Magnesium in PDB 8rhl: Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)

Enzymatic activity of Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)

All present enzymatic activity of Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A):
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A), PDB code: 8rhl was solved by M.G.Goetz, K.Godwin, R.Price, R.Dorn, G.Merrill-Steskal, H.Hansen, W.Klemmer, G.Produturi, M.Rocha, M.Palmer, L.Molacek, Z.Strater, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.21, 303.14, 143.23, 90, 113.09, 90
R / Rfree (%) 18.4 / 22.8

Other elements in 8rhl:

The structure of Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A) (pdb code 8rhl). 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 A Linear Biarylether Epoxyketone (Compound 15A), PDB code: 8rhl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8rhl

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)


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 A Linear Biarylether Epoxyketone (Compound 15A) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:74.2
occ:1.00
 O G:MET125 2.3 78.7 1.0
OG1 G:THR8 2.7 69.5 1.0
O G:ARG122 2.9 87.3 1.0
O G:ALA123 2.9 87.5 1.0
O G:TYR119 3.2 74.8 1.0
CG2 G:THR8 3.3 73.5 1.0
C G:MET125 3.4 78.5 1.0
C G:ALA123 3.5 83.0 1.0
CB G:THR8 3.5 72.2 1.0
CA G:ALA123 3.6 80.9 1.0
C G:ARG122 3.9 83.8 1.0
N G:THR8 3.9 76.2 1.0
CA G:ARG126 4.1 71.0 1.0
N G:ARG126 4.1 72.9 1.0
N G:ALA123 4.2 80.5 1.0
N G:MET125 4.3 85.0 1.0
CA G:THR8 4.3 75.1 1.0
C G:TYR119 4.4 73.6 1.0
CA G:MET125 4.5 85.9 1.0
N G:TYR124 4.5 85.3 1.0
CD G:PRO127 4.6 67.9 1.0
C G:ARG126 4.9 67.9 1.0
CB G:ALA123 4.9 79.5 1.0
C G:ILE7 4.9 79.6 1.0
C G:TYR124 4.9 83.3 1.0

Magnesium binding site 2 out of 8 in 8rhl

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)


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 A Linear Biarylether Epoxyketone (Compound 15A) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:84.0
occ:1.00
 O I:ASP177 2.7 70.3 1.0
O I:ALA174 2.8 76.2 1.0
O I:SER180 2.9 70.0 1.0
OXT I:ASP204 3.2 96.4 1.0
C I:ALA174 3.9 79.0 1.0
C I:ASP177 3.9 73.0 1.0
CA I:ASP175 4.0 81.8 1.0
C I:SER180 4.1 74.0 1.0
C I:ASP204 4.1 93.2 1.0
O I:ASP204 4.2 95.3 1.0
C I:ASP175 4.4 80.0 1.0
O I:ASP175 4.4 84.3 1.0
N I:ASP175 4.4 79.3 1.0
O I:ALA178 4.4 83.6 1.0
CA I:ALA178 4.6 75.5 1.0
NH2 Y:ARG19 4.6 89.7 1.0
C I:ALA178 4.7 76.8 1.0
N I:ALA178 4.7 72.2 1.0
OD1 I:ASP175 4.7 87.1 1.0
N I:ASP177 4.8 74.1 1.0
CA I:GLY181 4.8 76.7 1.0
N I:GLY181 4.8 74.4 1.0
CA I:ASP177 4.9 74.7 1.0
N I:SER180 5.0 75.4 1.0

Magnesium binding site 3 out of 8 in 8rhl

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)


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 A Linear Biarylether Epoxyketone (Compound 15A) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:100.5
occ:1.00
 O K:ASP168 2.4 69.4 1.0
O W:ASP204 2.4 109.9 1.0
O K:ALA165 2.8 70.6 1.0
C W:ASP204 3.0 105.9 1.0
O K:HIS166 3.1 73.5 1.0
C K:ASP168 3.2 73.7 1.0
O K:SER171 3.3 73.9 1.0
CA W:ASP204 3.4 97.1 1.0
CA K:ALA169 3.5 79.1 1.0
N K:ALA169 3.7 76.6 1.0
O K:ALA169 3.8 79.4 1.0
OXT W:ASP204 3.8 114.5 1.0
C K:ALA169 3.8 79.9 1.0
NH1 K:ARG19 3.8 88.3 1.0
C K:ALA165 3.9 72.3 1.0
C K:HIS166 3.9 72.5 1.0
CB W:ASP204 4.2 96.1 1.0
N K:ASP168 4.4 71.4 1.0
CA K:ASP168 4.4 72.2 1.0
C K:SER171 4.5 72.4 1.0
CA K:HIS166 4.5 73.5 1.0
C K:ARG167 4.5 71.9 1.0
N K:HIS166 4.6 71.4 1.0
N W:ASP204 4.6 93.6 1.0
O K:ARG167 4.7 70.4 1.0
N K:TYR170 4.7 78.4 1.0
NE1 W:TRP182 4.7 79.2 1.0
N K:SER171 4.7 73.5 1.0
N K:ARG167 4.8 70.5 1.0
CB K:ALA169 4.8 80.0 1.0
O K:ALA164 4.9 71.7 1.0
CZ K:ARG19 4.9 87.2 1.0
CA K:ALA165 4.9 72.2 1.0

