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Potassium in PDB 5lf3: Human 20S Proteasome Complex with Bortezomib at 2.1 Angstrom

Enzymatic activity of Human 20S Proteasome Complex with Bortezomib at 2.1 Angstrom

All present enzymatic activity of Human 20S Proteasome Complex with Bortezomib at 2.1 Angstrom:
3.4.25.1;

Protein crystallography data

The structure of Human 20S Proteasome Complex with Bortezomib at 2.1 Angstrom, PDB code: 5lf3 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) 170.45 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.370, 202.720, 314.900, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.6

Other elements in 5lf3:

The structure of Human 20S Proteasome Complex with Bortezomib at 2.1 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms
Chlorine (Cl) 51 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Human 20S Proteasome Complex with Bortezomib at 2.1 Angstrom (pdb code 5lf3). 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 Bortezomib at 2.1 Angstrom, PDB code: 5lf3:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5lf3

Go back to Potassium Binding Sites List in 5lf3
Potassium binding site 1 out of 6 in the Human 20S Proteasome Complex with Bortezomib at 2.1 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 Bortezomib at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K303

b:37.7
occ:1.00
 O G:MET131 2.5 34.1 1.0
O G:TYR125 2.6 32.6 1.0
O G:ASN128 2.6 33.0 1.0
O G:HOH480 2.7 34.8 1.0
OG1 G:THR14 2.8 35.0 1.0
CG2 G:THR14 3.5 32.5 1.0
C G:ASN128 3.7 30.9 1.0
C G:TYR125 3.7 29.7 1.0
CB G:THR14 3.7 32.8 1.0
C G:MET131 3.7 32.4 1.0
O F:HOH479 4.0 33.3 1.0
CA G:ALA129 4.1 32.6 1.0
C G:ALA129 4.1 32.3 1.0
O G:ALA129 4.1 31.5 1.0
SD G:MET131 4.3 34.0 1.0
N G:ALA129 4.3 31.2 1.0
N G:MET131 4.4 30.6 1.0
CA G:TYR125 4.5 30.8 1.0
CA G:ARG132 4.5 30.6 1.0
N G:THR14 4.5 31.5 1.0
CD G:PRO133 4.5 33.1 1.0
N G:ARG132 4.6 31.2 1.0
N G:THR126 4.6 30.0 1.0
N G:ASN128 4.7 30.1 1.0
CA G:MET131 4.7 31.5 1.0
N G:GLU130 4.8 31.7 1.0
CA G:THR14 4.8 32.3 1.0
CA G:THR126 4.8 30.9 1.0
CA G:ASN128 4.8 30.9 1.0
C G:ARG132 4.8 30.8 1.0
CG G:MET131 4.8 31.9 1.0
C G:THR126 4.9 31.2 1.0
N G:PRO133 4.9 30.4 1.0
CB G:TYR125 5.0 30.4 1.0

Potassium binding site 2 out of 6 in 5lf3

Go back to Potassium Binding Sites List in 5lf3
Potassium binding site 2 out of 6 in the Human 20S Proteasome Complex with Bortezomib at 2.1 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 Bortezomib at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K302

b:49.4
occ:1.00
 O L:ALA183 2.6 50.8 1.0
O L:THR189 2.6 48.5 1.0
O L:HOH447 2.6 47.0 1.0
O L:ASP186 2.6 52.4 1.0
O L:HOH433 3.2 45.1 1.0
O L:HOH460 3.4 49.9 1.0
C L:ALA183 3.5 48.5 1.0
C L:ASP186 3.7 46.5 1.0
CA L:ALA183 3.8 48.5 1.0
C L:THR189 3.8 46.1 1.0
O L:VAL187 3.9 42.9 1.0
CA L:VAL187 4.0 44.1 1.0
C L:VAL187 4.1 42.8 1.0
NH1 L:ARG28 4.1 44.1 1.0
OXT L:ASP213 4.2 52.3 1.0
N L:VAL187 4.3 45.9 1.0
CB L:ALA183 4.4 49.2 1.0
N L:THR189 4.4 42.8 1.0
CA L:THR189 4.6 44.3 1.0
O L:ALA182 4.7 48.7 1.0
N L:GLY190 4.7 46.2 1.0
NH2 V:ARG19 4.7 46.3 1.0
N L:GLU184 4.7 48.6 1.0
CA L:GLY190 4.7 46.8 1.0
N L:ASP186 4.8 45.4 1.0
N L:TYR188 4.9 41.7 1.0
CA L:ASP186 4.9 46.0 1.0
N L:ALA183 5.0 48.8 1.0

