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Magnesium in PDB 5l5v: 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18

Enzymatic activity of 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18

All present enzymatic activity of 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18:
3.4.25.1;

Protein crystallography data

The structure of 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18, PDB code: 5l5v 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.240, 300.970, 145.640, 90.00, 112.84, 90.00
R / Rfree (%) 18.6 / 20.8

Other elements in 5l5v:

The structure of 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 (pdb code 5l5v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18, PDB code: 5l5v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5l5v

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Magnesium binding site 1 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:49.7
occ:1.00
 O G:MET125 2.3 44.1 1.0
O G:ARG122 2.5 42.8 1.0
OG1 G:THR8 2.6 38.8 1.0
O G:TYR119 2.8 35.5 1.0
CG2 G:THR8 3.2 42.9 1.0
O G:ALA123 3.3 50.0 1.0
C G:MET125 3.4 45.3 1.0
CB G:THR8 3.5 41.4 1.0
C G:ARG122 3.6 43.2 1.0
C G:ALA123 3.7 46.1 1.0
CA G:ALA123 3.7 44.4 1.0
C G:TYR119 4.0 37.1 1.0
N G:ALA123 4.1 43.8 1.0
N G:THR8 4.1 43.3 1.0
N G:MET125 4.2 47.1 1.0
CA G:ARG126 4.3 41.6 1.0
N G:ARG126 4.3 42.8 1.0
CA G:MET125 4.4 48.4 1.0
CA G:THR8 4.4 42.6 1.0
CD G:PRO127 4.6 37.5 1.0
N G:TYR124 4.6 46.5 1.0
CA G:TYR119 4.7 35.9 1.0
CA G:ARG122 4.9 45.0 1.0
C G:ARG126 4.9 40.6 1.0
N G:THR120 4.9 37.3 1.0
N G:ARG122 5.0 42.5 1.0
C G:TYR124 5.0 46.4 1.0

Magnesium binding site 2 out of 9 in 5l5v

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Magnesium binding site 2 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:61.5
occ:1.00
 O I:SER180 2.6 48.6 1.0
O I:ASP177 2.6 44.6 1.0
O I:ALA174 3.0 48.5 1.0
OXT I:ASP204 3.5 58.0 1.0
O I:HOH401 3.7 46.5 1.0
C I:SER180 3.8 47.7 1.0
C I:ASP177 3.8 45.1 1.0
C I:ALA174 4.1 48.3 1.0
O I:ALA178 4.3 49.6 1.0
CD1 Y:ILE26 4.4 56.1 1.0
CA I:ALA178 4.4 46.5 1.0
C I:ALA178 4.4 48.0 1.0
C I:ASP204 4.5 56.6 1.0
CA I:ASP175 4.5 49.8 1.0
O I:ASP204 4.5 59.7 1.0
N I:ALA178 4.6 44.9 1.0
N I:SER180 4.6 45.7 1.0
CA I:GLY181 4.6 48.2 1.0
N I:GLY181 4.7 46.6 1.0
N I:ASP175 4.7 48.0 1.0
N I:ASP177 4.7 45.6 1.0
CA I:SER180 4.8 46.8 1.0
NH1 Y:ARG19 4.8 64.1 1.0
CA I:ASP177 4.8 46.2 1.0
C I:ASP175 4.9 50.7 1.0
NH2 Y:ARG19 5.0 59.9 1.0

Magnesium binding site 3 out of 9 in 5l5v

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Magnesium binding site 3 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:59.0
occ:1.00
 O Y:ASP167 2.2 50.5 1.0
O Y:ALA164 2.3 46.3 1.0
O I:ASP204 2.3 59.7 1.0
O Y:SER170 2.6 51.0 1.0
C I:ASP204 3.2 56.6 1.0
C Y:ASP167 3.3 48.4 1.0
C Y:ALA164 3.4 44.8 1.0
NH1 Y:ARG19 3.6 64.1 1.0
CA I:ASP204 3.7 56.6 1.0
CA Y:ALA168 3.7 50.0 1.0
C Y:SER170 3.8 50.3 1.0
O Y:ALA168 3.9 50.7 1.0
C Y:ALA168 3.9 50.7 1.0
N Y:ALA168 3.9 49.0 1.0
CB I:ASP204 3.9 56.7 1.0
O Y:HIS165 4.0 49.3 1.0
OXT I:ASP204 4.1 58.0 1.0
CA Y:ALA164 4.2 45.5 1.0
N Y:SER170 4.2 48.1 1.0
C Y:HIS165 4.3 47.2 1.0
N Y:HIS165 4.4 45.1 1.0
CA Y:ASP167 4.5 47.4 1.0
CZ Y:ARG19 4.5 62.4 1.0
N Y:ASP167 4.5 48.5 1.0
CA Y:SER170 4.5 48.5 1.0
O Y:ALA163 4.6 44.4 1.0
CA Y:HIS165 4.7 46.1 1.0
N Y:TYR169 4.7 51.0 1.0
N Y:GLY171 4.8 50.8 1.0
C Y:ARG166 4.8 48.5 1.0
NH2 Y:ARG19 4.8 59.9 1.0
CA Y:GLY171 4.9 52.7 1.0
CG I:ASP204 4.9 57.5 1.0
N Y:ARG166 5.0 47.0 1.0
CB Y:SER170 5.0 47.0 1.0

