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Magnesium in PDB 5jhr: Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27

Enzymatic activity of Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27

All present enzymatic activity of Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27, PDB code: 5jhr 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.290, 300.810, 144.540, 90.00, 112.95, 90.00
R / Rfree (%) 18.1 / 20.6

Other elements in 5jhr:

The structure of Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27 (pdb code 5jhr). 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 the Peptidic Epoxyketone Inhibitor 27, PDB code: 5jhr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5jhr

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27


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 the Peptidic Epoxyketone Inhibitor 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:53.9
occ:1.00
 O G:MET125 2.4 52.2 1.0
O G:ARG122 2.4 49.7 1.0
OG1 G:THR8 2.6 46.3 1.0
O G:TYR119 2.7 45.5 1.0
CG2 G:THR8 3.3 49.7 1.0
O G:ALA123 3.3 51.5 1.0
CB G:THR8 3.5 48.8 1.0
C G:MET125 3.5 50.2 1.0
C G:ARG122 3.5 49.7 1.0
CA G:ALA123 3.6 49.2 1.0
C G:ALA123 3.6 50.1 1.0
C G:TYR119 3.9 44.2 1.0
N G:ALA123 4.0 49.1 1.0
N G:THR8 4.1 51.6 1.0
N G:MET125 4.2 52.5 1.0
N G:ARG126 4.3 47.1 1.0
CA G:ARG126 4.4 45.8 1.0
CA G:MET125 4.4 53.4 1.0
CA G:THR8 4.4 50.2 1.0
N G:TYR124 4.6 51.3 1.0
CD G:PRO127 4.6 43.3 1.0
CA G:TYR119 4.7 42.7 1.0
CA G:ARG122 4.8 51.3 1.0
N G:ARG122 4.9 48.8 1.0
N G:THR120 4.9 44.3 1.0
CB G:ALA123 4.9 48.8 1.0
C G:ARG126 5.0 45.9 1.0
C G:TYR124 5.0 52.6 1.0

Magnesium binding site 2 out of 8 in 5jhr

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27


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 the Peptidic Epoxyketone Inhibitor 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:50.2
occ:1.00
 O I:ASP177 2.4 53.7 1.0
O I:SER180 2.6 52.5 1.0
O I:ALA174 2.8 55.9 1.0
C I:ASP177 3.5 52.4 1.0
OXT I:ASP204 3.7 57.3 1.0
C I:SER180 3.8 52.7 1.0
C I:ALA174 3.9 55.8 1.0
O I:ALA178 4.0 57.2 1.0
CA I:ASP175 4.2 56.4 1.0
CA I:ALA178 4.2 51.5 1.0
C I:ALA178 4.2 52.8 1.0
N I:ALA178 4.3 50.9 1.0
N I:ASP177 4.5 51.9 1.0
C I:ASP175 4.5 54.5 1.0
N I:ASP175 4.5 55.7 1.0
N I:SER180 4.5 50.7 1.0
CA I:ASP177 4.6 52.3 1.0
O I:ASP175 4.6 55.4 1.0
C I:ASP204 4.6 64.5 1.0
NH1 Y:ARG19 4.7 62.8 1.0
O I:ASP204 4.7 68.7 1.0
CA I:GLY181 4.7 52.3 1.0
N I:GLY181 4.7 52.2 1.0
CA I:SER180 4.7 51.9 1.0
OD1 I:ASP175 4.9 62.0 1.0
NH2 Y:ARG19 5.0 62.5 1.0
N I:LEU179 5.0 51.9 1.0

Magnesium binding site 3 out of 8 in 5jhr

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27


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 the Peptidic Epoxyketone Inhibitor 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:50.1
occ:1.00
 O Y:ASP168 2.1 56.0 1.0
O I:ASP204 2.3 68.7 1.0
O Y:ALA165 2.4 52.9 1.0
O Y:SER171 2.8 52.4 1.0
C I:ASP204 3.1 64.5 1.0
C Y:ASP168 3.1 52.0 1.0
CA Y:ALA169 3.5 53.9 1.0
C Y:ALA165 3.6 51.3 1.0
CA I:ASP204 3.6 64.2 1.0
N Y:ALA169 3.7 52.7 1.0
C Y:ALA169 3.7 53.9 1.0
O Y:ALA169 3.7 55.3 1.0
OXT I:ASP204 3.9 57.3 1.0
C Y:SER171 3.9 54.5 1.0
O Y:HIS166 3.9 51.1 1.0
NH1 Y:ARG19 4.0 62.8 1.0
CB I:ASP204 4.1 66.2 1.0
C Y:HIS166 4.2 53.0 1.0
N Y:SER171 4.3 52.2 1.0
CA Y:ASP168 4.3 50.2 1.0
N Y:ASP168 4.4 50.4 1.0
CA Y:ALA165 4.4 51.9 1.0
N Y:HIS166 4.5 50.3 1.0
N Y:TYR170 4.5 53.5 1.0
CA Y:HIS166 4.6 52.2 1.0
CZ Y:ARG19 4.6 61.4 1.0
CA Y:SER171 4.6 52.3 1.0
O Y:ALA164 4.7 48.7 1.0
C Y:ARG167 4.7 52.2 1.0
CB Y:ALA169 4.8 55.1 1.0
NH2 Y:ARG19 4.8 62.5 1.0
N Y:ARG167 4.8 52.9 1.0
N Y:GLY172 5.0 57.0 1.0
O Y:ARG167 5.0 51.1 1.0
N I:ASP204 5.0 62.8 1.0

