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Potassium in PDB 5lex: Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom

Enzymatic activity of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom

All present enzymatic activity of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom:
3.4.25.1;

Protein crystallography data

The structure of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom, PDB code: 5lex was solved by J.Schrader, F.Henneberg, R.Mata, K.Tittmann, T.R.Schneider, H.Stark, G.Bourenkov, A.Chari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 170.89 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.860, 203.150, 316.020, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.1

Other elements in 5lex:

The structure of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom (pdb code 5lex). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom, PDB code: 5lex:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5lex

Go back to Potassium Binding Sites List in 5lex
Potassium binding site 1 out of 6 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K301

b:64.8
occ:1.00
 O G:MET131 2.5 53.9 1.0
O G:TYR125 2.6 49.8 1.0
O G:ASN128 2.6 53.2 1.0
O G:HOH423 2.7 53.8 1.0
OG1 G:THR14 2.7 56.4 1.0
CG2 G:THR14 3.5 51.7 1.0
C G:ASN128 3.6 49.3 1.0
C G:TYR125 3.6 46.8 1.0
CB G:THR14 3.7 52.5 1.0
C G:MET131 3.7 52.4 1.0
CA G:ALA129 4.0 50.5 1.0
C G:ALA129 4.0 50.9 1.0
O G:ALA129 4.0 53.0 1.0
O F:HOH314 4.2 50.0 1.0
N G:ALA129 4.2 49.2 1.0
N G:MET131 4.3 49.4 1.0
SD G:MET131 4.3 57.2 1.0
CA G:TYR125 4.4 46.6 1.0
CA G:ARG132 4.5 46.6 1.0
N G:THR14 4.5 48.1 1.0
CD G:PRO133 4.5 47.7 1.0
N G:ARG132 4.6 49.4 1.0
N G:ASN128 4.6 45.3 1.0
CA G:MET131 4.6 51.3 1.0
N G:THR126 4.6 46.4 1.0
N G:GLU130 4.6 51.5 1.0
CA G:ASN128 4.7 48.2 1.0
CA G:THR14 4.8 50.4 1.0
C G:ARG132 4.8 45.2 1.0
CA G:THR126 4.8 45.1 1.0
CG G:MET131 4.8 53.0 1.0
CB G:TYR125 4.8 47.3 1.0
N G:PRO133 4.9 45.7 1.0
C G:THR126 4.9 45.8 1.0
O G:HOH488 4.9 57.0 1.0

Potassium binding site 2 out of 6 in 5lex

Go back to Potassium Binding Sites List in 5lex
Potassium binding site 2 out of 6 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K302

b:74.3
occ:1.00
 O L:ALA183 2.6 81.1 1.0
O L:HOH433 2.6 63.8 1.0
O L:THR189 2.6 76.6 1.0
O L:ASP186 2.6 74.5 1.0
O L:HOH467 3.3 76.5 1.0
C L:ALA183 3.5 74.6 1.0
C L:ASP186 3.7 65.6 1.0
CA L:ALA183 3.7 73.2 1.0
C L:THR189 3.7 67.7 1.0
O L:VAL187 4.0 59.0 1.0
CA L:VAL187 4.0 61.1 1.0
O L:HOH417 4.1 58.7 1.0
OXT L:ASP213 4.1 76.5 1.0
C L:VAL187 4.1 59.4 1.0
NH1 L:ARG28 4.2 66.8 1.0
CB L:ALA183 4.3 74.6 1.0
N L:THR189 4.3 62.9 1.0
N L:VAL187 4.3 62.9 1.0
CA L:THR189 4.6 65.4 1.0
N L:GLY190 4.7 67.4 1.0
CA L:GLY190 4.7 67.9 1.0
N L:GLU184 4.7 73.4 1.0
O L:ALA182 4.7 72.1 1.0
NH2 V:ARG19 4.9 66.0 1.0
N L:ASP186 4.9 65.9 1.0
CA L:ASP186 4.9 65.6 1.0
N L:TYR188 4.9 58.8 1.0
CB L:THR189 5.0 66.0 1.0

