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Magnesium in PDB 5d0t: Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132

Enzymatic activity of Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132

All present enzymatic activity of Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132, PDB code: 5d0t 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.860, 300.140, 145.060, 90.00, 113.26, 90.00
R / Rfree (%) 19.5 / 21.8

Other elements in 5d0t:

The structure of Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132 (pdb code 5d0t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132, PDB code: 5d0t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 5d0t

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Magnesium binding site 1 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.0
occ:1.00
 O G:MET125 2.3 45.7 1.0
OG1 G:THR8 2.6 38.3 1.0
O G:ARG122 2.8 43.3 1.0
O G:ALA123 3.1 49.8 1.0
O G:TYR119 3.1 40.7 1.0
CG2 G:THR8 3.3 44.7 1.0
C G:MET125 3.4 49.4 1.0
CB G:THR8 3.5 44.1 1.0
C G:ALA123 3.5 47.9 1.0
CA G:ALA123 3.7 46.4 1.0
C G:ARG122 3.8 44.8 1.0
N G:THR8 4.0 45.7 1.0
CA G:ARG126 4.1 44.1 1.0
N G:ARG126 4.1 45.6 1.0
N G:ALA123 4.2 44.6 1.0
N G:MET125 4.2 50.7 1.0
C G:TYR119 4.3 41.1 1.0
CA G:THR8 4.4 45.9 1.0
CA G:MET125 4.4 52.7 1.0
CD G:PRO127 4.5 40.9 1.0
N G:TYR124 4.6 49.0 1.0
O G:HOH411 4.6 38.2 1.0
C G:ARG126 4.8 42.7 1.0
C G:TYR124 4.9 49.2 1.0
CB G:ALA123 5.0 46.1 1.0

Magnesium binding site 2 out of 11 in 5d0t

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Magnesium binding site 2 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:67.4
occ:1.00
 O I:ASP177 2.3 45.6 1.0
O I:SER180 2.7 49.6 1.0
O I:ALA174 3.3 49.5 1.0
C I:ASP177 3.4 47.4 1.0
OXT I:ASP204 3.5 62.3 1.0
O I:ALA178 3.7 53.7 1.0
CA I:ALA178 3.9 47.3 1.0
NH1 Y:ARG19 3.9 66.8 1.0
C I:ALA178 3.9 49.9 1.0
C I:SER180 3.9 48.6 1.0
N I:ALA178 4.1 47.1 1.0
O I:ASP204 4.3 55.0 1.0
C I:ASP204 4.3 59.5 1.0
N I:SER180 4.4 45.2 1.0
NH2 Y:ARG19 4.4 68.3 1.0
C I:ALA174 4.5 51.1 1.0
CZ Y:ARG19 4.6 64.0 1.0
CA I:ASP177 4.6 47.6 1.0
N I:ASP177 4.6 47.7 1.0
N I:LEU179 4.7 48.3 1.0
CA I:SER180 4.7 47.0 1.0
CA I:ASP175 4.8 53.3 1.0
N I:GLY181 4.9 47.9 1.0
CG2 Y:VAL26 4.9 48.9 1.0
C I:ASP175 4.9 52.4 1.0
O I:ASP175 5.0 49.9 1.0
CA I:GLY181 5.0 49.3 1.0

