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Magnesium in PDB 4y8j: Yeast 20S Proteasome in Complex with Ac-Lll-Ep

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with Ac-Lll-Ep, PDB code: 4y8j 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.190, 299.330, 144.940, 90.00, 112.97, 90.00
R / Rfree (%) 19.8 / 22.4

Other elements in 4y8j:

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

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Ac-Lll-Ep (pdb code 4y8j). 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-Lll-Ep, PDB code: 4y8j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4y8j

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:69.4
occ:1.00
 O G:MET125 2.4 46.0 1.0
OG1 G:THR8 2.9 40.0 1.0
O G:ALA123 3.0 53.3 1.0
O G:ARG122 3.0 42.3 1.0
O G:TYR119 3.3 40.1 1.0
CG2 G:THR8 3.4 48.4 1.0
C G:MET125 3.4 49.7 1.0
C G:ALA123 3.6 50.0 1.0
CB G:THR8 3.7 46.3 1.0
CA G:ALA123 3.7 47.7 1.0
N G:THR8 4.0 46.1 1.0
C G:ARG122 4.0 46.4 1.0
CA G:ARG126 4.1 45.4 1.0
N G:ARG126 4.1 47.5 1.0
N G:MET125 4.2 50.2 1.0
O G:HOH408 4.2 49.5 1.0
N G:ALA123 4.4 46.2 1.0
CA G:MET125 4.4 51.6 1.0
CA G:THR8 4.5 48.6 1.0
CD G:PRO127 4.5 43.1 1.0
C G:TYR119 4.5 42.9 1.0
N G:TYR124 4.6 50.9 1.0
C G:ARG126 4.9 44.8 1.0
C G:TYR124 4.9 49.6 1.0
C G:ILE7 4.9 49.2 1.0
CB G:ALA123 5.0 47.2 1.0
CA G:ILE7 5.0 50.3 1.0

Magnesium binding site 2 out of 7 in 4y8j

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:56.1
occ:1.00
 O I:SER180 2.5 47.6 1.0
O I:ASP177 2.5 42.6 1.0
O I:ALA174 2.7 47.2 1.0
O I:HOH413 3.2 49.8 1.0
C I:SER180 3.7 46.2 1.0
C I:ASP177 3.7 44.3 1.0
OXT I:ASP204 3.7 50.0 1.0
C I:ALA174 3.8 49.2 1.0
CA I:ASP175 4.1 49.5 1.0
O I:ALA178 4.3 47.8 1.0
N I:ASP175 4.4 48.9 1.0
C I:ALA178 4.5 46.6 1.0
CA I:ALA178 4.5 44.7 1.0
C I:ASP175 4.5 48.5 1.0
CA I:GLY181 4.5 46.8 1.0
N I:ALA178 4.5 43.5 1.0
N I:SER180 4.6 45.3 1.0
N I:GLY181 4.6 46.8 1.0
N I:ASP177 4.6 44.1 1.0
C I:ASP204 4.7 54.2 1.0
OD1 I:ASP175 4.7 47.7 1.0
CA I:SER180 4.7 45.7 1.0
O I:ASP175 4.7 46.7 1.0
CA I:ASP177 4.7 45.2 1.0
NH1 Y:ARG19 4.7 55.5 1.0
O I:ASP204 4.7 57.1 1.0
CA I:ALA174 4.9 49.6 1.0
NH2 Y:ARG19 4.9 56.1 1.0

