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Potassium in PDB 5lez: Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom

Enzymatic activity of Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom

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

Protein crystallography data

The structure of Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom, PDB code: 5lez 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) 170.81 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.860, 203.230, 315.220, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.2

Other elements in 5lez:

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

Magnesium (Mg) 10 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 6 in 5lez

Go back to Potassium Binding Sites List in 5lez
Potassium binding site 1 out of 6 in the Human 20S Proteasome Complex with Oprozomib 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 Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K301

b:59.5
occ:1.00
 O G:MET131 2.5 52.2 1.0
O G:TYR125 2.5 47.6 1.0
O G:ASN128 2.6 50.8 1.0
O G:HOH440 2.6 46.1 1.0
OG1 G:THR14 2.7 52.8 1.0
CG2 G:THR14 3.5 49.0 1.0
C G:ASN128 3.6 46.7 1.0
C G:TYR125 3.6 44.7 1.0
CB G:THR14 3.7 49.1 1.0
C G:MET131 3.7 49.6 1.0
CA G:ALA129 4.0 47.1 1.0
C G:ALA129 4.1 46.5 1.0
O G:ALA129 4.1 46.8 1.0
O F:HOH322 4.1 42.9 1.0
N G:ALA129 4.2 45.9 1.0
SD G:MET131 4.3 55.1 1.0
CA G:TYR125 4.3 45.8 1.0
N G:MET131 4.4 46.3 1.0
N G:THR14 4.5 45.5 1.0
CA G:ARG132 4.5 45.1 1.0
N G:ASN128 4.5 44.3 1.0
N G:ARG132 4.6 47.6 1.0
CD G:PRO133 4.6 45.9 1.0
N G:THR126 4.6 44.0 1.0
CA G:MET131 4.6 49.7 1.0
CA G:ASN128 4.7 46.3 1.0
CA G:THR14 4.7 47.5 1.0
CA G:THR126 4.7 44.2 1.0
N G:GLU130 4.7 45.9 1.0
CB G:TYR125 4.8 46.6 1.0
C G:THR126 4.8 44.0 1.0
C G:ARG132 4.8 44.2 1.0
CG G:MET131 4.8 51.4 1.0
N G:PRO133 4.9 44.0 1.0
O G:HOH506 4.9 48.7 1.0
N G:GLN127 4.9 44.0 1.0

Potassium binding site 2 out of 6 in 5lez

Go back to Potassium Binding Sites List in 5lez
Potassium binding site 2 out of 6 in the Human 20S Proteasome Complex with Oprozomib 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 Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K302

b:77.1
occ:1.00
 O L:HOH436 2.5 62.5 1.0
O L:ALA183 2.6 82.3 1.0
O L:THR189 2.6 75.3 1.0
O L:ASP186 2.6 74.1 1.0
O L:HOH475 3.3 66.0 1.0
C L:ALA183 3.5 74.1 1.0
C L:THR189 3.7 66.2 1.0
C L:ASP186 3.7 65.8 1.0
CA L:ALA183 3.8 72.3 1.0
O L:VAL187 4.0 60.7 1.0
O L:HOH424 4.0 56.0 1.0
OXT L:ASP213 4.0 73.7 1.0
CA L:VAL187 4.0 61.8 1.0
NH1 L:ARG28 4.1 67.0 1.0
C L:VAL187 4.1 60.2 1.0
N L:VAL187 4.3 64.0 1.0
N L:THR189 4.3 61.5 1.0
CB L:ALA183 4.4 72.5 1.0
CA L:THR189 4.6 64.5 1.0
N L:GLY190 4.6 65.8 1.0
CA L:GLY190 4.7 66.3 1.0
N L:GLU184 4.7 73.6 1.0
O L:ALA182 4.8 68.8 1.0
N L:ASP186 4.8 64.7 1.0
N L:TYR188 4.9 58.6 1.0
CA L:ASP186 4.9 64.8 1.0
NH2 V:ARG19 4.9 64.9 1.0
C L:ASP213 5.0 73.6 1.0

Potassium binding site 3 out of 6 in 5lez

Go back to Potassium Binding Sites List in 5lez
Potassium binding site 3 out of 6 in the Human 20S Proteasome Complex with Oprozomib 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 Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:K302

b:56.3
occ:1.00
 O N:HOH540 2.3 49.4 1.0
O N:MET164 2.5 49.8 1.0
O N:HOH516 2.6 44.5 1.0
O N:SER170 2.6 47.4 1.0
O N:ASP167 2.6 43.1 1.0
O N:HOH480 3.3 58.6 1.0
C N:ASP167 3.6 38.9 1.0
C N:SER170 3.7 41.6 1.0
C N:MET164 3.7 44.9 1.0
NH1 N:ARG19 3.8 40.5 1.0
CA N:GLY168 4.0 38.9 1.0
N N:GLY168 4.1 39.4 1.0
O N:HOH406 4.2 76.4 1.0
O N:GLY168 4.2 39.3 1.0
C N:GLY168 4.3 38.7 1.0
CZ N:ARG19 4.3 40.2 1.0
CA N:GLY171 4.4 39.7 1.0
CA N:MET164 4.4 41.4 1.0
N N:SER170 4.5 38.8 1.0
N N:GLY171 4.5 40.3 1.0
N N:ASP167 4.5 41.1 1.0
O N:GLU165 4.5 46.5 1.0
NH2 N:ARG19 4.6 41.8 1.0
C N:GLU165 4.6 45.7 1.0
CA N:SER170 4.6 39.5 1.0
CA N:ASP167 4.6 39.2 1.0
N N:GLU165 4.7 45.5 1.0
O a:HOH521 4.7 43.7 1.0
CA N:GLU165 4.8 49.0 1.0
CB N:MET164 4.9 41.1 1.0
O N:HOH511 5.0 49.5 1.0

