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Magnesium in PDB 4y8l: Yeast 20S Proteasome in Complex with Ac-Apll-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Apll-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with Ac-Apll-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Apll-Ep, PDB code: 4y8l was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.610, 299.760, 144.950, 90.00, 113.06, 90.00
R / Rfree (%) 20.8 / 22.4

Other elements in 4y8l:

The structure of Yeast 20S Proteasome in Complex with Ac-Apll-Ep also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep (pdb code 4y8l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep, PDB code: 4y8l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y8l

Go back to Magnesium Binding Sites List in 4y8l
Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast 20S Proteasome in Complex with Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:44.1
occ:1.00
 O G:MET125 2.3 41.7 1.0
O G:ARG122 2.3 43.0 1.0
O G:HOH420 2.3 40.1 1.0
O G:TYR119 2.5 34.2 1.0
OG1 G:THR8 2.6 39.6 1.0
CG2 G:THR8 3.3 43.0 1.0
C G:ARG122 3.4 43.2 1.0
O G:ALA123 3.4 43.5 1.0
C G:MET125 3.5 42.2 1.0
CB G:THR8 3.5 42.3 1.0
CA G:ALA123 3.7 43.1 1.0
C G:TYR119 3.7 36.3 1.0
C G:ALA123 3.7 44.2 1.0
N G:ALA123 4.0 42.7 1.0
N G:MET125 4.2 44.1 1.0
N G:THR8 4.3 43.4 1.0
N G:ARG126 4.3 39.7 1.0
CA G:ARG126 4.3 38.0 1.0
CA G:MET125 4.4 45.3 1.0
CA G:TYR119 4.5 36.1 1.0
CA G:THR8 4.5 43.3 1.0
CD G:PRO127 4.6 35.8 1.0
CA G:ARG122 4.6 45.2 1.0
N G:TYR124 4.7 45.6 1.0
N G:ARG122 4.7 43.1 1.0
N G:THR120 4.7 37.2 1.0
CA G:THR120 4.9 37.1 1.0
C G:ARG126 4.9 37.2 1.0
CB G:MET125 4.9 49.7 1.0
C G:THR120 4.9 37.8 1.0
CB G:TYR119 5.0 36.1 1.0

Magnesium binding site 2 out of 7 in 4y8l

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast 20S Proteasome in Complex with Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:49.6
occ:1.00
 O I:ASP177 2.4 41.6 1.0
O I:SER180 2.5 42.9 1.0
O I:HOH424 2.6 56.9 1.0
O I:ALA174 2.7 47.5 1.0
C I:ASP177 3.6 42.0 1.0
C I:SER180 3.7 42.1 1.0
C I:ALA174 3.7 47.0 1.0
OXT I:ASP204 3.9 49.4 1.0
CA I:ASP175 4.1 47.4 1.0
O I:ALA178 4.2 42.2 1.0
N I:ASP175 4.3 47.1 1.0
CA I:ALA178 4.4 41.7 1.0
C I:ALA178 4.4 42.2 1.0
N I:ALA178 4.4 41.8 1.0
N I:ASP177 4.4 41.8 1.0
C I:ASP175 4.4 44.9 1.0
N I:SER180 4.5 41.0 1.0
CA I:ASP177 4.5 42.7 1.0
N I:GLY181 4.6 41.5 1.0
CA I:GLY181 4.6 42.2 1.0
CA I:SER180 4.6 41.6 1.0
O I:ASP175 4.6 44.4 1.0
NH1 Y:ARG19 4.7 47.5 1.0
C I:ASP204 4.8 51.9 1.0
O I:ASP204 4.8 50.9 1.0
CA I:ALA174 4.8 46.3 1.0
OD1 I:ASP175 4.8 51.3 1.0
NH2 Y:ARG19 4.9 48.3 1.0

