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Magnesium in PDB 5l6a: Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17

Enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17

All present enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17, PDB code: 5l6a was solved by M.Groll, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.330, 300.520, 145.190, 90.00, 112.66, 90.00
R / Rfree (%) 18.6 / 21.3

Other elements in 5l6a:

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 (pdb code 5l6a). 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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17, PDB code: 5l6a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5l6a

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:56.6
occ:1.00
 O G:MET125 2.1 52.7 1.0
O G:ARG122 2.4 48.7 1.0
O G:TYR119 2.5 45.5 1.0
OG1 G:THR8 2.6 45.3 1.0
CG2 G:THR8 3.2 49.5 1.0
C G:MET125 3.3 52.1 1.0
O G:ALA123 3.5 53.9 1.0
CB G:THR8 3.5 48.9 1.0
C G:ARG122 3.6 50.4 1.0
C G:TYR119 3.7 44.7 1.0
C G:ALA123 3.7 52.8 1.0
CA G:ALA123 3.8 50.9 1.0
N G:ALA123 4.1 50.2 1.0
N G:ARG126 4.2 48.8 1.0
N G:MET125 4.2 53.8 1.0
CA G:ARG126 4.2 47.9 1.0
N G:THR8 4.3 50.7 1.0
CA G:MET125 4.3 55.1 1.0
CA G:TYR119 4.5 43.6 1.0
CD G:PRO127 4.5 45.1 1.0
CA G:THR8 4.5 50.9 1.0
N G:TYR124 4.6 54.7 1.0
N G:THR120 4.7 44.2 1.0
CA G:ARG122 4.8 52.9 1.0
C G:ARG126 4.8 46.5 1.0
N G:ARG122 4.8 51.2 1.0
CA G:THR120 4.9 43.9 1.0
CB G:MET125 4.9 59.7 1.0
N G:PRO127 4.9 44.6 1.0
C G:THR120 5.0 43.9 1.0
CB G:TYR119 5.0 44.1 1.0
C G:TYR124 5.0 53.7 1.0

Magnesium binding site 2 out of 8 in 5l6a

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:57.8
occ:1.00
 O I:ASP177 2.3 52.4 1.0
O I:SER180 2.5 52.9 1.0
O I:ALA174 3.1 54.3 1.0
C I:ASP177 3.5 54.3 1.0
OXT I:ASP204 3.7 61.5 1.0
C I:SER180 3.8 55.4 1.0
O I:ALA178 3.9 56.9 1.0
CA I:ALA178 4.0 54.6 1.0
C I:ALA178 4.0 53.5 1.0
N I:ALA178 4.2 54.2 1.0
C I:ALA174 4.2 55.0 1.0
CD1 Y:ILE26 4.3 54.7 1.0
N I:SER180 4.3 52.8 1.0
O I:ASP204 4.5 65.5 1.0
C I:ASP204 4.5 63.5 1.0
CA I:ASP177 4.6 54.7 1.0
CA I:SER180 4.6 54.4 1.0
N I:ASP177 4.6 55.9 1.0
N I:GLY181 4.7 54.7 1.0
N I:LEU179 4.7 53.1 1.0
CA I:ASP175 4.7 58.5 1.0
CA I:GLY181 4.7 56.9 1.0
NH1 Y:ARG19 4.7 68.1 1.0
NH2 Y:ARG19 4.9 66.2 1.0
N I:ASP175 4.9 55.5 1.0

Magnesium binding site 3 out of 8 in 5l6a

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:54.1
occ:1.00
 O Y:ASP167 2.2 54.1 1.0
O I:ASP204 2.2 65.5 1.0
O Y:ALA164 2.3 52.1 1.0
O Y:SER170 2.7 57.1 1.0
C I:ASP204 3.1 63.5 1.0
C Y:ASP167 3.3 52.0 1.0
NH1 Y:ARG19 3.4 68.1 1.0
C Y:ALA164 3.5 50.4 1.0
CA Y:ALA168 3.6 52.9 1.0
CA I:ASP204 3.7 65.0 1.0
N Y:ALA168 3.8 52.4 1.0
O Y:ALA168 3.9 55.5 1.0
C Y:ALA168 3.9 53.8 1.0
C Y:SER170 3.9 54.0 1.0
O Y:HIS165 3.9 51.1 1.0
CB I:ASP204 4.0 66.6 1.0
OXT I:ASP204 4.0 61.5 1.0
CA Y:ALA164 4.3 50.4 1.0
C Y:HIS165 4.3 50.6 1.0
N Y:SER170 4.4 52.2 1.0
CZ Y:ARG19 4.4 66.5 1.0
CA Y:ASP167 4.4 51.2 1.0
N Y:HIS165 4.5 51.4 1.0
N Y:ASP167 4.5 52.1 1.0
CA Y:HIS165 4.6 50.9 1.0
N Y:TYR169 4.7 54.2 1.0
CA Y:SER170 4.7 52.3 1.0
O Y:ALA163 4.7 48.0 1.0
C Y:ARG166 4.8 51.8 1.0
NH2 Y:ARG19 4.8 66.2 1.0
N Y:GLY171 4.9 54.9 1.0
CG I:ASP204 4.9 68.7 1.0
CA Y:GLY171 5.0 55.5 1.0
N Y:ARG166 5.0 50.0 1.0
CB Y:ALA168 5.0 52.3 1.0