Potassium binding site 4 out of 6 in 5lez

Go back to Potassium Binding Sites List in 5lez
Potassium binding site 4 out of 6 in the Human 20S Proteasome Complex with Oprozomib 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 Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
U:K302

b:62.3
occ:1.00
 O U:MET131 2.5 64.8 1.0
O U:ASN128 2.5 62.5 1.0
O U:TYR125 2.6 63.6 1.0
OG1 U:THR14 2.8 65.9 1.0
O U:HOH442 2.8 60.3 1.0
CG2 U:THR14 3.5 63.7 1.0
C U:ASN128 3.6 57.2 1.0
C U:TYR125 3.6 60.1 1.0
C U:MET131 3.7 61.2 1.0
CB U:THR14 3.7 62.3 1.0
CA U:ALA129 4.0 55.3 1.0
C U:ALA129 4.1 55.8 1.0
O U:ALA129 4.1 54.3 1.0
O T:HOH310 4.2 52.8 1.0
N U:ALA129 4.2 55.3 1.0
SD U:MET131 4.3 71.7 1.0
N U:MET131 4.3 59.2 1.0
CA U:TYR125 4.3 59.3 1.0
N U:THR14 4.5 59.7 1.0
CA U:ARG132 4.5 57.1 1.0
N U:ASN128 4.5 56.3 1.0
N U:ARG132 4.5 58.9 1.0
CD U:PRO133 4.6 58.3 1.0
N U:THR126 4.6 60.0 1.0
CA U:MET131 4.6 62.4 1.0
CA U:ASN128 4.6 57.2 1.0
N U:GLU130 4.7 58.5 1.0
CA U:THR14 4.7 60.8 1.0
CA U:THR126 4.8 58.8 1.0
CB U:TYR125 4.8 60.1 1.0
C U:ARG132 4.8 56.0 1.0
C U:THR126 4.8 58.6 1.0
CG U:MET131 4.9 64.8 1.0
O U:HOH441 4.9 59.6 1.0
N U:PRO133 4.9 57.0 1.0
N U:GLN127 5.0 56.6 1.0

Potassium binding site 5 out of 6 in 5lez

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Potassium binding site 5 out of 6 in the Human 20S Proteasome Complex with Oprozomib 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 Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:K301

b:67.4
occ:1.00
 O Z:HOH429 2.4 53.2 1.0
O Z:ALA183 2.6 58.6 1.0
O Z:THR189 2.6 56.4 1.0
O Z:ASP186 2.6 52.2 1.0
O Z:HOH445 3.3 59.5 1.0
C Z:ALA183 3.5 52.6 1.0
C Z:THR189 3.7 49.3 1.0
C Z:ASP186 3.7 47.2 1.0
CA Z:ALA183 3.8 50.0 1.0
O Z:VAL187 4.0 45.1 1.0
CA Z:VAL187 4.0 46.9 1.0
OXT Z:ASP213 4.1 62.8 1.0
C Z:VAL187 4.1 45.6 1.0
NH1 Z:ARG28 4.1 52.7 1.0
O Z:HOH428 4.2 55.9 1.0
N Z:THR189 4.3 45.3 1.0
N Z:VAL187 4.3 47.0 1.0
CB Z:ALA183 4.3 50.2 1.0
CA Z:THR189 4.5 46.9 1.0
N Z:GLY190 4.6 49.1 1.0
CA Z:GLY190 4.6 50.0 1.0
N Z:GLU184 4.7 51.9 1.0
O Z:ALA182 4.7 49.2 1.0
N Z:ASP186 4.8 47.6 1.0
N Z:TYR188 4.9 45.2 1.0
CA Z:ASP186 4.9 46.4 1.0
OD1 Z:ASP213 5.0 55.2 1.0
CB Z:THR189 5.0 47.4 1.0

Potassium binding site 6 out of 6 in 5lez

Go back to Potassium Binding Sites List in 5lez
Potassium binding site 6 out of 6 in the Human 20S Proteasome Complex with Oprozomib 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 Human 20S Proteasome Complex with Oprozomib in Mg-Acetate at 2.2 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
b:K301

b:60.7
occ:1.00
 O b:HOH497 2.5 53.0 1.0
O b:HOH478 2.5 44.6 1.0
O b:MET164 2.5 56.3 1.0
O b:SER170 2.6 56.4 1.0
O b:ASP167 2.6 51.2 1.0
O b:HOH461 3.3 69.4 1.0
C b:ASP167 3.6 46.2 1.0
C b:MET164 3.7 51.0 1.0
C b:SER170 3.7 48.6 1.0
NH1 b:ARG19 3.8 49.5 1.0
CA b:GLY168 4.0 46.0 1.0
N b:GLY168 4.1 45.4 1.0
O b:GLY168 4.3 46.1 1.0
C b:GLY168 4.3 45.2 1.0
CZ b:ARG19 4.4 49.7 1.0
CA b:MET164 4.4 47.7 1.0
CA b:GLY171 4.4 48.9 1.0
O M:HOH362 4.4 48.3 1.0
N b:SER170 4.5 46.8 1.0
N b:ASP167 4.5 46.4 1.0
O b:GLU165 4.5 47.7 1.0
N b:GLY171 4.5 48.4 1.0
C b:GLU165 4.6 49.4 1.0
NH2 b:ARG19 4.6 49.9 1.0
CA b:ASP167 4.6 45.5 1.0
CA b:SER170 4.6 47.7 1.0
N b:GLU165 4.7 51.2 1.0
CA b:GLU165 4.8 52.9 1.0
CB b:MET164 4.9 48.4 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 14:09:59 2024

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