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Magnesium in PDB 4y8h: Yeast 20S Proteasome in Complex with N3-Apal-Ep

Enzymatic activity of Yeast 20S Proteasome in Complex with N3-Apal-Ep

All present enzymatic activity of Yeast 20S Proteasome in Complex with N3-Apal-Ep:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with N3-Apal-Ep, PDB code: 4y8h 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.320, 300.790, 145.460, 90.00, 113.64, 90.00
R / Rfree (%) 20.1 / 21.4

Other elements in 4y8h:

The structure of Yeast 20S Proteasome in Complex with N3-Apal-Ep also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with N3-Apal-Ep (pdb code 4y8h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with N3-Apal-Ep, PDB code: 4y8h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4y8h

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:41.9
occ:1.00
 O G:MET125 2.2 42.4 1.0
O G:HOH406 2.2 38.6 1.0
O G:ARG122 2.4 40.4 1.0
O G:TYR119 2.4 38.0 1.0
OG1 G:THR8 2.6 39.9 1.0
C G:ARG122 3.4 40.9 1.0
C G:MET125 3.4 45.0 1.0
O G:ALA123 3.4 45.8 1.0
CG2 G:THR8 3.5 42.6 1.0
C G:TYR119 3.6 36.8 1.0
CB G:THR8 3.6 41.8 1.0
CA G:ALA123 3.6 42.0 1.0
C G:ALA123 3.6 45.2 1.0
N G:ALA123 4.0 40.1 1.0
N G:MET125 4.1 45.8 1.0
CA G:MET125 4.3 48.9 1.0
CA G:TYR119 4.3 36.6 1.0
N G:ARG126 4.4 41.5 1.0
N G:THR8 4.4 41.8 1.0
CA G:ARG126 4.5 37.7 1.0
N G:TYR124 4.5 47.9 1.0
N G:ARG122 4.6 40.5 1.0
N G:THR120 4.6 35.4 1.0
CA G:ARG122 4.6 44.2 1.0
CA G:THR8 4.6 42.2 1.0
CD G:PRO127 4.7 29.8 1.0
CB G:MET125 4.7 56.2 1.0
CA G:THR120 4.8 35.3 1.0
C G:THR120 4.8 36.6 1.0
CB G:TYR119 4.9 38.1 1.0
N G:GLN121 5.0 36.7 1.0
CB G:ALA123 5.0 40.6 1.0
C G:TYR124 5.0 45.6 1.0

Magnesium binding site 2 out of 8 in 4y8h

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:58.9
occ:1.00
 O I:ASP177 2.4 41.1 1.0
O I:SER180 2.7 46.2 1.0
O I:ALA174 2.8 41.2 1.0
O I:HOH422 3.6 41.1 1.0
O I:HOH437 3.6 48.5 1.0
C I:ASP177 3.6 40.1 1.0
OXT I:ASP204 3.8 52.0 1.0
C I:ALA174 3.8 42.6 1.0
C I:SER180 3.9 44.2 1.0
CA I:ASP175 4.2 44.6 1.0
CA I:ALA178 4.3 38.7 1.0
N I:ALA178 4.4 38.1 1.0
C I:ALA178 4.4 40.1 1.0
O I:ALA178 4.4 41.1 1.0
N I:ASP175 4.4 44.1 1.0
C I:ASP175 4.5 43.0 1.0
N I:ASP177 4.5 40.1 1.0
O I:ASP175 4.6 44.5 1.0
N I:SER180 4.6 40.6 1.0
CA I:ASP177 4.6 41.3 1.0
C I:ASP204 4.6 43.9 1.0
O I:ASP204 4.7 54.0 1.0
CA I:GLY181 4.7 42.9 1.0
N I:GLY181 4.8 43.3 1.0
NH2 Y:ARG19 4.8 60.9 1.0
NH1 Y:ARG19 4.8 61.1 1.0
CA I:SER180 4.8 42.5 1.0
OD1 I:ASP175 4.8 47.2 1.0
CA I:ALA174 4.9 40.2 1.0