Magnesium binding site 3 out of 7 in 4y8j

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:49.7
occ:1.00
 O I:ASP204 2.1 57.1 1.0
O Y:ASP168 2.2 42.4 1.0
O Y:HOH407 2.5 58.3 1.0
O Y:ALA165 2.6 45.0 1.0
O Y:SER171 2.7 53.9 1.0
C I:ASP204 3.0 54.2 1.0
C Y:ASP168 3.2 42.4 1.0
CA Y:ALA169 3.4 42.3 1.0
O Y:ALA169 3.5 46.3 1.0
C Y:ALA169 3.6 44.0 1.0
CA I:ASP204 3.7 55.6 1.0
N Y:ALA169 3.7 42.9 1.0
C Y:ALA165 3.7 44.7 1.0
C Y:SER171 3.8 46.9 1.0
OXT I:ASP204 3.9 50.0 1.0
NH1 Y:ARG19 3.9 55.5 1.0
CB I:ASP204 4.1 56.4 1.0
O Y:HIS166 4.1 46.6 1.0
N Y:SER171 4.2 43.4 1.0
CZ Y:ARG19 4.4 53.7 1.0
N Y:TYR170 4.5 42.2 1.0
CA Y:ASP168 4.5 40.8 1.0
C Y:HIS166 4.5 44.3 1.0
N Y:ASP168 4.5 42.8 1.0
CA Y:SER171 4.6 43.3 1.0
CA Y:ALA165 4.6 44.4 1.0
NH2 Y:ARG19 4.7 56.1 1.0
N Y:HIS166 4.7 44.4 1.0
CB Y:ALA169 4.8 41.2 1.0
CA Y:HIS166 4.8 43.5 1.0
O Y:ALA164 4.8 43.6 1.0
N Y:GLY172 4.8 48.8 1.0
C Y:ARG167 4.9 43.7 1.0
CA Y:GLY172 4.9 49.4 1.0
CB Y:SER171 5.0 41.4 1.0

Magnesium binding site 4 out of 7 in 4y8j

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:55.7
occ:1.00
 O K:ASP168 2.2 44.8 1.0
O K:ALA165 2.3 45.9 1.0
O W:ASP204 2.3 53.7 1.0
O K:SER171 2.8 46.3 1.0
C W:ASP204 3.1 51.7 1.0
C K:ASP168 3.2 43.6 1.0
C K:ALA165 3.5 46.7 1.0
CA K:ALA169 3.6 42.5 1.0
CA W:ASP204 3.6 50.5 1.0
N K:ALA169 3.7 43.1 1.0
O K:ALA169 3.8 46.8 1.0
C K:ALA169 3.8 44.9 1.0
O K:HIS166 3.8 43.4 1.0
C K:SER171 3.9 45.2 1.0
OXT W:ASP204 4.0 52.3 1.0
CB W:ASP204 4.0 49.9 1.0
C K:HIS166 4.2 46.0 1.0
NH1 K:ARG19 4.2 49.0 1.0
N K:ASP168 4.3 44.5 1.0
N K:SER171 4.3 44.9 1.0
CA K:ASP168 4.3 42.9 1.0
CA K:ALA165 4.4 46.6 1.0
N K:HIS166 4.4 46.5 1.0
CA K:HIS166 4.5 47.0 1.0
O K:ALA164 4.6 46.5 1.0
N K:TYR170 4.6 44.9 1.0
CA K:SER171 4.6 43.8 1.0
CZ K:ARG19 4.7 48.7 1.0
C K:ARG167 4.7 44.4 1.0
N K:ARG167 4.8 45.1 1.0
N K:GLY172 4.9 44.9 1.0
NH2 K:ARG19 4.9 52.6 1.0
N W:ASP204 4.9 51.9 1.0
CB K:ALA169 4.9 40.6 1.0
CB K:SER171 5.0 43.4 1.0
CA K:GLY172 5.0 47.0 1.0