Magnesium binding site 4 out of 9 in 5l5v

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Magnesium binding site 4 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:53.8
occ:1.00
 OE1 J:GLN118 3.2 38.5 1.0
O J:THR124 3.4 39.1 1.0
CB J:ASP120 3.7 39.6 1.0
OD2 J:ASP120 3.8 49.0 1.0
N J:ASP120 3.8 36.2 1.0
CG J:ASP120 3.8 43.6 1.0
CD J:GLN118 4.1 36.2 1.0
CB J:THR124 4.1 39.5 1.0
CG J:GLN118 4.1 35.3 1.0
CE1 J:HIS133 4.3 40.1 1.0
O J:GLN118 4.3 36.6 1.0
CG2 J:THR124 4.3 38.5 1.0
CA J:ASP120 4.3 37.1 1.0
C J:THR124 4.4 37.7 1.0
C J:ILE119 4.5 35.5 1.0
OD1 J:ASP120 4.6 50.0 1.0
C J:GLN118 4.6 34.8 1.0
CA J:ILE119 4.7 32.9 1.0
N J:ILE119 4.8 34.3 1.0
CA J:THR124 4.9 38.1 1.0
CB J:GLN118 4.9 34.7 1.0
ND1 J:HIS133 4.9 39.1 1.0
CG1 I:VAL35 5.0 49.9 1.0

Magnesium binding site 5 out of 9 in 5l5v

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Magnesium binding site 5 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:62.0
occ:1.00
 O K:ASP167 2.2 47.6 1.0
O W:ASP204 2.2 60.1 1.0
O K:ALA164 2.3 45.6 1.0
O K:SER170 2.6 47.6 1.0
C W:ASP204 3.1 56.7 1.0
C K:ASP167 3.3 48.7 1.0
C K:ALA164 3.4 47.4 1.0
NH1 K:ARG19 3.6 59.5 1.0
CA W:ASP204 3.6 56.9 1.0
CA K:ALA168 3.7 51.4 1.0
C K:SER170 3.8 49.6 1.0
O K:ALA168 3.9 50.9 1.0
C K:ALA168 3.9 51.0 1.0
N K:ALA168 3.9 49.2 1.0
CB W:ASP204 3.9 57.7 1.0
O K:HIS165 4.0 49.0 1.0
OXT W:ASP204 4.0 55.4 1.0
CA K:ALA164 4.2 47.2 1.0
N K:SER170 4.3 49.7 1.0
C K:HIS165 4.3 48.5 1.0
N K:HIS165 4.4 46.6 1.0
CA K:ASP167 4.5 48.6 1.0
CZ K:ARG19 4.5 58.8 1.0
N K:ASP167 4.5 50.1 1.0
CA K:SER170 4.6 48.4 1.0
CA K:HIS165 4.6 48.2 1.0
O K:ALA163 4.7 47.4 1.0
N K:TYR169 4.7 51.4 1.0
C K:ARG166 4.8 51.2 1.0
N K:GLY171 4.8 49.6 1.0
NH2 K:ARG19 4.9 60.9 1.0
CG W:ASP204 4.9 57.9 1.0
CA K:GLY171 4.9 50.8 1.0
N K:ARG166 5.0 47.4 1.0

Magnesium binding site 6 out of 9 in 5l5v

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Magnesium binding site 6 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:58.4
occ:1.00
 OXT L:ASP222 2.1 74.8 1.0
O V:ILE163 2.1 46.4 1.0
O V:ASP166 2.2 45.6 1.0
O V:SER169 2.2 47.5 1.0
O V:HOH402 2.4 42.1 1.0
C L:ASP222 3.1 71.8 1.0
C V:ILE163 3.2 46.8 1.0
C V:ASP166 3.2 44.7 1.0
C V:SER169 3.4 46.0 1.0
CA L:ASP222 3.7 68.0 1.0
NH1 V:ARG19 3.8 56.5 1.0
O V:GLY162 3.8 44.0 1.0
CA V:LEU167 3.9 45.0 1.0
CA V:ILE163 4.0 45.8 1.0
N V:LEU167 4.0 44.5 1.0
O L:ASP222 4.1 74.9 1.0
N V:ASP166 4.1 44.0 1.0
CB L:ASP222 4.2 67.4 1.0
N V:TRP164 4.3 46.7 1.0
N V:SER169 4.3 45.5 1.0
CA V:GLY170 4.3 47.2 1.0
CA V:ASP166 4.3 44.2 1.0
N V:GLY170 4.3 46.1 1.0
C V:LEU167 4.3 44.4 1.0
CA V:SER169 4.3 46.1 1.0
C V:TRP164 4.4 49.5 1.0
O V:TRP164 4.4 53.1 1.0
CZ V:ARG19 4.5 54.8 1.0
O V:LEU167 4.5 45.3 1.0
CA V:TRP164 4.5 49.0 1.0
NH2 V:ARG19 4.7 55.8 1.0
CB V:SER169 4.7 46.8 1.0
N V:ASN165 4.7 47.1 1.0
C V:GLY162 4.8 44.9 1.0
N V:ILE163 4.9 44.8 1.0
CG2 V:ILE163 4.9 47.5 1.0
C V:ASN165 5.0 44.5 1.0

