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Magnesium in PDB 8bzl: Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42

Enzymatic activity of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42

All present enzymatic activity of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42:
3.4.25.1;

Protein crystallography data

The structure of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42, PDB code: 8bzl was solved by F.Henneberg, A.Chari, E.Jankowska, J.Witkowska, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.12 / 2.14
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.915, 203.262, 316.421, 90, 90, 90
R / Rfree (%) 19.6 / 22.6

Other elements in 8bzl:

The structure of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 also contains other interesting chemical elements:

Potassium (K) 6 atoms
Chlorine (Cl) 54 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 (pdb code 8bzl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42, PDB code: 8bzl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8bzl

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Magnesium binding site 1 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg302

b:38.5
occ:1.00
 O 3:HOH450 1.9 41.0 1.0
O 3:SER180 2.2 44.2 1.0
O 3:ASP177 2.3 43.4 1.0
O 3:HOH427 2.5 36.4 1.0
O 3:VAL174 2.6 40.9 1.0
C 3:SER180 3.4 43.8 1.0
C 3:ASP177 3.5 43.2 1.0
C 3:VAL174 3.6 41.4 1.0
OXT 3:ASP204 3.9 48.7 1.0
O 3:HOH480 4.0 73.0 1.0
O 3:HOH404 4.1 36.3 1.0
CA 3:ASP175 4.3 43.2 1.0
N 3:SER180 4.3 42.6 1.0
CA 3:GLY181 4.3 44.3 1.0
N 3:GLY181 4.3 43.9 1.0
O 3:ALA178 4.4 42.5 1.0
N 3:ASP177 4.4 44.0 1.0
N 3:ASP175 4.4 42.3 1.0
CA 3:SER180 4.4 43.1 1.0
C 3:ALA178 4.4 42.3 1.0
CA 3:ASP177 4.4 43.7 1.0
N 3:ALA178 4.4 43.1 1.0
CD1 K:ILE26 4.5 41.6 1.0
CA 3:ALA178 4.5 42.9 1.0
CA 3:VAL174 4.6 40.8 1.0
C 3:ASP175 4.7 43.3 1.0
CB 3:VAL174 4.7 40.6 1.0
OD1 3:ASP175 4.8 44.2 1.0
CB 3:ASP177 4.8 44.1 1.0
C 3:ASP204 4.9 49.0 1.0
N 3:VAL179 5.0 41.8 1.0
O 3:ASP175 5.0 43.3 1.0
CB 3:SER180 5.0 44.0 1.0

Magnesium binding site 2 out of 10 in 8bzl

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Magnesium binding site 2 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg303

b:42.3
occ:1.00
 O H:HOH525 2.2 39.8 1.0
O H:HOH434 2.2 41.6 1.0
O N:HOH412 2.2 38.2 1.0
O N:HOH479 2.2 38.0 1.0
O N:HOH413 2.2 40.8 1.0
OE1 H:GLN91 2.4 38.1 1.0
CD H:GLN91 3.4 36.7 1.0
OD1 N:ASP51 3.6 25.3 1.0
O N:ASP93 3.7 34.7 1.0
NE2 H:GLN91 3.7 35.3 1.0
O N:HOH536 3.9 54.4 1.0
O H:HOH452 4.0 20.6 1.0
O H:HOH460 4.0 39.7 1.0
OD2 N:ASP51 4.1 24.6 1.0
CG N:ASP51 4.3 24.6 1.0
O N:HOH426 4.5 30.9 1.0
ND1 H:HIS116 4.7 27.3 1.0
CG H:GLN91 4.7 35.1 1.0
O N:HOH555 4.7 64.9 1.0
C N:ASP93 4.8 34.7 1.0

Magnesium binding site 3 out of 10 in 8bzl

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Magnesium binding site 3 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg304

