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Potassium in PDB 5lf6: Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde at 2.1 Angstrom

Enzymatic activity of Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde at 2.1 Angstrom

All present enzymatic activity of Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde at 2.1 Angstrom:
3.4.25.1;

Protein crystallography data

The structure of Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde at 2.1 Angstrom, PDB code: 5lf6 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) 171.02 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.870, 203.480, 315.630, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.7

Other elements in 5lf6:

The structure of Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde at 2.1 Angstrom also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms
Chlorine (Cl) 55 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde at 2.1 Angstrom (pdb code 5lf6). 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 Z-Lly-Ketoaldehyde at 2.1 Angstrom, PDB code: 5lf6:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 5lf6

Go back to Potassium Binding Sites List in 5lf6
Potassium binding site 1 out of 6 in the Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde 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 Z-Lly-Ketoaldehyde at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K303

b:38.5
occ:1.00
 O G:MET131 2.5 38.7 1.0
O G:TYR125 2.6 40.4 1.0
O G:ASN128 2.6 40.5 1.0
O G:HOH468 2.6 37.2 1.0
OG1 G:THR14 2.8 40.1 1.0
CG2 G:THR14 3.6 39.0 1.0
C G:ASN128 3.7 37.5 1.0
C G:TYR125 3.7 36.0 1.0
C G:MET131 3.7 35.9 1.0
CB G:THR14 3.7 38.9 1.0
O F:HOH466 3.9 36.9 1.0
O G:ALA129 4.1 36.8 1.0
CA G:ALA129 4.1 37.5 1.0
C G:ALA129 4.1 36.7 1.0
SD G:MET131 4.2 39.5 1.0
N G:ALA129 4.3 37.3 1.0
N G:MET131 4.4 34.6 1.0
CD G:PRO133 4.4 34.3 1.0
CA G:TYR125 4.4 36.2 1.0
CA G:ARG132 4.4 34.0 1.0
N G:ARG132 4.5 34.9 1.0
N G:THR14 4.5 37.1 1.0
CA G:MET131 4.7 35.5 1.0
N G:THR126 4.7 35.2 1.0
N G:GLU130 4.7 36.2 1.0
N G:ASN128 4.8 35.1 1.0
CA G:THR14 4.8 37.8 1.0
CA G:ASN128 4.8 36.1 1.0
CG G:MET131 4.8 37.0 1.0
C G:ARG132 4.8 33.8 1.0
CA G:THR126 4.8 34.9 1.0
N G:PRO133 4.9 33.6 1.0
C G:THR126 4.9 35.2 1.0
CB G:TYR125 4.9 36.2 1.0

Potassium binding site 2 out of 6 in 5lf6

Go back to Potassium Binding Sites List in 5lf6
Potassium binding site 2 out of 6 in the Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde 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 Z-Lly-Ketoaldehyde at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K302

b:58.6
occ:1.00
 O L:ALA183 2.6 62.6 1.0
O L:THR189 2.6 60.2 1.0
O L:ASP186 2.6 57.9 1.0
O L:HOH461 2.7 48.1 1.0
O L:HOH423 3.1 56.7 1.0
O V:HOH454 3.3 48.5 1.0
C L:ALA183 3.5 59.2 1.0
C L:THR189 3.7 55.1 1.0
C L:ASP186 3.8 52.1 1.0
CA L:ALA183 3.8 59.1 1.0
O L:VAL187 3.9 52.3 1.0
CA L:VAL187 4.0 51.2 1.0
C L:VAL187 4.1 51.2 1.0
OXT L:ASP213 4.1 57.8 1.0
NH1 L:ARG28 4.2 53.0 1.0
CB L:ALA183 4.3 59.1 1.0
N L:VAL187 4.4 51.0 1.0
N L:THR189 4.4 54.1 1.0
CA L:THR189 4.6 55.5 1.0
N L:GLY190 4.6 53.5 1.0
CA L:GLY190 4.7 53.3 1.0
O L:ALA182 4.7 58.0 1.0
N L:GLU184 4.7 59.5 1.0
NH2 V:ARG19 4.8 55.8 1.0
N L:TYR188 4.9 51.4 1.0
N L:ASP186 4.9 52.8 1.0
CA L:ASP186 4.9 52.8 1.0

Potassium binding site 3 out of 6 in 5lf6

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Potassium binding site 3 out of 6 in the Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde 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 Z-Lly-Ketoaldehyde at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
N:K306

b:44.9
occ:1.00
 O N:HOH536 2.4 47.4 1.0
O N:MET164 2.5 43.8 1.0
O N:HOH478 2.5 40.9 1.0
O N:SER170 2.6 42.4 1.0
O N:ASP167 2.6 39.8 1.0
C N:ASP167 3.6 35.6 1.0
O N:HOH412 3.6 59.4 1.0
O N:HOH516 3.7 55.1 1.0
NH1 N:ARG19 3.7 32.2 1.0
C N:MET164 3.7 39.2 1.0
C N:SER170 3.7 36.7 1.0
CA N:GLY168 4.1 34.7 1.0
N N:GLY168 4.2 35.7 1.0
CZ N:ARG19 4.2 32.6 1.0
C N:GLY168 4.3 35.0 1.0
O N:GLY168 4.4 36.2 1.0
O N:GLU165 4.4 38.7 1.0
CA N:GLY171 4.4 35.5 1.0
NH2 N:ARG19 4.4 32.7 1.0
CA N:MET164 4.4 36.0 1.0
N N:ASP167 4.5 35.1 1.0
N N:GLY171 4.5 36.4 1.0
O a:HOH525 4.6 41.8 1.0
C N:GLU165 4.6 38.2 1.0
N N:SER170 4.6 33.7 1.0
CA N:ASP167 4.6 34.9 1.0
N N:GLU165 4.7 39.9 1.0
CA N:SER170 4.7 34.9 1.0
CA N:GLU165 4.8 41.4 1.0