Potassium binding site 3 out of 6 in 5lex

Go back to Potassium Binding Sites List in 5lex
Potassium binding site 3 out of 6 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:K302

b:58.8
occ:1.00
 O N:HOH540 2.4 51.9 1.0
O N:MET164 2.5 49.8 1.0
O N:SER170 2.6 46.9 1.0
O N:HOH501 2.6 46.9 1.0
O N:ASP167 2.6 43.2 1.0
O N:HOH468 3.5 59.0 1.0
C N:ASP167 3.6 39.9 1.0
C N:MET164 3.6 44.6 1.0
C N:SER170 3.7 43.2 1.0
NH1 N:ARG19 3.7 38.8 1.0
O N:HOH416 4.0 63.1 1.0
CA N:GLY168 4.1 39.3 1.0
N N:GLY168 4.1 41.6 1.0
CZ N:ARG19 4.3 39.6 1.0
CA N:GLY171 4.3 41.1 1.0
O N:GLU165 4.4 45.8 1.0
CA N:MET164 4.4 42.1 1.0
C N:GLY168 4.4 39.5 1.0
O N:GLY168 4.5 40.4 1.0
N N:GLY171 4.5 42.4 1.0
N N:ASP167 4.5 41.5 1.0
C N:GLU165 4.5 46.4 1.0
N N:SER170 4.5 40.1 1.0
O a:HOH508 4.6 46.5 1.0
CA N:ASP167 4.6 40.5 1.0
N N:GLU165 4.6 45.6 1.0
CA N:SER170 4.7 41.8 1.0
NH2 N:ARG19 4.7 39.9 1.0
CA N:GLU165 4.8 48.4 1.0
CB N:MET164 4.9 41.6 1.0
N N:ARG166 5.0 44.8 1.0
C N:ARG166 5.0 43.7 1.0

Potassium binding site 4 out of 6 in 5lex

Go back to Potassium Binding Sites List in 5lex
Potassium binding site 4 out of 6 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
U:K301

b:64.3
occ:1.00
 O U:ASN128 2.5 64.6 1.0
O U:MET131 2.5 66.9 1.0
O U:TYR125 2.5 63.8 1.0
O U:HOH448 2.7 56.4 1.0
OG1 U:THR14 2.8 67.1 1.0
C U:ASN128 3.5 59.8 1.0
CG2 U:THR14 3.6 64.6 1.0
C U:TYR125 3.6 59.1 1.0
C U:MET131 3.7 64.1 1.0
CB U:THR14 3.7 64.3 1.0
CA U:ALA129 4.0 59.5 1.0
C U:ALA129 4.1 59.8 1.0
O U:ALA129 4.1 58.0 1.0
O T:HOH315 4.1 57.7 1.0
SD U:MET131 4.2 74.1 1.0
N U:ALA129 4.2 60.2 1.0
CA U:TYR125 4.3 58.9 1.0
N U:MET131 4.3 62.0 1.0
N U:ASN128 4.4 58.3 1.0
CA U:ARG132 4.5 60.0 1.0
CA U:ASN128 4.6 59.2 1.0
CA U:MET131 4.6 64.8 1.0
N U:THR126 4.6 58.4 1.0
N U:ARG132 4.6 61.2 1.0
N U:THR14 4.6 60.2 1.0
N U:GLU130 4.6 61.9 1.0
CD U:PRO133 4.6 60.7 1.0
CB U:TYR125 4.7 59.5 1.0
CG U:MET131 4.8 67.6 1.0
CA U:THR126 4.8 59.2 1.0
C U:ARG132 4.8 58.7 1.0
CA U:THR14 4.8 62.0 1.0
C U:THR126 4.8 59.6 1.0
N U:PRO133 4.9 59.5 1.0
N U:GLN127 5.0 58.2 1.0