Potassium binding site 3 out of 6 in 5lf3

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Potassium binding site 3 out of 6 in the Human 20S Proteasome Complex with Bortezomib at 2.1 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 Bortezomib at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:K303

b:46.0
occ:1.00
 O N:HOH543 2.5 43.5 1.0
O N:MET164 2.5 43.6 1.0
O N:SER170 2.6 40.8 1.0
O N:ASP167 2.6 42.0 1.0
O N:HOH452 2.6 44.0 1.0
O N:HOH487 2.9 64.4 1.0
C N:ASP167 3.6 38.6 1.0
C N:SER170 3.7 38.0 1.0
C N:MET164 3.7 40.0 1.0
NH1 N:ARG19 3.7 36.5 1.0
O a:HOH544 4.0 86.8 1.0
CA N:GLY168 4.1 37.8 1.0
N N:GLY168 4.2 38.5 1.0
O N:GLY168 4.2 37.5 1.0
CZ N:ARG19 4.2 35.9 1.0
C N:GLY168 4.3 37.3 1.0
CA N:GLY171 4.4 37.3 1.0
CA N:MET164 4.5 37.7 1.0
O N:GLU165 4.5 41.3 1.0
N N:GLY171 4.5 37.2 1.0
NH2 N:ARG19 4.5 36.0 1.0
N N:SER170 4.5 36.9 1.0
N N:ASP167 4.6 37.9 1.0
O a:HOH519 4.6 37.6 1.0
CA N:SER170 4.6 37.4 1.0
C N:GLU165 4.6 42.1 1.0
CA N:ASP167 4.7 37.5 1.0
N N:GLU165 4.7 42.2 1.0
CA N:GLU165 4.9 43.9 1.0

Potassium binding site 4 out of 6 in 5lf3

Go back to Potassium Binding Sites List in 5lf3
Potassium binding site 4 out of 6 in the Human 20S Proteasome Complex with Bortezomib at 2.1 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 Bortezomib at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
U:K302

b:46.1
occ:1.00
 O U:MET131 2.5 51.9 1.0
O U:ASN128 2.6 51.6 1.0
O U:TYR125 2.6 52.2 1.0
O U:HOH453 2.7 45.0 1.0
OG1 U:THR14 2.8 52.2 1.0
CG2 U:THR14 3.6 51.0 1.0
C U:ASN128 3.7 47.0 1.0
C U:TYR125 3.7 48.5 1.0
C U:MET131 3.7 48.9 1.0
CB U:THR14 3.7 50.3 1.0
O T:HOH326 3.9 44.4 1.0
CA U:ALA129 4.1 46.9 1.0
C U:ALA129 4.1 47.6 1.0
O U:ALA129 4.1 47.5 1.0
SD U:MET131 4.2 51.3 1.0
N U:ALA129 4.3 47.3 1.0
N U:MET131 4.4 47.8 1.0
CA U:TYR125 4.5 47.9 1.0
CA U:ARG132 4.5 47.3 1.0
N U:THR14 4.5 47.6 1.0
N U:ARG132 4.5 48.4 1.0
CD U:PRO133 4.6 49.9 1.0
N U:ASN128 4.6 45.4 1.0
N U:THR126 4.6 47.1 1.0
CA U:MET131 4.7 48.8 1.0
N U:GLU130 4.7 47.9 1.0
CA U:ASN128 4.7 46.2 1.0
CA U:THR14 4.8 49.1 1.0
CA U:THR126 4.8 47.3 1.0
CG U:MET131 4.8 49.3 1.0
C U:ARG132 4.8 47.7 1.0
C U:THR126 4.9 47.0 1.0
CB U:TYR125 5.0 49.3 1.0
N U:PRO133 5.0 48.4 1.0