Magnesium binding site 4 out of 8 in 5jhr

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27


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 the Peptidic Epoxyketone Inhibitor 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:30.0
occ:1.00
 OE1 J:GLN118 3.5 48.1 1.0
O J:THR124 3.7 47.4 1.0
CB J:ASP120 3.7 42.0 1.0
CG J:ASP120 3.9 45.1 1.0
OD2 J:ASP120 4.0 49.7 1.0
N J:ASP120 4.0 39.7 1.0
CB J:THR124 4.2 44.5 1.0
CD J:GLN118 4.2 45.3 1.0
CG J:GLN118 4.3 44.0 1.0
CE1 J:HIS133 4.3 40.1 1.0
CG2 J:THR124 4.4 44.0 1.0
CA J:ASP120 4.5 40.2 1.0
O J:GLN118 4.5 39.8 1.0
CG2 J:VAL126 4.6 51.4 1.0
OD1 J:ASP120 4.6 49.8 1.0
C J:THR124 4.7 44.3 1.0
O J:HOH301 4.7 27.5 1.0
C J:ILE119 4.7 39.3 1.0
CG1 I:VAL35 4.9 53.1 1.0
C J:GLN118 4.9 40.7 1.0
CA J:ILE119 5.0 39.3 1.0

Magnesium binding site 5 out of 8 in 5jhr

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27


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 the Peptidic Epoxyketone Inhibitor 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:55.3
occ:1.00
 O K:ASP168 2.2 53.4 1.0
O K:ALA165 2.2 54.9 1.0
O W:ASP204 2.2 66.0 1.0
O K:SER171 2.5 53.5 1.0
C W:ASP204 3.1 62.4 1.0
C K:ASP168 3.3 52.1 1.0
C K:ALA165 3.4 55.0 1.0
CA W:ASP204 3.6 59.5 1.0
CA K:ALA169 3.7 53.2 1.0
C K:SER171 3.7 53.0 1.0
O K:ALA169 3.8 57.1 1.0
C K:ALA169 3.8 55.1 1.0
N K:ALA169 3.9 52.2 1.0
CB W:ASP204 3.9 58.6 1.0
OXT W:ASP204 4.0 62.0 1.0
NH1 K:ARG19 4.0 60.0 1.0
O K:HIS166 4.0 55.2 1.0
N K:SER171 4.2 50.0 1.0
CA K:ALA165 4.2 55.4 1.0
C K:HIS166 4.3 55.7 1.0
N K:HIS166 4.3 53.6 1.0
N K:ASP168 4.4 52.6 1.0
CA K:ASP168 4.4 51.9 1.0
CA K:SER171 4.5 51.3 1.0
CA K:HIS166 4.5 55.3 1.0
CZ K:ARG19 4.5 59.0 1.0
O K:ALA164 4.6 53.7 1.0
N K:TYR170 4.6 54.6 1.0
N K:GLY172 4.7 54.2 1.0
NH2 K:ARG19 4.7 61.0 1.0
C K:ARG167 4.8 53.3 1.0
CA K:GLY172 4.8 55.1 1.0
CB K:SER171 4.8 50.5 1.0
N K:ARG167 4.9 53.9 1.0
CG W:ASP204 4.9 59.1 1.0
N W:ASP204 5.0 60.0 1.0

Magnesium binding site 6 out of 8 in 5jhr

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27


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 the Peptidic Epoxyketone Inhibitor 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:72.2
occ:1.00
 O V:ASP166 2.0 56.9 1.0
O V:ILE163 2.2 57.4 1.0
OXT L:ASP222 2.2 68.7 1.0
O V:SER169 2.7 54.3 1.0
C V:ASP166 3.1 56.3 1.0
C L:ASP222 3.1 67.7 1.0
C V:ILE163 3.3 59.5 1.0
CA L:ASP222 3.7 66.3 1.0
N V:LEU167 3.8 56.1 1.0
CA V:LEU167 3.8 54.6 1.0
O V:GLY162 3.8 58.5 1.0
O V:TRP164 3.8 58.3 1.0
C V:SER169 3.9 54.5 1.0
O L:ASP222 3.9 70.9 1.0
N V:ASP166 3.9 55.2 1.0
C V:TRP164 3.9 59.8 1.0
CA V:ASP166 4.1 54.9 1.0
N V:TRP164 4.1 59.4 1.0
CA V:ILE163 4.2 59.7 1.0
NH1 V:ARG19 4.2 60.6 1.0
CA V:TRP164 4.2 60.1 1.0
CB L:ASP222 4.3 66.3 1.0
C V:LEU167 4.3 53.8 1.0
N V:ASN165 4.4 58.2 1.0
C V:ASN165 4.5 55.6 1.0
N V:SER169 4.6 53.6 1.0
O V:LEU167 4.7 53.2 1.0
CA V:SER169 4.7 53.5 1.0
CD2 V:LEU167 4.8 53.0 1.0
CA V:GLY170 4.8 57.6 1.0
CZ V:ARG19 4.8 58.7 1.0
N V:GLY170 4.8 55.6 1.0
C V:GLY162 4.8 58.0 1.0
O L:ARG221 4.8 65.1 1.0
NH2 V:ARG19 4.9 60.9 1.0
CB V:ASP166 4.9 54.6 1.0
N L:ASP222 5.0 65.5 1.0
CA V:ASN165 5.0 57.1 1.0