Magnesium binding site 4 out of 8 in 8rhl

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)


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 A Linear Biarylether Epoxyketone (Compound 15A) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:68.3
occ:1.00
 O N:SER169 2.6 80.1 1.0
O N:ILE163 2.7 70.8 1.0
O N:ASP166 3.1 65.3 1.0
NH1 N:ARG19 3.4 75.5 1.0
CD1 a:LEU34 3.7 66.9 1.0
C N:SER169 3.8 79.4 1.0
C N:ILE163 3.8 71.7 1.0
CG2 N:ILE163 4.0 71.8 1.0
CA N:GLY170 4.2 80.6 1.0
CZ N:ARG19 4.2 73.2 1.0
C N:ASP166 4.3 68.8 1.0
NH2 N:ARG19 4.4 73.1 1.0
N N:GLY170 4.4 79.8 1.0
CA N:ILE163 4.5 70.7 1.0
O N:GLY167 4.5 66.8 1.0
CA N:GLY167 4.7 70.4 1.0
C N:GLY167 4.8 69.9 1.0
N N:LYS164 4.8 72.3 1.0
CB N:ILE163 4.8 70.8 1.0
N N:GLY167 4.9 69.4 1.0
CA N:SER169 4.9 76.0 1.0
N N:SER169 5.0 76.8 1.0
CG a:LEU34 5.0 68.6 1.0

Magnesium binding site 5 out of 8 in 8rhl

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)


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 A Linear Biarylether Epoxyketone (Compound 15A) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:104.8
occ:1.00
 OXT L:ASP222 2.3 115.2 1.0
O V:ASP166 2.4 77.7 1.0
O V:ILE163 2.6 79.2 1.0
C L:ASP222 2.9 108.8 1.0
O V:TRP164 3.1 79.0 1.0
C V:ASP166 3.2 78.9 1.0
C V:TRP164 3.6 77.1 1.0
CA L:ASP222 3.6 104.3 1.0
O V:SER169 3.6 73.8 1.0
O L:ASP222 3.7 110.7 1.0
C V:ILE163 3.7 81.3 1.0
N V:LEU167 3.8 79.0 1.0
CA V:LEU167 3.8 80.9 1.0
N V:ASP166 4.0 77.0 1.0
CD2 V:LEU167 4.1 80.3 1.0
CA V:TRP164 4.1 78.0 1.0
N V:ASN165 4.2 75.0 1.0
CA V:ASP166 4.2 78.5 1.0
N V:TRP164 4.3 79.0 1.0
O L:ARG221 4.3 88.1 1.0
C V:ASN165 4.3 75.4 1.0
O V:GLY162 4.4 78.3 1.0
CD1 L:ILE35 4.5 84.0 1.0
CB L:ASP222 4.5 103.8 1.0
C V:LEU167 4.5 81.3 1.0
N L:ASP222 4.7 100.4 1.0
NH1 V:ARG19 4.7 87.9 1.0
O V:LEU167 4.7 87.9 1.0
CA V:ASN165 4.8 74.2 1.0
C V:SER169 4.8 77.8 1.0
CA V:ILE163 4.9 81.4 1.0
O V:ASN165 4.9 73.4 1.0
C L:ARG221 4.9 92.7 1.0
CB V:LEU167 5.0 80.4 1.0
NH1 L:ARG28 5.0 100.8 1.0

Magnesium binding site 6 out of 8 in 8rhl

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)


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 A Linear Biarylether Epoxyketone (Compound 15A) within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg201

b:64.2
occ:1.00
 OE1 X:GLN118 3.5 70.7 1.0
O X:THR124 3.7 72.4 1.0
CB X:ASP120 3.9 72.9 1.0
N X:ASP120 4.1 71.4 1.0
CG X:GLN118 4.1 69.7 1.0
CG X:ASP120 4.2 73.4 1.0
CD X:GLN118 4.2 70.2 1.0
O X:GLN118 4.2 74.3 1.0
CE1 X:HIS133 4.2 74.5 1.0
OD2 X:ASP120 4.2 74.2 1.0
CB X:THR124 4.4 70.0 1.0
CG2 X:THR124 4.5 70.8 1.0
CG1 W:VAL35 4.5 74.7 1.0
CA X:ASP120 4.6 71.0 1.0
C X:GLN118 4.6 71.2 1.0
C X:THR124 4.7 70.7 1.0
C X:ILE119 4.7 69.3 1.0
OD1 X:ASP120 4.8 74.0 1.0
CB X:GLN118 4.9 70.2 1.0
CA X:ILE119 5.0 69.7 1.0
N X:ILE119 5.0 69.5 1.0
NE2 X:HIS133 5.0 72.4 1.0
CD2 W:LEU28 5.0 69.5 1.0