Magnesium binding site 3 out of 7 in 4y8l

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast 20S Proteasome in Complex with Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:41.4
occ:1.00
 O Y:ASP168 2.2 38.6 1.0
O Y:SER171 2.3 42.8 1.0
O I:ASP204 2.4 50.9 1.0
O Y:HOH1102 2.4 37.4 1.0
O Y:ALA165 2.5 39.8 1.0
C I:ASP204 3.2 51.9 1.0
C Y:ASP168 3.2 37.5 1.0
C Y:SER171 3.4 41.3 1.0
O Y:ALA169 3.5 36.9 1.0
CA Y:ALA169 3.6 36.9 1.0
C Y:ALA169 3.6 37.3 1.0
C Y:ALA165 3.6 39.5 1.0
CA I:ASP204 3.7 52.6 1.0
NH1 Y:ARG19 3.7 47.5 1.0
N Y:ALA169 3.8 37.1 1.0
N Y:SER171 3.9 38.6 1.0
CB I:ASP204 4.0 53.4 1.0
OXT I:ASP204 4.1 49.4 1.0
CA Y:SER171 4.2 39.2 1.0
CZ Y:ARG19 4.3 47.0 1.0
CA Y:ALA165 4.3 39.3 1.0
N Y:TYR170 4.3 37.9 1.0
O Y:HIS166 4.4 39.2 1.0
N Y:GLY172 4.4 43.0 1.0
CA Y:ASP168 4.5 36.7 1.0
N Y:ASP168 4.6 37.9 1.0
NH2 Y:ARG19 4.6 48.3 1.0
CA Y:GLY172 4.6 44.1 1.0
C Y:HIS166 4.6 39.3 1.0
O Y:ALA164 4.6 38.5 1.0
N Y:HIS166 4.7 38.6 1.0
CB Y:SER171 4.7 38.5 1.0
CA Y:HIS166 4.9 38.9 1.0
C Y:TYR170 4.9 38.7 1.0
CB Y:ALA169 5.0 36.8 1.0
CG I:ASP204 5.0 53.1 1.0

Magnesium binding site 4 out of 7 in 4y8l

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast 20S Proteasome in Complex with Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:47.6
occ:1.00
 O K:ASP168 2.2 41.8 1.0
O W:ASP204 2.2 50.7 1.0
O K:ALA165 2.3 43.9 1.0
O K:SER171 2.4 44.6 1.0
C W:ASP204 3.1 49.7 1.0
C K:ASP168 3.3 40.7 1.0
C K:ALA165 3.4 43.8 1.0
C K:SER171 3.6 43.2 1.0
CA W:ASP204 3.6 48.2 1.0
CA K:ALA169 3.7 40.5 1.0
O K:ALA169 3.7 44.5 1.0
C K:ALA169 3.8 41.7 1.0
CB W:ASP204 3.9 47.8 1.0
N K:ALA169 3.9 40.4 1.0
NH1 K:ARG19 4.0 48.5 1.0
OXT W:ASP204 4.0 50.0 1.0
N K:SER171 4.1 41.3 1.0
O K:HIS166 4.2 44.8 1.0
CA K:ALA165 4.2 43.4 1.0
CA K:SER171 4.4 41.4 1.0
C K:HIS166 4.4 44.3 1.0
N K:HIS166 4.4 43.3 1.0
CZ K:ARG19 4.4 48.5 1.0
CA K:ASP168 4.5 40.5 1.0
N K:ASP168 4.5 41.0 1.0
O K:ALA164 4.5 43.5 1.0
N K:GLY172 4.5 44.6 1.0
N K:TYR170 4.6 41.1 1.0
CA K:HIS166 4.6 44.5 1.0
CA K:GLY172 4.7 45.7 1.0
NH2 K:ARG19 4.7 51.3 1.0
CB K:SER171 4.8 40.5 1.0
CG W:ASP204 4.8 48.1 1.0
O W:HOH314 4.9 60.9 1.0
C K:ARG167 5.0 41.9 1.0
N W:ASP204 5.0 47.7 1.0
N K:ARG167 5.0 43.3 1.0

Magnesium binding site 5 out of 7 in 4y8l

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Yeast 20S Proteasome in Complex with Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:47.7
occ:1.00
 O V:ASP166 2.1 48.6 1.0
O V:ILE163 2.2 52.5 1.0
OXT L:ASP222 2.3 56.1 1.0
O V:SER169 2.3 51.3 1.0
O V:HOH402 2.5 45.8 1.0
C V:ASP166 3.2 49.5 1.0
C L:ASP222 3.2 57.2 1.0
C V:ILE163 3.2 53.5 1.0
C V:SER169 3.5 51.4 1.0
O V:GLY162 3.7 49.1 1.0
CA L:ASP222 3.9 56.7 1.0
N V:LEU167 3.9 50.1 1.0
CA V:LEU167 3.9 50.1 1.0
O L:ASP222 4.0 57.8 1.0
NH1 V:ARG19 4.0 52.0 1.0
CA V:ILE163 4.0 54.9 1.0
N V:ASP166 4.0 49.3 1.0
N V:TRP164 4.1 52.6 1.0
CA V:ASP166 4.2 49.2 1.0
C V:TRP164 4.2 53.8 1.0
N V:SER169 4.3 48.0 1.0
C V:LEU167 4.3 48.9 1.0
O V:TRP164 4.3 51.8 1.0
CB L:ASP222 4.4 56.3 1.0
N V:GLY170 4.4 53.5 1.0
CA V:TRP164 4.4 54.7 1.0
CA V:SER169 4.4 49.8 1.0
CA V:GLY170 4.4 54.6 1.0
CZ V:ARG19 4.4 52.2 1.0
NH2 V:ARG19 4.4 52.5 1.0
O V:LEU167 4.5 47.5 1.0
N V:ASN165 4.5 51.9 1.0
C V:GLY162 4.6 52.1 1.0
C V:ASN165 4.7 49.6 1.0
CB V:SER169 4.8 49.0 1.0
N V:ILE163 4.8 53.0 1.0
CB V:ASP166 4.9 48.8 1.0
N V:GLY168 5.0 48.9 1.0