Magnesium binding site 7 out of 9 in 5l5v

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Magnesium binding site 7 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:47.5
occ:1.00
 O N:SER169 2.7 44.2 1.0
O N:ILE163 2.8 43.0 1.0
O N:ASP166 3.0 42.1 1.0
NH1 N:ARG19 3.6 42.9 1.0
CD1 a:LEU34 3.7 48.0 1.0
C N:SER169 3.9 41.5 1.0
C N:ILE163 3.9 42.1 1.0
CG2 N:ILE163 4.0 40.8 1.0
C N:ASP166 4.0 40.2 1.0
CZ N:ARG19 4.1 42.2 1.0
CA N:GLY167 4.1 41.2 1.0
NH2 N:ARG19 4.2 41.8 1.0
CA N:GLY170 4.4 42.0 1.0
O N:GLY167 4.4 43.0 1.0
N N:GLY167 4.5 40.8 1.0
C N:GLY167 4.5 41.9 1.0
CA N:ILE163 4.5 41.4 1.0
N N:GLY170 4.6 41.2 1.0
CB N:ILE163 4.9 40.4 1.0
N N:SER169 4.9 39.8 1.0
CA N:SER169 4.9 39.3 1.0
CG a:LEU34 4.9 48.3 1.0
NE N:ARG19 4.9 43.1 1.0
N N:LYS164 5.0 43.2 1.0

Magnesium binding site 8 out of 9 in 5l5v

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Magnesium binding site 8 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


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 Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:63.3
occ:1.00
 O Z:VAL198 2.6 48.4 1.0
O Z:THR192 2.8 61.4 1.0
O Z:ASP222 3.2 71.6 1.0
O Z:HIS195 3.3 52.2 1.0
NH2 Z:ARG28 3.6 58.5 1.0
CG2 Z:THR192 3.6 60.1 1.0
C Z:THR192 3.8 61.4 1.0
C Z:VAL198 3.8 53.3 1.0
OD1 Z:ASP222 4.0 69.0 1.0
O Z:ILE196 4.1 61.8 1.0
NH2 H:ARG19 4.2 62.7 1.0
CA Z:THR192 4.2 61.6 1.0
C Z:ASP222 4.3 72.7 1.0
CA Z:ILE196 4.3 56.2 1.0
C Z:HIS195 4.3 52.1 1.0
C Z:ILE196 4.4 56.8 1.0
CB Z:THR192 4.6 60.0 1.0
CZ Z:ARG28 4.6 60.8 1.0
CA Z:GLY199 4.6 55.1 1.0
N Z:GLY199 4.7 53.3 1.0
NH1 Z:ARG28 4.7 66.0 1.0
N Z:VAL198 4.7 51.8 1.0
O Z:LYS220 4.7 69.2 1.0
N Z:ILE196 4.8 54.5 1.0
OXT Z:ASP222 4.8 69.4 1.0
CA Z:VAL198 4.8 53.7 1.0
CG Z:ASP222 4.9 69.1 1.0
N Z:GLU193 5.0 60.0 1.0

Magnesium binding site 9 out of 9 in 5l5v

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Magnesium binding site 9 out of 9 in the 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 'Yeast 20S Proteasome with Human BETA5I (1-138; V31M) and Human BETA6 (97-111; 118-133) in Complex with Epoxyketone Inhibitor 18 within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg201

b:42.3
occ:1.00
 O b:ILE163 2.6 44.0 1.0
O b:SER169 2.7 43.5 1.0
O b:ASP166 3.0 41.7 1.0
CD1 M:LEU34 3.6 45.8 1.0
C b:ILE163 3.8 42.8 1.0
NH1 b:ARG19 3.8 45.9 1.0
C b:SER169 3.9 41.8 1.0
CG2 b:ILE163 3.9 43.1 1.0
C b:ASP166 4.0 41.5 1.0
CA b:GLY167 4.1 42.0 1.0
CZ b:ARG19 4.2 44.8 1.0
NH2 b:ARG19 4.4 44.7 1.0
CA b:ILE163 4.4 41.5 1.0
CA b:GLY170 4.4 43.0 1.0
N b:GLY167 4.5 41.5 1.0
O b:GLY167 4.5 42.6 1.0
C b:GLY167 4.6 42.9 1.0
N b:GLY170 4.6 42.2 1.0
CB b:ILE163 4.8 41.9 1.0
N b:LYS164 4.8 42.8 1.0
CG M:LEU34 4.9 46.8 1.0
N b:SER169 4.9 40.4 1.0
CA b:SER169 4.9 40.5 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 19:32:16 2024

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