Magnesium binding site 3 out of 8 in 4y8h

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:46.9
occ:1.00
 O Y:ASP168 2.1 41.8 1.0
O Y:SER171 2.3 44.0 1.0
O I:ASP204 2.3 54.0 1.0
O Y:ALA165 2.4 39.0 1.0
O Y:HOH410 2.5 30.7 1.0
C Y:ASP168 3.2 39.0 1.0
C I:ASP204 3.2 43.9 1.0
C Y:SER171 3.5 42.7 1.0
C Y:ALA165 3.6 41.6 1.0
CA Y:ALA169 3.6 35.1 1.0
C Y:ALA169 3.6 36.5 1.0
NH1 Y:ARG19 3.6 61.1 1.0
O Y:ALA169 3.6 35.6 1.0
CA I:ASP204 3.8 48.4 1.0
N Y:ALA169 3.8 35.9 1.0
N Y:SER171 3.9 42.5 1.0
CB I:ASP204 4.0 46.4 1.0
OXT I:ASP204 4.2 52.0 1.0
CA Y:SER171 4.2 41.9 1.0
CA Y:ALA165 4.3 42.3 1.0
O Y:HIS166 4.3 40.4 1.0
N Y:TYR170 4.3 39.5 1.0
CZ Y:ARG19 4.3 58.0 1.0
CA Y:ASP168 4.4 39.5 1.0
N Y:GLY172 4.5 42.0 1.0
N Y:ASP168 4.5 40.2 1.0
C Y:HIS166 4.6 39.8 1.0
N Y:HIS166 4.6 41.2 1.0
O Y:ALA164 4.6 42.5 1.0
CA Y:GLY172 4.7 41.8 1.0
NH2 Y:ARG19 4.7 60.9 1.0
CB Y:SER171 4.8 40.9 1.0
CA Y:HIS166 4.8 40.3 1.0
C Y:TYR170 4.9 44.3 1.0
CB Y:ALA169 5.0 35.0 1.0

Magnesium binding site 4 out of 8 in 4y8h

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:44.3
occ:1.00
 O K:ASP168 2.2 40.4 1.0
O W:ASP204 2.3 39.8 1.0
O K:ALA165 2.3 38.0 1.0
O K:SER171 2.5 46.0 1.0
C W:ASP204 3.1 29.8 1.0
C K:ASP168 3.3 38.2 1.0
C K:ALA165 3.5 41.5 1.0
CA W:ASP204 3.5 39.6 1.0
CA K:ALA169 3.6 37.1 1.0
C K:SER171 3.7 45.9 1.0
NH1 K:ARG19 3.7 53.2 1.0
C K:ALA169 3.7 41.1 1.0
O K:ALA169 3.8 42.2 1.0
N K:ALA169 3.8 37.1 1.0
CB W:ASP204 3.9 42.2 1.0
OXT W:ASP204 4.0 37.6 1.0
O K:HIS166 4.0 39.9 1.0
N K:SER171 4.1 46.8 1.0
CA K:ALA165 4.3 42.7 1.0
C K:HIS166 4.4 40.0 1.0
CA K:SER171 4.4 45.1 1.0
CA K:ASP168 4.5 37.2 1.0
CZ K:ARG19 4.5 53.7 1.0
N K:HIS166 4.5 40.5 1.0
N K:TYR170 4.5 44.8 1.0
N K:ASP168 4.5 37.1 1.0
O K:ALA164 4.6 41.9 1.0
CA K:HIS166 4.6 40.6 1.0
N K:GLY172 4.7 44.7 1.0
NH2 K:ARG19 4.8 58.0 1.0
CA K:GLY172 4.8 44.1 1.0
N W:ASP204 4.9 39.9 1.0
C K:ARG167 4.9 36.8 1.0
CB K:SER171 5.0 43.0 1.0
CG W:ASP204 5.0 43.6 1.0

Magnesium binding site 5 out of 8 in 4y8h

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:55.9
occ:1.00
 O V:ASP166 2.2 42.1 1.0
O V:ILE163 2.3 50.1 1.0
OXT L:ASP222 2.4 56.8 1.0
O V:SER169 2.8 44.9 1.0
C L:ASP222 3.1 59.6 1.0
C V:ASP166 3.1 43.7 1.0
C V:ILE163 3.3 51.2 1.0
CA L:ASP222 3.6 57.2 1.0
O V:TRP164 3.7 50.1 1.0
N V:ASP166 3.8 42.3 1.0
C V:TRP164 3.8 48.2 1.0
N V:LEU167 3.8 44.1 1.0
O L:ASP222 3.8 62.6 1.0
CA V:LEU167 3.9 43.4 1.0
O V:GLY162 3.9 46.7 1.0
C V:SER169 4.0 42.7 1.0
CA V:ASP166 4.0 42.7 1.0
N V:TRP164 4.1 48.5 1.0
CA V:TRP164 4.2 48.1 1.0
N V:ASN165 4.3 46.4 1.0
NH1 V:ARG19 4.3 60.9 1.0
CA V:ILE163 4.3 53.9 1.0
CB L:ASP222 4.4 55.2 1.0
C V:ASN165 4.4 42.9 1.0
C V:LEU167 4.5 40.5 1.0
O L:ARG221 4.5 50.4 1.0
N V:SER169 4.6 38.8 1.0
CD2 V:LEU167 4.7 40.3 1.0
NH2 V:ARG19 4.8 58.6 1.0
CZ V:ARG19 4.8 59.1 1.0
N L:ASP222 4.9 54.2 1.0
CA V:ASN165 4.9 45.2 1.0
CA V:SER169 4.9 39.3 1.0
C V:GLY162 4.9 48.0 1.0
O V:LEU167 4.9 39.3 1.0
CB V:ASP166 4.9 42.1 1.0
N V:GLY170 5.0 43.1 1.0
CA V:GLY170 5.0 44.7 1.0