Magnesium binding site 7 out of 8 in 8rhl

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)


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 A Linear Biarylether Epoxyketone (Compound 15A) within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:90.3
occ:1.00
 O Y:ASP168 2.1 71.9 1.0
O Y:ALA165 2.3 83.9 1.0
O I:ASP204 2.4 95.3 1.0
O Y:SER171 2.9 80.1 1.0
O Y:HIS166 3.1 78.0 1.0
C Y:ASP168 3.2 73.3 1.0
C I:ASP204 3.2 93.2 1.0
C Y:ALA165 3.5 82.8 1.0
CA I:ASP204 3.5 91.6 1.0
CA Y:ALA169 3.7 73.8 1.0
NH1 Y:ARG19 3.8 92.6 1.0
N Y:ALA169 3.8 74.7 1.0
C Y:HIS166 3.8 79.4 1.0
C Y:ALA169 3.9 73.5 1.0
O Y:ALA169 3.9 71.0 1.0
CB I:ASP204 4.0 91.5 1.0
C Y:SER171 4.1 79.3 1.0
OXT I:ASP204 4.2 96.4 1.0
N Y:HIS166 4.2 80.9 1.0
N Y:ASP168 4.2 74.6 1.0
CA Y:HIS166 4.3 80.2 1.0
CA Y:ASP168 4.3 73.7 1.0
CA Y:ALA165 4.4 81.5 1.0
N Y:SER171 4.5 75.7 1.0
O Y:ALA164 4.5 81.9 1.0
C Y:ARG167 4.5 76.8 1.0
N Y:ARG167 4.6 77.4 1.0
N Y:TYR170 4.7 72.8 1.0
O Y:ARG167 4.8 74.1 1.0
CA Y:SER171 4.8 77.4 1.0
CZ Y:ARG19 4.8 90.2 1.0
N I:ASP204 4.9 90.0 1.0

Magnesium binding site 8 out of 8 in 8rhl

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with A Linear Biarylether Epoxyketone (Compound 15A)


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 A Linear Biarylether Epoxyketone (Compound 15A) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:98.1
occ:1.00
 O Z:VAL198 2.5 70.6 1.0
O Z:THR192 2.7 81.9 1.0
O Z:HIS195 3.0 69.9 1.0
O Z:ASP222 3.4 106.9 1.0
NH2 Z:ARG28 3.5 87.6 1.0
C Z:THR192 3.7 81.4 1.0
C Z:VAL198 3.8 74.4 1.0
CG2 Z:THR192 3.8 80.8 1.0
O Z:ILE196 3.9 81.1 1.0
C Z:HIS195 4.0 74.0 1.0
CA Z:THR192 4.1 79.9 1.0
CA Z:ILE196 4.1 77.5 1.0
C Z:ILE196 4.2 77.8 1.0
NH2 H:ARG19 4.2 98.1 1.0
OD1 Z:ASP222 4.3 89.0 1.0
C Z:ASP222 4.4 104.6 1.0
N Z:ILE196 4.5 74.4 1.0
CB Z:THR192 4.5 79.5 1.0
CZ Z:ARG28 4.5 85.0 1.0
N Z:VAL198 4.5 74.6 1.0
N Z:GLY199 4.6 75.9 1.0
CA Z:GLY199 4.6 78.3 1.0
CA Z:VAL198 4.7 72.9 1.0
NH1 Z:ARG28 4.8 87.7 1.0
OXT Z:ASP222 4.8 106.1 1.0
O Z:LYS220 4.9 87.8 1.0
N Z:GLU193 4.9 82.5 1.0

Reference:

M.G.Gotz, K.Godwin, R.Price, R.Dorn, G.Merrill-Steskal, W.Klemmer, H.Hansen, G.Produturi, M.Rocha, M.Palmer, L.Molacek, Z.Strater, M.Groll. Macrocyclic Oxindole Peptide Epoxyketones-A Comparative Study of Macrocyclic Inhibitors of the 20S Proteasome. Acs Med.Chem.Lett. V. 15 533 2024.
ISSN: ISSN 1948-5875
PubMed: 38628795
DOI: 10.1021/ACSMEDCHEMLETT.4C00017
Page generated: Fri Oct 4 17:39:47 2024

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