Magnesium binding site 6 out of 7 in 4y8l

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Yeast 20S Proteasome in Complex with Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:39.3
occ:1.00
 O N:SER169 2.5 36.4 1.0
O N:ILE163 2.6 38.1 1.0
O N:ASP166 2.7 37.7 1.0
CD1 a:LEU34 3.6 39.0 1.0
NH1 N:ARG19 3.7 37.7 1.0
C N:SER169 3.7 35.4 1.0
C N:ASP166 3.7 36.7 1.0
C N:ILE163 3.7 39.3 1.0
CA N:GLY167 4.0 35.1 1.0
CG2 N:ILE163 4.1 38.1 1.0
O N:GLY167 4.3 35.2 1.0
N N:GLY167 4.3 35.6 1.0
C N:GLY167 4.3 34.4 1.0
CA N:ILE163 4.4 38.4 1.0
CZ N:ARG19 4.4 38.0 1.0
CA N:GLY170 4.5 37.9 1.0
N N:SER169 4.5 34.1 1.0
N N:GLY170 4.5 36.4 1.0
CA N:SER169 4.6 33.7 1.0
NH2 N:ARG19 4.7 37.8 1.0
N N:LYS164 4.8 40.5 1.0
CG a:LEU34 4.8 39.6 1.0
O N:LYS164 4.8 42.4 1.0
CB N:ILE163 4.9 37.9 1.0
CA N:ASP166 4.9 36.8 1.0
N N:ASP166 4.9 37.0 1.0
C N:LYS164 4.9 41.6 1.0
CA N:LYS164 5.0 42.0 1.0

Magnesium binding site 7 out of 7 in 4y8l

Go back to Magnesium Binding Sites List in 4y8l
Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Apll-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Yeast 20S Proteasome in Complex with Ac-Apll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:57.7
occ:1.00
 O Z:HOH430 2.3 44.0 1.0
O Z:VAL198 2.5 48.0 1.0
O Z:THR192 2.6 53.7 1.0
O Z:HIS195 2.8 38.9 1.0
NH2 Z:ARG28 3.6 51.5 1.0
C Z:THR192 3.7 51.0 1.0
C Z:VAL198 3.7 45.8 1.0
CG2 Z:THR192 3.8 50.5 1.0
C Z:HIS195 3.8 39.1 1.0
O Z:ILE196 3.8 40.7 1.0
O Z:ASP222 3.9 58.0 1.0
CA Z:ILE196 4.0 38.8 1.0
CA Z:THR192 4.0 49.9 1.0
C Z:ILE196 4.1 39.1 1.0
N Z:VAL198 4.3 42.8 1.0
N Z:ILE196 4.3 38.7 1.0
NH2 H:ARG19 4.5 53.0 1.0
CB Z:THR192 4.5 50.3 1.0
OD1 Z:ASP222 4.5 56.9 1.0
CA Z:VAL198 4.5 43.9 1.0
N Z:GLY199 4.6 46.2 1.0
CZ Z:ARG28 4.7 50.3 1.0
CA Z:GLY199 4.7 47.4 1.0
C Z:ASP222 4.8 57.5 1.0
N Z:GLU193 4.9 51.2 1.0
NH1 Z:ARG28 4.9 52.2 1.0
N Z:GLN197 5.0 39.3 1.0
N Z:HIS195 5.0 41.6 1.0

Reference:

E.M.Huber, G.De Bruin, W.Heinemeyer, G.Paniagua Soriano, H.S.Overkleeft, M.Groll. Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors. J.Am.Chem.Soc. V. 137 7835 2015.
ISSN: ESSN 1520-5126
PubMed: 26020686
DOI: 10.1021/JACS.5B03688
Page generated: Tue Aug 12 03:57:25 2025

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