b:33.6
occ:1.00
 O H:ASP166 2.1 28.3 1.0
O H:SER169 2.1 29.6 1.0
O H:ILE163 2.3 29.1 1.0
O Z:ASP213 2.4 42.5 1.0
O Z:HOH502 2.7 42.8 1.0
C H:ASP166 3.2 28.4 1.0
C H:SER169 3.3 28.9 1.0
C Z:ASP213 3.4 43.1 1.0
C H:ILE163 3.4 28.8 1.0
CA Z:ASP213 3.9 43.8 1.0
N H:SER169 3.9 27.5 1.0
NH1 H:ARG19 3.9 34.4 1.0
CA H:LEU167 4.0 28.9 1.0
N H:LEU167 4.0 28.4 1.0
CA H:SER169 4.1 27.7 1.0
CB Z:ASP213 4.1 44.4 1.0
C H:LEU167 4.2 28.1 1.0
N H:ASP166 4.2 28.6 1.0
CA H:ILE163 4.2 27.8 1.0
O H:GLY162 4.2 27.0 1.0
O Z:HOH417 4.2 43.6 1.0
N H:GLY170 4.3 29.3 1.0
CA H:ASP166 4.3 28.1 1.0
O H:LEU167 4.3 28.4 1.0
OXT Z:ASP213 4.3 42.8 1.0
N H:PHE164 4.4 29.6 1.0
CB H:SER169 4.4 27.1 1.0
CA H:GLY170 4.4 31.1 1.0
CZ H:ARG19 4.6 34.5 1.0
CA H:PHE164 4.6 30.9 1.0
C H:PHE164 4.6 30.8 1.0
N H:GLY168 4.8 27.5 1.0
N H:ASN165 4.8 30.0 1.0
NH2 H:ARG19 4.9 35.4 1.0
O H:PHE164 5.0 31.7 1.0
CG2 H:ILE163 5.0 29.1 1.0

Magnesium binding site 4 out of 10 in 8bzl

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Magnesium binding site 4 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:33.6
occ:1.00
 O I:HOH470 2.1 38.0 1.0
O I:SER180 2.2 29.6 1.0
O I:VAL174 2.3 25.7 1.0
O I:ASP177 2.3 27.6 1.0
O I:HOH411 2.6 28.9 1.0
C I:VAL174 3.3 25.9 1.0
C I:SER180 3.4 28.6 1.0
C I:ASP177 3.5 28.1 1.0
O I:HOH448 3.8 35.7 1.0
O I:HOH403 4.0 30.8 1.0
CA I:ASP175 4.1 28.3 1.0
N I:ASP175 4.1 27.0 1.0
N I:ASP177 4.2 28.1 1.0
OXT I:ASP204 4.2 34.7 1.0
CA I:GLY181 4.2 29.4 1.0
N I:GLY181 4.3 28.2 1.0
N I:SER180 4.3 27.9 1.0
CA I:ASP177 4.3 28.1 1.0
CA I:VAL174 4.3 25.0 1.0
CA I:SER180 4.4 28.5 1.0
CB I:VAL174 4.4 24.9 1.0
O I:HOH489 4.4 48.4 1.0
N I:ALA178 4.5 28.7 1.0
C I:ASP175 4.5 28.2 1.0
CD1 Y:ILE26 4.5 27.8 1.0
C I:ALA178 4.6 28.6 1.0
O I:ALA178 4.6 29.3 1.0
OD1 I:ASP175 4.6 31.8 1.0
CA I:ALA178 4.6 29.0 1.0
CB I:ASP177 4.7 28.2 1.0
CG2 I:VAL174 4.8 25.0 1.0
CB I:SER180 4.9 28.6 1.0
O I:ASP175 4.9 28.7 1.0
N I:ARG176 4.9 27.7 1.0

Magnesium binding site 5 out of 10 in 8bzl

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Magnesium binding site 5 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:44.8
occ:1.00
 O J:HOH413 2.2 43.3 1.0
O J:HOH419 2.2 43.8 1.0
O J:HOH503 2.2 44.3 1.0
O K:HOH480 2.2 42.7 1.0
O J:HOH454 2.2 43.7 1.0
O J:HOH539 2.2 44.1 1.0
O J:PRO97 4.1 34.4 1.0
O K:HOH462 4.2 42.4 1.0
OE2 J:GLU49 4.2 42.9 1.0
O K:HOH439 4.2 29.0 1.0
OD1 J:ASP52 4.3 34.6 1.0
OD2 J:ASP52 4.4 33.1 1.0
O K:HOH494 4.4 38.3 1.0
CE1 J:HIS99 4.6 33.4 0.6
CE K:LYS91 4.7 40.0 1.0
CG J:ASP52 4.8 33.2 1.0
ND1 J:HIS99 4.8 33.2 0.6

