TYR69 3.8 46.6 1.0
CZ U:ARG111 4.1 42.5 1.0
NE U:ARG111 4.4 41.2 1.0
CA U:ARG111 4.7 39.1 1.0
O U:ARG111 4.8 41.1 1.0
OD2 O:ASP87 4.9 51.0 1.0
ND2 U:ASN114 4.9 43.9 1.0
CG U:ARG111 5.0 38.6 1.0

Chlorine binding site 4 out of 6 in 4y8l

Go back to Chlorine Binding Sites List in 4y8l
Chlorine binding site 4 out of 6 in the Yeast 20S Proteasome in Complex with Ac-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 Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl201

b:69.2
occ:1.00
 NE2 b:GLN53 2.9 38.4 1.0
NH2 b:ARG45 3.0 35.4 1.0
NH1 b:ARG45 3.2 35.4 1.0
CZ b:ARG45 3.5 35.0 1.0
CG2 b:THR31 3.8 41.5 1.0
CB b:ALA49 4.0 34.5 1.0
CD b:GLN53 4.0 37.1 1.0
C27 f:05W5 4.1 67.1 1.0
C28 f:05W5 4.2 68.2 1.0
CG b:GLN53 4.3 36.2 1.0
O V:THR119 4.5 43.7 1.0
CA b:ALA49 4.6 34.7 1.0
C26 f:05W5 4.6 67.6 1.0
O b:ALA49 4.7 35.7 1.0
OD1 V:ASP120 4.7 52.9 1.0
CB M:TYR228 4.8 62.0 1.0
NE b:ARG45 4.9 34.7 1.0
CD2 M:TYR228 4.9 58.5 1.0
O b:ASP32 4.9 41.8 1.0

Chlorine binding site 5 out of 6 in 4y8l

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Chlorine binding site 5 out of 6 in the Yeast 20S Proteasome in Complex with Ac-Apll-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-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Cl101

b:30.0
occ:1.00
 O4 d:05W5 3.0 52.6 1.0
N N:SER129 3.3 31.9 1.0
C24 d:05W5 3.5 65.4 1.0
CA N:GLY128 3.6 32.4 1.0
O N:HOH1145 3.6 55.1 1.0
N N:GLY47 3.8 30.8 1.0
CB N:THR1 3.9 59.6 1.0
C N:GLY128 3.9 32.4 1.0
C17 d:05W5 4.0 60.1 1.0
CB N:SER46 4.0 32.7 1.0
C22 d:05W5 4.1 64.5 1.0
O7 d:05W5 4.1 64.7 1.0
N N:THR1 4.2 63.1 1.0
CB N:SER129 4.3 32.6 1.0
OG N:SER46 4.3 34.0 1.0
O N:THR1 4.3 44.4 1.0
CA N:SER129 4.3 32.2 1.0
OG1 N:THR1 4.4 57.0 1.0
CA N:GLY47 4.4 30.6 1.0
OG N:SER129 4.4 34.4 1.0
CA N:THR1 4.5 57.9 1.0
O N:HOH1121 4.5 35.9 1.0
C N:SER46 4.6 31.1 1.0
CA N:SER46 4.7 32.2 1.0
N N:GLY128 4.7 33.0 1.0
C N:THR1 4.8 48.4 1.0
CG2 N:THR1 4.9 60.7 1.0

Chlorine binding site 6 out of 6 in 4y8l

Go back to Chlorine Binding Sites List in 4y8l
Chlorine binding site 6 out of 6 in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Yeast 20S Proteasome in Complex with Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Cl101

b:30.0
occ:1.00
 O4 f:05W5 3.1 55.1 1.0
O7 f:05W5 3.1 68.0 1.0
N b:SER129 3.3 34.2 1.0
CA b:GLY128 3.5 32.9 1.0
C b:GLY128 3.8 33.4 1.0
N b:GLY47 3.9 30.8 1.0
CB b:THR1 4.0 60.5 1.0
CB b:SER46 4.1 32.5 1.0
C24 f:05W5 4.1 70.4 1.0
C17 f:05W5 4.2 63.2 1.0
N b:THR1 4.2 66.7 1.0
O a:HOH343 4.2 56.1 1.0
CB b:SER129 4.2 36.2 1.0
CA b:SER129 4.3 35.7 1.0
O b:THR1 4.3 46.8 1.0
OG b:SER46 4.3 33.4 1.0
C22 f:05W5 4.3 68.5 1.0
OG b:SER129 4.4 37.5 1.0
CA b:GLY47 4.4 30.7 1.0
CA b:THR1 4.5 60.4 1.0
OG1 b:THR1 4.6 56.7 1.0
C b:SER46 4.6 31.3 1.0
N b:GLY128 4.7 33.3 1.0
CA b:SER46 4.7 32.0 1.0
C b:THR1 4.8 52.1 1.0
CG2 b:THR1 5.0 60.2 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 03:55:11 2024

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