Magnesium binding site 5 out of 7 in 4y8j

Go back to Magnesium Binding Sites List in 4y8j
Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:57.9
occ:1.00
 O V:ASP166 2.1 51.0 1.0
O V:ILE163 2.3 57.0 1.0
OXT L:ASP222 2.3 55.9 1.0
O V:SER169 2.6 56.7 1.0
C V:ASP166 3.1 51.2 1.0
C L:ASP222 3.1 59.2 1.0
C V:ILE163 3.3 56.0 1.0
CA L:ASP222 3.7 59.5 1.0
O V:GLY162 3.8 51.3 1.0
C V:SER169 3.8 52.4 1.0
N V:ASP166 3.8 53.4 1.0
N V:LEU167 3.9 50.5 1.0
O L:ASP222 3.9 65.0 1.0
CA V:LEU167 3.9 50.5 1.0
C V:TRP164 3.9 57.2 1.0
O V:TRP164 4.0 57.1 1.0
CA V:ASP166 4.1 52.0 1.0
N V:TRP164 4.1 54.8 1.0
NH1 V:ARG19 4.2 54.7 1.0
CA V:ILE163 4.2 56.6 1.0
CA V:TRP164 4.3 56.5 1.0
N V:ASN165 4.3 57.3 1.0
CB L:ASP222 4.4 61.5 1.0
C V:LEU167 4.5 50.4 1.0
C V:ASN165 4.5 52.7 1.0
N V:SER169 4.5 49.2 1.0
CA V:SER169 4.7 50.6 1.0
CZ V:ARG19 4.7 52.5 1.0
N V:GLY170 4.7 53.3 1.0
CA V:GLY170 4.7 54.5 1.0
C V:GLY162 4.8 54.5 1.0
NH2 V:ARG19 4.8 55.5 1.0
O L:ARG221 4.8 59.3 1.0
CD2 V:LEU167 4.8 48.8 1.0
O V:LEU167 4.9 49.1 1.0
CA V:ASN165 4.9 54.1 1.0
CB V:ASP166 4.9 50.2 1.0
N V:ILE163 5.0 55.5 1.0

Magnesium binding site 6 out of 7 in 4y8j

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:55.9
occ:1.00
 O N:SER169 2.5 51.4 1.0
O N:ILE163 2.7 49.1 1.0
O N:ASP166 3.0 48.0 1.0
NH1 N:ARG19 3.6 47.0 1.0
CD1 a:LEU34 3.7 45.8 1.0
C N:SER169 3.7 45.9 1.0
C N:ILE163 3.8 48.9 1.0
CG2 N:ILE163 4.0 47.7 1.0
C N:ASP166 4.1 44.9 1.0
CZ N:ARG19 4.2 46.8 1.0
CA N:GLY167 4.3 43.2 1.0
CA N:GLY170 4.3 47.7 1.0
O N:GLY167 4.4 42.3 1.0
NH2 N:ARG19 4.4 46.5 1.0
N N:GLY170 4.5 47.0 1.0
CA N:ILE163 4.5 48.1 1.0
C N:GLY167 4.5 43.1 1.0
N N:GLY167 4.6 42.5 1.0
N N:SER169 4.7 42.3 1.0
CA N:SER169 4.7 41.9 1.0
O a:HOH313 4.8 48.6 1.0
N N:LYS164 4.9 49.9 1.0
CB N:ILE163 4.9 47.5 1.0
CG a:LEU34 5.0 46.0 1.0

Magnesium binding site 7 out of 7 in 4y8j

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome in Complex with Ac-Lll-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-Lll-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:72.3
occ:1.00
 O Z:VAL198 2.4 48.3 1.0
O Z:THR192 2.7 47.2 1.0
O Z:HIS195 3.0 44.7 1.0
NH2 Z:ARG28 3.5 57.9 1.0
CG2 Z:THR192 3.5 54.3 1.0
C Z:VAL198 3.6 49.6 1.0
C Z:THR192 3.7 53.5 1.0
O Z:ASP222 3.7 57.3 1.0
CA Z:THR192 3.9 53.0 1.0
O Z:ILE196 4.0 49.1 1.0
C Z:HIS195 4.1 44.2 1.0
CA Z:ILE196 4.2 44.4 1.0
C Z:ILE196 4.3 45.1 1.0
CB Z:THR192 4.3 53.0 1.0
OD1 Z:ASP222 4.3 55.0 1.0
N Z:VAL198 4.4 46.1 1.0
N Z:GLY199 4.5 50.8 1.0
CA Z:GLY199 4.5 51.8 1.0
CZ Z:ARG28 4.5 56.0 1.0
CA Z:VAL198 4.5 48.0 1.0
NH2 H:ARG19 4.6 57.3 1.0
N Z:ILE196 4.6 43.8 1.0
C Z:ASP222 4.6 58.0 1.0
NH1 Z:ARG28 4.8 57.9 1.0
O Z:LYS220 4.8 54.5 1.0
N Z:GLU193 4.9 55.0 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 03:55:41 2025

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