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Chlorine in PDB 5l66: Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib

Enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib

All present enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib, PDB code: 5l66 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.310, 301.130, 145.750, 90.00, 112.92, 90.00
R / Rfree (%) 18.2 / 21

Other elements in 5l66:

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib (pdb code 5l66). 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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib, PDB code: 5l66:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5l66

Go back to Chlorine Binding Sites List in 5l66
Chlorine binding site 1 out of 4 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:41.5
occ:1.00
 OH H:TYR69 2.8 43.0 1.0
NH1 G:ARG111 3.0 42.6 1.0
OD1 G:ASN114 3.2 50.1 1.0
CD G:ARG111 3.6 41.9 1.0
CZ H:TYR69 3.7 43.2 1.0
CE2 H:TYR69 3.7 42.3 1.0
CB G:ASN114 3.8 43.1 1.0
CG G:ASN114 3.8 44.8 1.0
CZ G:ARG111 4.1 42.2 1.0
NE G:ARG111 4.3 41.7 1.0
CA G:ARG111 4.7 42.5 1.0
O G:ARG111 4.8 45.9 1.0
CG G:ARG111 4.9 41.5 1.0
CE1 H:TYR69 4.9 43.6 1.0
OD2 A:ASP87 5.0 55.2 1.0
CD2 H:TYR69 5.0 41.3 1.0

Chlorine binding site 2 out of 4 in 5l66

Go back to Chlorine Binding Sites List in 5l66
Chlorine binding site 2 out of 4 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl203

b:51.0
occ:1.00
 NH2 N:ARG45 3.0 41.5 1.0
NE2 N:GLN53 3.2 38.1 1.0
NH1 N:ARG45 3.4 41.4 1.0
CG2 N:THR31 3.6 46.4 1.0
CZ N:ARG45 3.6 41.3 1.0
C25 N:BO2201 3.9 34.2 1.0
CB N:ALA49 4.1 38.5 1.0
CD N:GLN53 4.3 37.6 1.0
C24 N:BO2201 4.3 33.5 1.0
OD1 H:ASP120 4.4 72.6 1.0
CG N:GLN53 4.5 37.8 1.0
O H:THR119 4.6 44.3 1.0
O N:ASP32 4.7 47.0 1.0
C23 N:BO2201 4.7 33.9 1.0
CB a:TYR228 4.7 54.2 1.0
CA N:ALA49 4.8 38.4 1.0
CD2 a:TYR228 4.9 48.1 1.0
NE N:ARG45 4.9 42.0 1.0
OG1 N:THR20 5.0 49.6 1.0

Chlorine binding site 3 out of 4 in 5l66

Go back to Chlorine Binding Sites List in 5l66
Chlorine binding site 3 out of 4 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl301

b:44.1
occ:1.00
 OH V:TYR69 2.9 46.9 1.0
NH1 U:ARG111 3.0 52.4 1.0
OD1 U:ASN114 3.1 47.6 1.0
CB U:ASN114 3.6 45.3 1.0
CG U:ASN114 3.7 47.0 1.0
CZ V:TYR69 3.7 48.7 1.0
CD U:ARG111 3.7 45.7 1.0
CE2 V:TYR69 3.8 49.2 1.0
CZ U:ARG111 4.1 50.5 1.0
NE U:ARG111 4.4 48.9 1.0
CA U:ARG111 4.7 43.1 1.0
O U:ARG111 4.8 45.3 1.0
ND2 U:ASN114 4.9 47.2 1.0
OD2 O:ASP87 5.0 59.6 1.0

Chlorine binding site 4 out of 4 in 5l66

Go back to Chlorine Binding Sites List in 5l66
Chlorine binding site 4 out of 4 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl202

b:56.0
occ:1.00
 NH2 b:ARG45 3.0 40.0 1.0
NE2 b:GLN53 3.1 39.3 1.0
NH1 b:ARG45 3.5 41.9 1.0
CG2 b:THR31 3.6 46.6 1.0
CZ b:ARG45 3.7 40.2 1.0
C25 b:BO2201 4.1 38.3 1.0
CB b:ALA49 4.2 39.2 1.0
CD b:GLN53 4.2 38.8 1.0
OD1 V:ASP120 4.3 69.0 1.0
CG b:GLN53 4.5 38.5 1.0
O V:THR119 4.5 45.0 1.0
C24 b:BO2201 4.6 37.8 1.0
CB M:TYR228 4.6 53.6 1.0
O b:ASP32 4.7 47.5 1.0
CD2 M:TYR228 4.8 48.3 1.0
CA b:ALA49 4.9 39.8 1.0
CG M:TYR228 5.0 50.9 1.0
C23 b:BO2201 5.0 38.2 1.0

Reference:

E.M.Huber, W.Heinemeyer, G.De Bruin, H.S.Overkleeft, M.Groll. A Humanized Yeast Proteasome Identifies Unique Binding Modes of Inhibitors For the Immunosubunit Beta 5I. Embo J. V. 35 2602 2016.
ISSN: ESSN 1460-2075
PubMed: 27789522
DOI: 10.15252/EMBJ.201695222
Page generated: Fri Jul 26 11:10:55 2024

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