Potassium binding site 4 out of 6 in 5lf6

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Potassium binding site 4 out of 6 in the Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde 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 Z-Lly-Ketoaldehyde at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
U:K302

b:46.9
occ:1.00
 O U:MET131 2.5 50.5 1.0
O U:ASN128 2.5 53.6 1.0
O U:TYR125 2.6 54.2 1.0
O U:HOH447 2.7 50.5 1.0
OG1 U:THR14 2.8 55.2 1.0
CG2 U:THR14 3.6 51.9 1.0
C U:ASN128 3.6 51.4 1.0
C U:TYR125 3.7 51.3 1.0
C U:MET131 3.7 48.0 1.0
CB U:THR14 3.7 51.5 1.0
CA U:ALA129 4.0 50.2 1.0
O U:ALA129 4.1 47.7 1.0
C U:ALA129 4.1 49.5 1.0
O T:HOH315 4.2 42.4 1.0
SD U:MET131 4.2 55.1 1.0
N U:ALA129 4.3 50.8 1.0
N U:MET131 4.4 46.6 1.0
CA U:TYR125 4.4 50.3 1.0
CD U:PRO133 4.5 48.5 1.0
CA U:ARG132 4.5 46.8 1.0
N U:THR14 4.5 49.5 1.0
N U:ARG132 4.6 47.7 1.0
N U:ASN128 4.6 50.2 1.0
CA U:MET131 4.7 48.4 1.0
N U:THR126 4.7 50.7 1.0
N U:GLU130 4.7 49.4 1.0
CA U:ASN128 4.7 51.0 1.0
CG U:MET131 4.8 51.0 1.0
CA U:THR14 4.8 50.5 1.0
CA U:THR126 4.8 50.3 1.0
C U:THR126 4.8 50.1 1.0
C U:ARG132 4.9 47.0 1.0
CB U:TYR125 4.9 49.9 1.0
O U:HOH426 4.9 48.8 1.0
N U:PRO133 4.9 48.3 1.0
N U:GLN127 5.0 49.5 1.0

Potassium binding site 5 out of 6 in 5lf6

Go back to Potassium Binding Sites List in 5lf6
Potassium binding site 5 out of 6 in the Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde 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 Z-Lly-Ketoaldehyde at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:K302

b:44.3
occ:1.00
 O Z:HOH452 2.6 44.5 1.0
O Z:ALA183 2.6 44.5 1.0
O Z:THR189 2.6 43.0 1.0
O Z:ASP186 2.6 43.0 1.0
O H:HOH452 3.2 45.2 1.0
O Z:HOH446 3.2 47.5 1.0
C Z:ALA183 3.5 41.7 1.0
C Z:THR189 3.7 41.2 1.0
C Z:ASP186 3.8 38.9 1.0
CA Z:ALA183 3.8 41.0 1.0
O Z:VAL187 3.9 39.0 1.0
CA Z:VAL187 4.0 38.5 1.0
C Z:VAL187 4.1 38.7 1.0
NH1 Z:ARG28 4.3 43.1 1.0
OXT Z:ASP213 4.3 47.7 1.0
CB Z:ALA183 4.3 40.8 1.0
N Z:THR189 4.4 41.2 1.0
N Z:VAL187 4.4 38.3 1.0
CA Z:THR189 4.6 40.9 1.0
N Z:GLY190 4.6 41.2 1.0
CA Z:GLY190 4.7 40.9 1.0
O Z:ALA182 4.7 40.3 1.0
N Z:GLU184 4.8 40.8 1.0
N Z:TYR188 4.8 39.3 1.0
N Z:ASP186 4.9 38.4 1.0
NH2 H:ARG19 4.9 36.0 1.0
CA Z:ASP186 4.9 38.6 1.0

Potassium binding site 6 out of 6 in 5lf6

Go back to Potassium Binding Sites List in 5lf6
Potassium binding site 6 out of 6 in the Human 20S Proteasome Complex with Z-Lly-Ketoaldehyde 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 Z-Lly-Ketoaldehyde at 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
b:K305

b:49.8
occ:1.00
 O b:MET164 2.5 45.3 1.0
O b:SER170 2.6 48.5 1.0
O b:HOH455 2.6 48.6 1.0
O b:ASP167 2.7 42.5 1.0
O b:HOH493 2.7 64.3 1.0
O b:HOH438 3.2 66.4 1.0
C b:ASP167 3.6 37.0 1.0
NH1 b:ARG19 3.7 38.6 1.0
C b:MET164 3.7 41.9 1.0
C b:SER170 3.7 42.3 1.0
CA b:GLY168 4.2 38.0 1.0
CZ b:ARG19 4.2 37.7 1.0
N b:GLY168 4.2 37.7 1.0
O b:GLU165 4.4 39.8 1.0
CA b:GLY171 4.4 42.4 1.0
NH2 b:ARG19 4.4 38.0 1.0
O M:HOH490 4.4 44.2 1.0
C b:GLY168 4.4 37.5 1.0
O b:GLY168 4.4 36.9 1.0
CA b:MET164 4.4 39.6 1.0
N b:GLY171 4.5 42.4 1.0
N b:ASP167 4.5 37.6 1.0
N b:SER170 4.6 39.7 1.0
C b:GLU165 4.6 40.5 1.0
CA b:ASP167 4.7 36.4 1.0
CA b:SER170 4.7 41.5 1.0
N b:GLU165 4.7 42.2 1.0
CA b:GLU165 4.9 43.5 1.0
NE b:ARG19 5.0 37.4 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 14:11:44 2024

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