Magnesium binding site 6 out of 10 in 8bzl

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Magnesium binding site 6 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg305

b:44.4
occ:1.00
 O K:ASP167 2.3 35.9 1.0
O 3:ASP204 2.3 48.4 1.0
O K:THR164 2.4 36.8 1.0
O K:SER170 2.4 38.1 1.0
O K:HOH454 2.5 42.5 1.0
C K:ASP167 3.3 35.2 1.0
C 3:ASP204 3.3 49.0 1.0
C K:THR164 3.4 36.4 1.0
C K:SER170 3.6 37.7 1.0
CA 3:ASP204 3.6 49.3 1.0
CA K:ALA168 3.7 36.1 1.0
C K:ALA168 3.8 36.1 1.0
O K:ALA168 3.8 36.2 1.0
CB 3:ASP204 3.9 49.7 1.0
NH1 K:ARG19 3.9 39.1 1.0
N K:ALA168 3.9 35.3 1.0
CA K:THR164 4.0 35.6 1.0
N K:SER170 4.1 36.4 1.0
CA K:SER170 4.3 36.8 1.0
N K:ASP167 4.4 35.2 1.0
CA K:ASP167 4.4 34.7 1.0
OXT 3:ASP204 4.5 48.7 1.0
CZ K:ARG19 4.5 39.6 1.0
N K:TYR169 4.5 35.8 1.0
CB K:THR164 4.5 36.5 1.0
N K:TYR165 4.6 36.9 1.0
N K:GLY171 4.6 38.3 1.0
O K:TYR165 4.7 37.1 1.0
C K:TYR165 4.8 37.1 1.0
NH2 K:ARG19 4.8 40.7 1.0
CA K:GLY171 4.8 39.7 1.0
CB K:SER170 4.8 36.3 1.0
O K:ALA163 4.9 34.4 1.0
CA K:TYR165 5.0 37.7 1.0

Magnesium binding site 7 out of 10 in 8bzl

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Magnesium binding site 7 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg303

b:48.4
occ:1.00
 O V:HOH489 2.2 48.1 1.0
O V:HOH435 2.2 49.2 1.0
O b:HOH408 2.2 46.0 1.0
O b:HOH441 2.2 45.7 1.0
O b:HOH420 2.2 47.7 1.0
OE1 V:GLN91 2.3 47.0 1.0
CD V:GLN91 3.4 46.1 1.0
O b:ASP93 3.5 44.1 1.0
OD1 b:ASP51 3.6 31.9 1.0
NE2 V:GLN91 3.7 45.6 1.0
OD2 b:ASP51 4.1 30.7 1.0
O V:HOH432 4.2 24.1 1.0
CG b:ASP51 4.2 31.0 1.0
O b:HOH503 4.3 52.7 1.0
O b:HOH419 4.5 51.5 1.0
O b:HOH510 4.5 67.0 1.0
O V:HOH495 4.6 51.7 1.0
C b:ASP93 4.6 42.3 1.0
CG V:GLN91 4.7 45.2 1.0
ND1 V:HIS116 4.9 34.3 1.0

Magnesium binding site 8 out of 10 in 8bzl

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Magnesium binding site 8 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg304

b:51.1
occ:1.00
 O V:ASP166 2.1 41.4 1.0
O V:SER169 2.2 43.1 1.0
O V:ILE163 2.4 40.2 1.0
O L:ASP213 2.4 56.8 1.0
O V:HOH465 2.5 46.6 1.0
C V:ASP166 3.2 40.7 1.0
C V:SER169 3.4 42.7 1.0
C L:ASP213 3.4 57.0 1.0
C V:ILE163 3.5 40.2 1.0
CA V:LEU167 3.9 41.6 1.0
CA L:ASP213 3.9 56.9 1.0
N V:LEU167 4.0 40.8 1.0
NH1 V:ARG19 4.0 48.7 1.0
N V:SER169 4.0 41.4 1.0
N V:ASP166 4.1 40.6 1.0
O L:HOH426 4.1 53.5 1.0
CA V:SER169 4.1 41.6 1.0
C V:LEU167 4.2 41.5 1.0
O V:GLY162 4.2 38.0 1.0
CB L:ASP213 4.2 57.2 1.0
CA V:ASP166 4.2 40.2 1.0
CA V:ILE163 4.2 39.6 1.0
O V:LEU167 4.3 42.1 1.0
OXT L:ASP213 4.3 57.8 1.0
N V:GLY170 4.3 43.0 1.0
N V:PHE164 4.4 41.0 1.0
CB V:SER169 4.5 41.5 1.0
CA V:GLY170 4.5 44.5 1.0
C V:PHE164 4.6 41.7 1.0
CA V:PHE164 4.6 42.1 1.0
CZ V:ARG19 4.6 49.3 1.0
N V:ASN165 4.7 41.1 1.0
N V:GLY168 4.8 41.1 1.0
O V:PHE164 4.9 42.1 1.0
NH2 V:ARG19 4.9 50.5 1.0
CB V:ASP166 5.0 39.5 1.0
C V:ASN165 5.0 40.7 1.0