Magnesium binding site 4 out of 8 in 5l6a

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:51.2
occ:1.00
 OE1 J:GLN118 3.2 51.5 1.0
O J:THR124 3.4 43.7 1.0
CB J:ASP120 3.7 45.6 1.0
OD2 J:ASP120 3.7 55.6 1.0
CG J:ASP120 3.8 48.5 1.0
N J:ASP120 3.8 43.4 1.0
CD J:GLN118 4.1 46.5 1.0
CB J:THR124 4.1 47.3 1.0
CG J:GLN118 4.1 44.8 1.0
CE1 J:HIS133 4.2 46.7 1.0
CG2 J:THR124 4.3 46.9 1.0
O J:GLN118 4.3 43.0 1.0
CA J:ASP120 4.3 44.6 1.0
C J:THR124 4.4 44.5 1.0
C J:ILE119 4.5 43.1 1.0
OD1 J:ASP120 4.5 49.5 1.0
C J:GLN118 4.7 42.8 1.0
CA J:ILE119 4.7 41.1 1.0
ND1 J:HIS133 4.8 45.0 1.0
N J:ILE119 4.9 41.6 1.0
CA J:THR124 4.9 45.8 1.0
CG1 I:VAL35 5.0 59.2 1.0
CB J:GLN118 5.0 43.8 1.0

Magnesium binding site 5 out of 8 in 5l6a

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:51.9
occ:1.00
 O K:ASP167 2.2 53.7 1.0
O K:ALA164 2.3 52.4 1.0
O W:ASP204 2.3 61.4 1.0
O K:SER170 2.7 54.8 1.0
C W:ASP204 3.1 59.0 1.0
C K:ASP167 3.2 52.2 1.0
C K:ALA164 3.5 50.2 1.0
NH1 K:ARG19 3.5 64.1 1.0
CA K:ALA168 3.6 54.9 1.0
CA W:ASP204 3.6 59.4 1.0
N K:ALA168 3.8 53.1 1.0
O K:HIS165 3.8 52.3 1.0
C K:ALA168 3.8 54.5 1.0
O K:ALA168 3.9 55.5 1.0
C K:SER170 3.9 53.3 1.0
CB W:ASP204 4.0 59.4 1.0
OXT W:ASP204 4.0 62.2 1.0
C K:HIS165 4.2 51.4 1.0
CA K:ALA164 4.3 50.0 1.0
N K:SER170 4.3 54.4 1.0
CA K:ASP167 4.4 51.9 1.0
N K:ASP167 4.4 52.2 1.0
N K:HIS165 4.4 49.1 1.0
CZ K:ARG19 4.5 63.5 1.0
CA K:HIS165 4.6 50.3 1.0
N K:TYR169 4.6 55.4 1.0
O K:ALA163 4.7 50.4 1.0
CA K:SER170 4.7 52.0 1.0
C K:ARG166 4.7 51.6 1.0
N K:GLY171 4.9 53.1 1.0
NH2 K:ARG19 4.9 64.8 1.0
N K:ARG166 4.9 50.3 1.0
CB K:ALA168 4.9 54.7 1.0
CG W:ASP204 5.0 60.8 1.0
CA K:GLY171 5.0 54.2 1.0
O K:ARG166 5.0 52.8 1.0