Magnesium binding site 3 out of 11 in 5d0t

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Magnesium binding site 3 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:54.5
occ:1.00
 O I:ASP204 2.2 55.0 1.0
O Y:ASN168 2.3 45.5 1.0
O Y:ALA165 2.5 43.2 1.0
O Y:SER171 3.0 51.5 1.0
C I:ASP204 3.1 59.5 1.0
C Y:ASN168 3.2 44.5 1.0
CA Y:ALA169 3.4 45.9 1.0
O Y:HIS166 3.6 48.1 1.0
CA I:ASP204 3.6 59.1 1.0
N Y:ALA169 3.7 46.4 1.0
C Y:ALA165 3.7 42.6 1.0
C Y:ALA169 3.8 46.0 1.0
O Y:ALA169 3.8 49.9 1.0
NH1 Y:ARG19 3.9 66.8 1.0
OXT I:ASP204 4.0 62.3 1.0
CB I:ASP204 4.1 59.7 1.0
C Y:HIS166 4.1 45.7 1.0
C Y:SER171 4.2 44.5 1.0
N Y:ASN168 4.3 47.1 1.0
CA Y:ASN168 4.3 44.2 1.0
N Y:HIS166 4.5 44.4 1.0
CA Y:ALA165 4.6 43.2 1.0
CA Y:HIS166 4.6 44.5 1.0
N Y:SER171 4.6 43.2 1.0
N Y:TYR170 4.7 44.8 1.0
CZ Y:ARG19 4.7 64.0 1.0
C Y:ARG167 4.7 47.6 1.0
CB Y:ALA169 4.8 45.4 1.0
O Y:ALA164 4.8 46.0 1.0
N Y:ARG167 4.9 45.1 1.0
N I:ASP204 4.9 57.7 1.0
CA Y:SER171 4.9 42.1 1.0

Magnesium binding site 4 out of 11 in 5d0t

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Magnesium binding site 4 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:42.8
occ:1.00
 OE1 J:GLN118 3.4 45.8 1.0
O J:THR124 3.8 44.7 1.0
CB J:ASP120 3.8 43.5 1.0
CG J:ASP120 4.0 45.6 1.0
OD2 J:ASP120 4.0 48.4 1.0
N J:ASP120 4.1 40.5 1.0
CD J:GLN118 4.2 42.8 1.0
CB J:THR124 4.2 45.0 1.0
CG J:GLN118 4.3 41.5 1.0
CE1 J:HIS133 4.4 42.9 1.0
CG2 J:THR124 4.4 46.2 1.0
O J:GLN118 4.5 38.9 1.0
CA J:ASP120 4.6 41.5 1.0
OD1 J:ASP120 4.7 49.3 1.0
C J:THR124 4.7 44.4 1.0
CG1 I:VAL35 4.8 48.7 1.0
C J:ILE119 4.8 40.6 1.0
OG I:SER30 4.9 61.3 1.0
CD2 I:LEU28 4.9 47.5 1.0
C J:GLN118 4.9 39.7 1.0

Magnesium binding site 5 out of 11 in 5d0t

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Magnesium binding site 5 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:68.1
occ:1.00
 O K:ASN168 2.2 46.6 1.0
O W:ASP204 2.3 58.4 1.0
O K:ALA165 2.3 44.9 1.0
O K:SER171 2.8 45.8 1.0
C K:ASN168 3.1 46.6 1.0
C W:ASP204 3.1 59.8 1.0
C K:ALA165 3.5 46.4 1.0
CA K:ALA169 3.5 49.2 1.0
CA W:ASP204 3.6 58.0 1.0
O K:HIS166 3.6 46.3 1.0
N K:ALA169 3.7 47.7 1.0
C K:ALA169 3.8 49.2 1.0
O K:ALA169 3.8 47.9 1.0
NH1 K:ARG19 3.9 64.8 1.0
C K:SER171 4.0 45.9 1.0
CB W:ASP204 4.0 57.3 1.0
OXT W:ASP204 4.1 61.4 1.0
C K:HIS166 4.1 46.5 1.0
N K:ASN168 4.3 45.7 1.0
CA K:ASN168 4.3 45.3 1.0
CA K:ALA165 4.4 47.5 1.0
N K:HIS166 4.4 44.5 1.0
N K:SER171 4.4 47.3 1.0
CA K:HIS166 4.5 45.5 1.0
N K:TYR170 4.6 48.7 1.0
CZ K:ARG19 4.7 62.4 1.0
O K:ALA164 4.7 46.8 1.0
C K:ARG167 4.7 46.5 1.0
CA K:SER171 4.7 45.8 1.0
N K:ARG167 4.8 47.5 1.0
CB K:ALA169 4.9 49.1 1.0
N K:GLY172 5.0 46.1 1.0
N W:ASP204 5.0 56.6 1.0