Magnesium binding site 9 out of 10 in 8bzl

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Magnesium binding site 9 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg301

b:51.3
occ:1.00
 O X:HOH430 2.2 48.9 1.0
O Y:HOH531 2.2 50.5 1.0
O X:HOH527 2.2 49.7 1.0
O X:HOH504 2.2 49.0 1.0
O X:HOH457 2.2 50.3 1.0
O X:HOH401 2.2 49.4 1.0
O Y:HOH534 4.0 57.7 1.0
O X:PRO97 4.0 37.2 1.0
O Y:HOH443 4.2 47.2 1.0
OE2 X:GLU49 4.3 46.0 1.0
O Y:HOH479 4.3 39.8 1.0
OD2 X:ASP52 4.4 32.4 1.0
OD1 X:ASP52 4.4 33.2 1.0
CE1 X:HIS99 4.5 35.4 0.6
ND1 X:HIS99 4.7 35.0 0.6
CE Y:LYS91 4.8 38.6 1.0
CG X:ASP52 4.8 32.5 1.0
CD X:PRO97 4.9 38.5 1.0
CG X:PRO97 5.0 37.9 1.0

Magnesium binding site 10 out of 10 in 8bzl

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Magnesium binding site 10 out of 10 in the Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Human 20S Proteasome in Complex with Peptide Activator Peptide BLM42 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg306

b:29.6
occ:1.00
 O Y:ASP167 2.2 24.7 1.0
O Y:SER170 2.3 28.3 1.0
O I:ASP204 2.4 35.1 1.0
O Y:THR164 2.4 25.8 1.0
O Y:HOH482 2.5 32.6 1.0
C Y:ASP167 3.2 25.1 1.0
C I:ASP204 3.4 35.0 1.0
C Y:THR164 3.5 25.4 1.0
C Y:SER170 3.5 26.9 1.0
CA Y:ALA168 3.7 26.1 1.0
CA I:ASP204 3.7 33.8 1.0
C Y:ALA168 3.7 25.9 1.0
O Y:ALA168 3.7 25.9 1.0
N Y:ALA168 3.9 25.2 1.0
NH1 Y:ARG19 3.9 26.8 1.0
CB I:ASP204 3.9 33.6 1.0
CA Y:THR164 4.0 24.6 1.0
N Y:SER170 4.0 25.7 1.0
CA Y:SER170 4.3 26.1 1.0
CA Y:ASP167 4.4 24.9 1.0
N Y:ASP167 4.4 25.3 1.0
N Y:TYR169 4.4 25.9 1.0
CZ Y:ARG19 4.5 27.1 1.0
OXT I:ASP204 4.5 34.7 1.0
CB Y:THR164 4.6 25.0 1.0
N Y:GLY171 4.6 26.2 1.0
N Y:TYR165 4.6 26.1 1.0
CB Y:SER170 4.7 25.4 1.0
O Y:TYR165 4.8 27.3 1.0
CA Y:GLY171 4.8 26.7 1.0
NH2 Y:ARG19 4.8 27.4 1.0
C Y:TYR165 4.8 27.0 1.0
O Y:ALA163 4.8 23.3 1.0
O I:HOH498 4.9 23.7 1.0

Reference:

M.Gizynska, P.Karpowicz, D.Sowik, K.Trepczyk, J.Witkowska, F.Hennenberg, A.Chari, A.Gieldon, K.Pierzynowska, L.Gaffke, G.Wegrzyn, E.Jankowska. Peptidic, BLM10-Based Activators of Human 20S Proteasome in Vitro and in Cellulo Enhance Degradation of Proteins Connected with Neurodegeneration. To Be Published.
Page generated: Thu Oct 3 19:58:50 2024

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