Potassium binding site 5 out of 6 in 5lex

Go back to Potassium Binding Sites List in 5lex
Potassium binding site 5 out of 6 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:K302

b:70.5
occ:1.00
 O Z:HOH418 2.4 61.1 1.0
O Z:ALA183 2.6 55.2 1.0
O Z:THR189 2.6 58.0 1.0
O Z:ASP186 2.6 51.1 1.0
O H:HOH470 3.4 62.8 1.0
C Z:ALA183 3.5 50.1 1.0
CA Z:ALA183 3.7 47.9 1.0
C Z:THR189 3.7 50.0 1.0
C Z:ASP186 3.7 45.1 1.0
O Z:HOH468 3.9 63.2 1.0
O Z:VAL187 4.0 41.4 1.0
CA Z:VAL187 4.1 45.0 1.0
C Z:VAL187 4.1 43.5 1.0
CB Z:ALA183 4.2 47.4 1.0
NH1 Z:ARG28 4.2 50.4 1.0
OXT Z:ASP213 4.3 59.1 1.0
N Z:THR189 4.3 45.9 1.0
N Z:VAL187 4.4 44.4 1.0
CA Z:THR189 4.5 47.2 1.0
CA Z:GLY190 4.6 48.8 1.0
N Z:GLY190 4.6 49.1 1.0
O Z:ALA182 4.7 45.8 1.0
N Z:GLU184 4.7 50.7 1.0
N Z:ASP186 4.8 45.7 1.0
CA Z:ASP186 4.9 45.3 1.0
N Z:TYR188 4.9 44.2 1.0
CB Z:THR189 4.9 49.3 1.0
N Z:ALA183 5.0 47.3 1.0

Potassium binding site 6 out of 6 in 5lex

Go back to Potassium Binding Sites List in 5lex
Potassium binding site 6 out of 6 in the Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Native Human 20S Proteasome in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
b:K302

b:63.6
occ:1.00
 O b:HOH508 2.5 54.7 1.0
O b:HOH466 2.6 48.5 1.0
O b:MET164 2.6 57.6 1.0
O b:SER170 2.6 60.9 1.0
O b:ASP167 2.6 52.9 1.0
O b:HOH420 3.4 65.7 1.0
C b:ASP167 3.6 46.1 1.0
C b:MET164 3.7 51.0 1.0
C b:SER170 3.7 51.4 1.0
NH1 b:ARG19 3.8 48.8 1.0
CA b:GLY168 4.0 46.1 1.0
N b:GLY168 4.1 46.0 1.0
O M:HOH403 4.3 51.6 1.0
O b:GLU165 4.4 51.1 1.0
C b:GLY168 4.4 45.1 1.0
CA b:MET164 4.4 49.4 1.0
CZ b:ARG19 4.4 49.6 1.0
CA b:GLY171 4.4 52.0 1.0
O b:GLY168 4.4 44.7 1.0
N b:ASP167 4.4 45.3 1.0
C b:GLU165 4.5 50.0 1.0
N b:GLY171 4.5 50.8 1.0
N b:SER170 4.6 48.2 1.0
CA b:ASP167 4.6 45.2 1.0
N b:GLU165 4.6 52.2 1.0
CA b:SER170 4.7 48.7 1.0
NH2 b:ARG19 4.7 49.4 1.0
CA b:GLU165 4.8 52.9 1.0
N b:ARG166 4.9 47.7 1.0
C b:ARG166 4.9 47.1 1.0
CB b:MET164 4.9 49.5 1.0

Reference:

J.Schrader, F.Henneberg, R.A.Mata, K.Tittmann, T.R.Schneider, H.Stark, G.Bourenkov, A.Chari. The Inhibition Mechanism of Human 20S Proteasomes Enables Next-Generation Inhibitor Design. Science V. 353 594 2016.
ISSN: ESSN 1095-9203
PubMed: 27493187
DOI: 10.1126/SCIENCE.AAF8993
Page generated: Mon Aug 12 14:08:46 2024

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