Magnesium binding site 6 out of 11 in 5d0t

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Magnesium binding site 6 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:67.3
occ:1.00
 OXT L:ASP222 2.2 75.5 1.0
O V:ILE163 2.2 50.4 1.0
O V:ASP166 2.2 50.5 1.0
O V:SER169 2.9 50.0 1.0
C L:ASP222 3.0 75.7 1.0
C V:ASP166 3.1 51.4 1.0
C V:ILE163 3.2 52.1 1.0
O V:TRP164 3.6 54.9 1.0
CA L:ASP222 3.7 73.6 1.0
C V:TRP164 3.7 53.6 1.0
N V:ASP166 3.8 48.3 1.0
N V:LEU167 3.9 51.4 1.0
O L:ASP222 3.9 74.8 1.0
O V:GLY162 3.9 48.8 1.0
CA V:LEU167 3.9 50.5 1.0
N V:TRP164 4.1 51.6 1.0
CA V:TRP164 4.1 53.2 1.0
C V:SER169 4.1 49.0 1.0
CA V:ASP166 4.1 50.3 1.0
CA V:ILE163 4.2 51.3 1.0
NH1 V:ARG19 4.3 62.3 1.0
N V:ASN165 4.3 52.1 1.0
CB L:ASP222 4.4 72.9 1.0
C V:ASN165 4.4 48.9 1.0
C V:LEU167 4.6 51.6 1.0
O L:ARG221 4.6 65.6 1.0
CD2 V:LEU167 4.7 48.5 1.0
CA V:ASN165 4.8 50.8 1.0
O V:LEU167 4.8 54.7 1.0
N V:SER169 4.9 48.0 1.0
CA V:GLY170 4.9 52.6 1.0
C V:GLY162 4.9 49.8 1.0
N L:ASP222 4.9 71.5 1.0
CZ V:ARG19 4.9 59.4 1.0
N V:GLY170 4.9 50.2 1.0
NH2 V:ARG19 5.0 62.3 1.0
CA V:SER169 5.0 48.1 1.0

Magnesium binding site 7 out of 11 in 5d0t

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Magnesium binding site 7 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg301

b:46.5
occ:1.00
 OD2 M:ASP188 2.5 40.4 1.0
OG M:SER10 2.7 41.2 1.0
CB M:SER10 3.2 37.9 1.0
OG1 M:THR9 3.3 34.9 1.0
CG M:ASP188 3.5 44.5 1.0
CB M:LEU184 3.7 43.7 1.0
CG2 M:THR9 3.7 38.0 1.0
CB M:ASP188 3.7 44.5 1.0
N M:SER10 3.7 37.0 1.0
CD1 M:LEU184 3.8 42.6 1.0
CD2 M:LEU184 3.9 43.4 1.0
CG M:LEU184 4.0 43.0 1.0
CA M:SER10 4.1 37.0 1.0
CB M:THR9 4.1 37.7 1.0
CB M:SER191 4.2 48.8 1.0
CB M:PHE146 4.3 51.8 1.0
OD2 M:ASP25 4.6 55.0 1.0
OD1 M:ASP188 4.7 46.7 1.0
CA M:LEU184 4.8 45.3 1.0
O M:LEU184 4.8 48.2 1.0
C M:THR9 4.8 36.7 1.0
N M:GLY147 4.9 46.8 1.0
C M:LEU184 5.0 46.2 1.0

Magnesium binding site 8 out of 11 in 5d0t

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Magnesium binding site 8 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:44.8
occ:1.00
 O N:SER169 2.5 39.8 1.0
O N:ILE163 2.5 40.1 1.0
O N:ASP166 2.8 46.1 1.0
NH1 N:ARG19 3.5 44.7 1.0
CD1 a:LEU34 3.6 48.2 1.0
C N:ILE163 3.7 42.3 1.0
C N:SER169 3.7 39.0 1.0
CG2 N:ILE163 3.9 41.0 1.0
C N:ASP166 3.9 42.5 1.0
CZ N:ARG19 4.2 44.3 1.0
CA N:GLY167 4.2 41.2 1.0
CA N:ILE163 4.3 42.0 1.0
CA N:GLY170 4.4 41.9 1.0
O N:GLY167 4.4 41.8 1.0
NH2 N:ARG19 4.5 47.0 1.0
N N:GLY170 4.5 40.5 1.0
N N:GLY167 4.5 41.2 1.0
C N:GLY167 4.5 40.5 1.0
CB N:ILE163 4.7 41.5 1.0
N N:LYS164 4.7 44.0 1.0
N N:SER169 4.8 39.2 1.0
CA N:SER169 4.8 37.3 1.0
CG a:LEU34 4.9 48.9 1.0
C N:LYS164 5.0 45.2 1.0
O N:LYS164 5.0 47.7 1.0