Magnesium binding site 6 out of 8 in 4y8h

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:45.4
occ:1.00
 O N:SER169 2.4 38.3 1.0
O N:ILE163 2.4 36.6 1.0
O N:ASP166 2.6 41.2 1.0
C N:ILE163 3.6 37.4 1.0
C N:SER169 3.6 36.5 1.0
C N:ASP166 3.7 38.0 1.0
NH1 N:ARG19 3.7 44.9 1.0
CD1 a:LEU34 3.8 36.6 1.0
CG2 N:ILE163 3.8 30.4 1.0
CA N:GLY167 4.0 36.5 1.0
CA N:ILE163 4.2 35.5 1.0
N N:GLY167 4.3 36.6 1.0
O N:GLY167 4.3 35.6 1.0
C N:GLY167 4.3 35.6 1.0
N N:SER169 4.4 33.5 1.0
CZ N:ARG19 4.4 42.5 1.0
CA N:GLY170 4.5 41.9 1.0
N N:GLY170 4.5 39.5 1.0
CA N:SER169 4.5 32.1 1.0
CB N:ILE163 4.6 33.8 1.0
NH2 N:ARG19 4.6 41.1 1.0
N N:LYS164 4.7 39.3 1.0
CA N:ASP166 4.9 37.5 1.0
O N:LYS164 4.9 41.6 1.0
C N:LYS164 4.9 41.9 1.0
N N:ASP166 4.9 38.1 1.0
CB N:SER169 4.9 28.8 1.0
CA N:LYS164 5.0 41.9 1.0
CG a:LEU34 5.0 38.8 1.0

Magnesium binding site 7 out of 8 in 4y8h

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with N3-Apal-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 N3-Apal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:59.4
occ:1.00
 OD1 N:ASP51 2.6 33.4 1.0
O N:ASN92 2.9 47.3 1.0
OE1 H:GLN91 3.2 69.4 1.0
CG N:ASP51 3.3 34.7 1.0
NE2 H:GLN91 3.4 64.1 1.0
OD2 N:ASP51 3.5 35.8 1.0
CD H:GLN91 3.7 64.1 1.0
CZ H:PHE88 4.0 31.7 1.0
O H:HOH304 4.1 29.7 1.0
C N:ASN92 4.1 44.4 1.0
CE1 H:PHE88 4.2 31.8 1.0
CD2 N:LEU93 4.5 36.4 1.0
CB N:ASP51 4.7 33.9 1.0
CB N:ASN92 4.8 45.9 1.0
CA N:LEU93 4.9 44.1 1.0
CE2 H:PHE88 4.9 30.8 1.0
N N:LEU93 5.0 45.5 1.0

Magnesium binding site 8 out of 8 in 4y8h

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with N3-Apal-Ep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Yeast 20S Proteasome in Complex with N3-Apal-Ep within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:56.8
occ:1.00
 O Z:VAL198 2.5 44.2 1.0
O Z:THR192 2.5 45.7 1.0
O Z:HIS195 2.6 37.0 1.0
C Z:THR192 3.5 47.5 1.0
C Z:HIS195 3.6 37.2 1.0
CG2 Z:THR192 3.7 39.7 1.0
C Z:VAL198 3.7 44.4 1.0
CA Z:THR192 3.8 45.1 1.0
NH2 Z:ARG28 3.9 55.1 1.0
CA Z:ILE196 3.9 39.4 1.0
O Z:ILE196 3.9 40.3 1.0
O Z:ASP222 4.0 57.1 1.0
C Z:ILE196 4.1 39.4 1.0
N Z:ILE196 4.2 37.9 1.0
N Z:VAL198 4.3 41.3 1.0
CB Z:THR192 4.4 42.6 1.0
CA Z:VAL198 4.5 43.2 1.0
OD1 Z:ASP222 4.6 51.9 1.0
N Z:GLY199 4.6 44.8 1.0
NH2 H:ARG19 4.6 49.0 1.0
CA Z:GLY199 4.7 45.8 1.0
N Z:GLU193 4.7 49.3 1.0
N Z:HIS195 4.7 39.5 1.0
CA Z:HIS195 4.8 37.7 1.0
O Z:ALA191 4.9 43.6 1.0
C Z:ASP222 4.9 54.6 1.0
CZ Z:ARG28 5.0 55.1 1.0
CB Z:VAL198 5.0 45.4 1.0
N Z:GLN197 5.0 38.5 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 03:55:23 2025

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