Magnesium binding site 6 out of 8 in 5l6a

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:63.0
occ:1.00
 OXT L:ASP222 2.0 76.3 1.0
O V:ILE163 2.1 55.3 1.0
O V:ASP166 2.2 46.3 1.0
O V:SER169 2.7 55.8 1.0
C L:ASP222 2.9 72.7 1.0
C V:ASP166 3.1 47.4 1.0
C V:ILE163 3.2 53.5 1.0
CA L:ASP222 3.7 70.0 1.0
O L:ASP222 3.8 81.2 1.0
C V:SER169 3.8 50.5 1.0
N V:LEU167 3.8 47.5 1.0
CA V:LEU167 3.9 48.4 1.0
N V:ASP166 3.9 48.0 1.0
O V:GLY162 3.9 52.6 1.0
O V:TRP164 3.9 64.0 1.0
C V:TRP164 4.0 54.4 1.0
NH1 V:ARG19 4.0 53.2 1.0
CA V:ASP166 4.1 47.8 1.0
CA V:ILE163 4.1 51.3 1.0
N V:TRP164 4.2 54.1 1.0
CA V:TRP164 4.3 53.0 1.0
CB L:ASP222 4.3 68.4 1.0
C V:LEU167 4.4 48.4 1.0
N V:ASN165 4.5 50.7 1.0
N V:SER169 4.5 47.3 1.0
CA V:SER169 4.7 47.9 1.0
C V:ASN165 4.7 48.0 1.0
CA V:GLY170 4.7 51.0 1.0
N V:GLY170 4.7 50.3 1.0
O L:ARG221 4.7 68.9 1.0
O V:LEU167 4.7 49.4 1.0
CZ V:ARG19 4.7 52.4 1.0
CD2 V:LEU167 4.8 46.3 1.0
C V:GLY162 4.9 50.8 1.0
NH2 V:ARG19 4.9 55.0 1.0
N L:ASP222 4.9 66.8 1.0
CB V:ASP166 5.0 47.4 1.0

Magnesium binding site 7 out of 8 in 5l6a

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:53.6
occ:1.00
 O N:SER169 2.6 47.1 1.0
O N:ILE163 2.7 45.7 1.0
O N:ASP166 3.0 46.5 1.0
NH1 N:ARG19 3.6 49.4 1.0
CD1 a:LEU34 3.7 54.7 1.0
C N:ILE163 3.8 45.7 1.0
C N:SER169 3.8 45.0 1.0
CG2 N:ILE163 3.8 46.7 1.0
C N:ASP166 4.0 44.8 1.0
CZ N:ARG19 4.1 47.4 1.0
CA N:GLY167 4.2 46.4 1.0
NH2 N:ARG19 4.3 46.7 1.0
CA N:GLY170 4.3 47.0 1.0
CA N:ILE163 4.4 46.0 1.0
O N:GLY167 4.4 45.7 1.0
N N:GLY170 4.5 44.2 1.0
C N:GLY167 4.5 45.5 1.0
N N:GLY167 4.5 45.6 1.0
CB N:ILE163 4.7 45.8 1.0
O N:HOH308 4.8 44.3 1.0
N N:LYS164 4.8 46.7 1.0
CA N:SER169 4.9 43.8 1.0
N N:SER169 4.9 43.9 1.0
CG a:LEU34 4.9 54.6 1.0
NE N:ARG19 4.9 48.4 1.0

Magnesium binding site 8 out of 8 in 5l6a

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17


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 with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Epoxyketone Inhibitor 17 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:77.0
occ:1.00
 O Z:VAL198 2.7 55.3 1.0
O Z:THR192 2.9 61.6 1.0
O Z:HIS195 3.0 59.6 1.0
O Z:ASP222 3.4 74.6 1.0
NH2 Z:ARG28 3.5 66.4 1.0
O Z:ILE196 3.7 66.3 1.0
CA Z:ILE196 3.8 60.1 1.0
C Z:VAL198 3.9 61.1 1.0
CG2 Z:THR192 3.9 68.6 1.0
C Z:ILE196 4.0 62.0 1.0
C Z:HIS195 4.0 59.2 1.0
C Z:THR192 4.0 65.0 1.0
NH2 H:ARG19 4.0 64.4 1.0
OD1 Z:ASP222 4.1 73.6 1.0
CA Z:THR192 4.4 67.0 1.0
N Z:ILE196 4.4 57.6 1.0
C Z:ASP222 4.4 76.0 1.0
N Z:VAL198 4.6 57.6 1.0
CZ Z:ARG28 4.6 64.8 1.0
CZ H:ARG19 4.8 62.9 1.0
NH1 Z:ARG28 4.8 65.6 1.0
CB Z:THR192 4.8 66.4 1.0
NH1 H:ARG19 4.8 65.1 1.0
CA Z:VAL198 4.8 59.8 1.0
N Z:GLY199 4.8 59.8 1.0
CA Z:GLY199 4.8 61.8 1.0
OXT Z:ASP222 4.9 70.8 1.0
N Z:GLN197 4.9 60.3 1.0
O Z:LYS220 5.0 64.9 1.0
CG Z:ASP222 5.0 70.9 1.0

Reference:

E.M.Huber, W.Heinemeyer, G.De Bruin, H.S.Overkleeft, M.Groll. A Humanized Yeast Proteasome Identifies Unique Binding Modes of Inhibitors For the Immunosubunit Beta 5I. Embo J. V. 35 2602 2016.
ISSN: ESSN 1460-2075
PubMed: 27789522
DOI: 10.15252/EMBJ.201695222
Page generated: Sun Sep 29 19:43:15 2024

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