Magnesium binding site 9 out of 11 in 5d0t

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Magnesium binding site 9 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


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 BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg201

b:38.0
occ:1.00
 O X:HOH319 2.0 44.0 1.0
OE1 X:GLN118 3.2 48.5 1.0
O X:THR124 3.7 47.8 1.0
CB X:ASP120 3.8 45.8 1.0
N X:ASP120 3.9 41.5 1.0
CD X:GLN118 4.0 44.9 1.0
CG X:GLN118 4.0 44.2 1.0
CG X:ASP120 4.0 48.8 1.0
CE1 X:HIS133 4.1 46.8 1.0
OD2 X:ASP120 4.2 51.4 1.0
O X:GLN118 4.2 44.1 1.0
CB X:THR124 4.4 49.4 1.0
CA X:ASP120 4.4 43.0 1.0
C X:ILE119 4.5 41.7 1.0
C X:GLN118 4.6 44.2 1.0
CG2 X:THR124 4.6 50.5 1.0
C X:THR124 4.7 49.5 1.0
OD1 X:ASP120 4.7 50.7 1.0
CA X:ILE119 4.7 40.5 1.0
N X:ILE119 4.8 42.6 1.0
CB X:GLN118 4.8 43.5 1.0
ND1 X:HIS133 4.8 44.6 1.0
CG1 W:VAL35 4.8 49.9 1.0
O X:HOH304 4.8 39.8 1.0
NE2 X:HIS133 5.0 48.4 1.0

Magnesium binding site 10 out of 11 in 5d0t

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Magnesium binding site 10 out of 11 in the Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Yeast 20S Proteasome BETA5-D166N Mutant in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:59.5
occ:1.00
 O Z:VAL198 2.5 50.3 1.0
O Z:THR192 2.8 61.4 1.0
O Z:ASP222 3.3 73.7 1.0
CG2 Z:THR192 3.3 62.0 1.0
NH2 Z:ARG28 3.6 62.8 1.0
O Z:HIS195 3.6 46.4 1.0
C Z:VAL198 3.7 52.6 1.0
C Z:THR192 3.7 62.1 1.0
OD1 Z:ASP222 3.9 66.1 1.0
CA Z:THR192 4.1 61.6 1.0
CB Z:THR192 4.3 61.3 1.0
CA Z:GLY199 4.3 54.2 1.0
NH2 H:ARG19 4.3 64.8 1.0
O Z:LYS220 4.3 61.8 1.0
C Z:ASP222 4.3 73.4 1.0
O Z:ILE196 4.4 54.8 1.0
CZ Z:ARG28 4.5 61.1 1.0
N Z:GLY199 4.5 53.1 1.0
NH1 Z:ARG28 4.5 62.6 1.0
C Z:HIS195 4.6 49.2 1.0
CA Z:ILE196 4.6 51.4 1.0
C Z:ILE196 4.7 50.3 1.0
N Z:VAL198 4.8 48.7 1.0
CA Z:VAL198 4.8 51.3 1.0
CG Z:ASP222 4.9 65.0 1.0
N Z:GLU193 4.9 59.8 1.0
OXT Z:ASP222 5.0 73.8 1.0

Reference:

E.M.Huber, W.Heinemeyer, X.Li, C.S.Arendt, M.Hochstrasser, M.Groll. A Unified Mechanism For Proteolysis and Autocatalytic Activation in the 20S Proteasome. Nat Commun V. 7 10900 2016.
ISSN: ESSN 2041-1723
PubMed: 26964885
DOI: 10.1038/NCOMMS10900
Page generated: Mon Dec 14 20:09:22 2020

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