Potassium binding site 5 out of 6 in 5lf3

Go back to Potassium Binding Sites List in 5lf3
Potassium binding site 5 out of 6 in the Human 20S Proteasome Complex with Bortezomib at 2.1 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 Bortezomib at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:K302

b:42.6
occ:1.00
 O Z:THR189 2.6 39.5 1.0
O Z:ALA183 2.6 41.1 1.0
O Z:ASP186 2.6 41.3 1.0
O Z:HOH1444 2.7 39.3 1.0
O Z:HOH1470 3.1 41.9 1.0
O Z:HOH1477 3.2 40.2 1.0
C Z:ALA183 3.5 38.1 1.0
C Z:THR189 3.7 38.0 1.0
C Z:ASP186 3.7 37.0 1.0
CA Z:ALA183 3.8 38.4 1.0
O Z:VAL187 3.9 36.5 1.0
CA Z:VAL187 4.0 36.4 1.0
C Z:VAL187 4.1 35.8 1.0
NH1 Z:ARG28 4.2 40.8 1.0
N Z:THR189 4.3 34.9 1.0
N Z:VAL187 4.3 36.7 1.0
OXT Z:ASP213 4.3 43.1 1.0
CB Z:ALA183 4.4 38.0 1.0
CA Z:THR189 4.5 36.0 1.0
O Z:ALA182 4.6 38.4 1.0
N Z:GLY190 4.6 38.3 1.0
N Z:GLU184 4.7 37.9 1.0
CA Z:GLY190 4.7 40.1 1.0
N Z:ASP186 4.8 37.2 1.0
NH2 H:ARG19 4.8 38.3 1.0
N Z:TYR188 4.9 34.9 1.0
CA Z:ASP186 4.9 36.0 1.0
N Z:ALA183 5.0 38.2 1.0
CB Z:THR189 5.0 36.4 1.0

Potassium binding site 6 out of 6 in 5lf3

Go back to Potassium Binding Sites List in 5lf3
Potassium binding site 6 out of 6 in the Human 20S Proteasome Complex with Bortezomib at 2.1 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 Bortezomib at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
b:K304

b:46.4
occ:1.00
 O b:HOH515 2.5 46.8 1.0
O b:MET164 2.5 45.1 1.0
O b:SER170 2.6 45.9 1.0
O b:ASP167 2.6 42.0 1.0
O b:HOH452 2.7 46.9 1.0
O b:HOH408 2.9 53.4 1.0
C b:ASP167 3.6 39.2 1.0
C b:MET164 3.7 42.7 1.0
C b:SER170 3.7 41.9 1.0
NH1 b:ARG19 3.8 38.6 1.0
CA b:GLY168 4.1 40.0 1.0
N b:GLY168 4.2 39.5 1.0
O b:GLY168 4.2 39.7 1.0
O M:HOH506 4.3 42.0 1.0
C b:GLY168 4.3 39.5 1.0
CZ b:ARG19 4.3 38.6 1.0
CA b:GLY171 4.4 41.6 1.0
CA b:MET164 4.4 40.1 1.0
O b:GLU165 4.5 44.6 1.0
N b:ASP167 4.5 39.7 1.0
N b:SER170 4.5 39.2 1.0
N b:GLY171 4.5 41.8 1.0
C b:GLU165 4.6 44.3 1.0
NH2 b:ARG19 4.6 39.0 1.0
CA b:SER170 4.6 40.3 1.0
CA b:ASP167 4.7 38.4 1.0
N b:GLU165 4.7 43.8 1.0
CA b:GLU165 4.9 47.0 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 14:11:16 2024

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