Magnesium binding site 7 out of 8 in 5jhr

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27


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 the Peptidic Epoxyketone Inhibitor 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:55.6
occ:1.00
 O N:ILE163 2.5 48.7 1.0
O N:SER169 2.7 48.6 1.0
O N:ASP166 3.0 48.7 1.0
C N:ILE163 3.6 50.6 1.0
CD1 a:LEU34 3.6 47.8 1.0
NH1 N:ARG19 3.7 53.1 1.0
C N:SER169 3.8 48.2 1.0
CG2 N:ILE163 3.9 50.3 1.0
C N:ASP166 4.1 48.1 1.0
CZ N:ARG19 4.3 51.2 1.0
CA N:GLY167 4.3 47.5 1.0
CA N:ILE163 4.4 50.2 1.0
CA N:GLY170 4.4 50.8 1.0
NH2 N:ARG19 4.4 50.8 1.0
N N:GLY170 4.6 50.3 1.0
O N:GLY167 4.6 46.2 1.0
N N:GLY167 4.6 47.6 1.0
N N:LYS164 4.6 51.0 1.0
C N:GLY167 4.7 46.2 1.0
CB N:ILE163 4.7 49.6 1.0
O N:LYS164 4.7 57.8 1.0
C N:LYS164 4.8 54.7 1.0
CA N:LYS164 4.8 53.9 1.0
CA N:SER169 4.9 45.5 1.0
N N:SER169 4.9 46.1 1.0
CG a:LEU34 4.9 49.2 1.0

Magnesium binding site 8 out of 8 in 5jhr

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with the Peptidic Epoxyketone Inhibitor 27


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 the Peptidic Epoxyketone Inhibitor 27 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:54.1
occ:1.00
 O Z:VAL198 2.7 55.6 1.0
O Z:HIS195 2.7 50.8 1.0
O Z:THR192 2.8 69.4 1.0
NH2 Z:ARG28 3.6 62.6 1.0
O Z:ASP222 3.7 71.8 1.0
C Z:HIS195 3.7 52.1 1.0
CA Z:ILE196 3.7 51.9 1.0
O Z:ILE196 3.7 54.1 1.0
C Z:THR192 3.8 64.4 1.0
C Z:VAL198 3.8 56.2 1.0
C Z:ILE196 3.9 51.9 1.0
CG2 Z:THR192 4.0 63.1 1.0
N Z:ILE196 4.1 51.6 1.0
CA Z:THR192 4.2 62.2 1.0
NH2 H:ARG19 4.2 66.5 1.0
N Z:VAL198 4.4 53.8 1.0
OD1 Z:ASP222 4.5 68.4 1.0
C Z:ASP222 4.6 72.5 1.0
CA Z:VAL198 4.6 55.1 1.0
CZ Z:ARG28 4.7 61.8 1.0
CB Z:THR192 4.7 63.0 1.0
N Z:GLY199 4.8 56.5 1.0
N Z:GLN197 4.8 51.8 1.0
NH1 H:ARG19 4.9 64.9 1.0
CA Z:GLY199 4.9 58.8 1.0
CA Z:HIS195 4.9 52.5 1.0
N Z:HIS195 4.9 53.0 1.0
CZ H:ARG19 4.9 64.4 1.0
NH1 Z:ARG28 5.0 65.1 1.0
OXT Z:ASP222 5.0 78.1 1.0
CB Z:ILE196 5.0 51.4 1.0

Reference:

B.T.Xin, G.De Bruin, E.M.Huber, A.Besse, B.I.Florea, D.V.Filippov, G.A.Van Der Marel, A.F.Kisselev, M.Van Der Stelt, C.Driessen, M.Groll, H.S.Overkleeft. Structure-Based Design of Beta 5C Selective Inhibitors of Human Constitutive Proteasomes. J.Med.Chem. V. 59 7177 2016.
ISSN: ISSN 0022-2623
PubMed: 27438186
DOI: 10.1021/ACS.JMEDCHEM.6B00705
Page generated: Sun Sep 29 17:44:50 2024

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