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Magnesium in PDB 5fgh: Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132

Enzymatic activity of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132

All present enzymatic activity of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132, PDB code: 5fgh 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.920, 299.860, 145.980, 90.00, 113.13, 90.00
R / Rfree (%) 17.8 / 20.6

Other elements in 5fgh:

The structure of Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 (pdb code 5fgh). 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 BETA5-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132, PDB code: 5fgh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5fgh

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) 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-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:63.0
occ:1.00
 O G:MET125 2.3 53.4 1.0
OG1 G:THR8 2.7 46.4 1.0
O G:ARG122 2.9 44.2 1.0
O G:TYR119 3.0 48.2 1.0
CG2 G:THR8 3.2 50.9 1.0
O G:ALA123 3.2 58.1 1.0
C G:MET125 3.4 55.1 1.0
CB G:THR8 3.5 49.8 1.0
C G:ALA123 3.7 53.8 1.0
CA G:ALA123 3.8 51.0 1.0
C G:ARG122 4.0 47.5 1.0
N G:THR8 4.0 54.4 1.0
CA G:ARG126 4.0 49.2 1.0
N G:ARG126 4.1 51.5 1.0
C G:TYR119 4.2 46.1 1.0
N G:MET125 4.3 57.0 1.0
CA G:THR8 4.4 52.0 1.0
N G:ALA123 4.4 48.3 1.0
CD G:PRO127 4.4 46.1 1.0
CA G:MET125 4.4 58.4 1.0
N G:TYR124 4.7 54.3 1.0
C G:ARG126 4.8 48.0 1.0
N G:PRO127 4.9 45.5 1.0
C G:TYR124 5.0 54.6 1.0
CA G:TYR119 5.0 44.5 1.0

Magnesium binding site 2 out of 8 in 5fgh

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) 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-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:77.1
occ:1.00
 O I:ASP177 2.5 53.0 1.0
O I:SER180 2.8 67.0 1.0
O I:ALA174 3.4 57.6 1.0
OXT I:ASP204 3.4 72.5 1.0
C I:ASP177 3.7 57.6 1.0
O I:ALA178 3.9 58.9 1.0
NH1 Y:ARG19 4.0 78.5 1.0
C I:SER180 4.1 58.5 1.0
CA I:ALA178 4.1 57.1 1.0
O I:ASP204 4.1 72.9 1.0
C I:ALA178 4.2 57.4 1.0
C I:ASP204 4.2 71.5 1.0
N I:ALA178 4.3 56.1 1.0
NH2 Y:ARG19 4.4 74.8 1.0
C I:ALA174 4.4 60.7 1.0
CZ Y:ARG19 4.6 75.2 1.0
CA I:ASP175 4.6 62.4 1.0
N I:SER180 4.7 55.7 1.0
N I:ASP177 4.7 59.1 1.0
O I:ASP175 4.8 65.6 1.0
CA I:ASP177 4.8 58.3 1.0
C I:ASP175 4.8 63.2 1.0
CA I:GLY181 4.9 59.0 1.0
CA I:SER180 5.0 57.0 1.0
N I:GLY181 5.0 56.6 1.0

Magnesium binding site 3 out of 8 in 5fgh

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) 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-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:67.5
occ:1.00
 O I:ASP204 2.3 72.9 1.0
O Y:ASP168 2.3 56.8 1.0
O Y:ALA165 2.4 54.1 1.0
O Y:SER171 2.9 60.6 1.0
C I:ASP204 3.2 71.5 1.0
C Y:ASP168 3.3 57.1 1.0
C Y:ALA165 3.6 54.7 1.0
CA Y:ALA169 3.6 59.0 1.0
CA I:ASP204 3.6 71.2 1.0
O Y:HIS166 3.8 59.3 1.0
N Y:ALA169 3.8 59.2 1.0
O Y:ALA169 3.8 63.1 1.0
C Y:ALA169 3.9 60.1 1.0
NH1 Y:ARG19 4.0 78.5 1.0
CB I:ASP204 4.0 72.0 1.0
C Y:SER171 4.1 57.0 1.0
OXT I:ASP204 4.1 72.5 1.0
C Y:HIS166 4.2 57.6 1.0
N Y:ASP168 4.4 59.3 1.0
CA Y:ALA165 4.5 55.7 1.0
CA Y:ASP168 4.5 56.1 1.0
N Y:HIS166 4.5 55.2 1.0
N Y:SER171 4.5 57.4 1.0
CA Y:HIS166 4.6 55.7 1.0
C Y:ARG167 4.7 59.8 1.0
CZ Y:ARG19 4.7 75.2 1.0
O Y:ALA164 4.8 54.2 1.0
N Y:TYR170 4.8 60.9 1.0
CA Y:SER171 4.8 55.1 1.0
N Y:ARG167 4.8 58.7 1.0
CB Y:ALA169 4.9 58.2 1.0
O Y:ARG167 4.9 63.4 1.0
NH2 Y:ARG19 5.0 74.8 1.0

Magnesium binding site 4 out of 8 in 5fgh

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) 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-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:50.0
occ:1.00
 OE1 J:GLN118 3.3 55.7 1.0
O J:THR124 3.7 53.5 1.0
CB J:ASP120 3.8 51.3 1.0
OD2 J:ASP120 3.9 65.1 1.0
CG J:ASP120 3.9 56.5 1.0
N J:ASP120 4.1 49.1 1.0
CD J:GLN118 4.1 50.4 1.0
CB J:THR124 4.3 53.9 1.0
CG J:GLN118 4.3 49.6 1.0
CG2 J:THR124 4.4 54.1 1.0
CE1 J:HIS133 4.4 50.6 1.0
O J:GLN118 4.5 46.9 1.0
CA J:ASP120 4.6 48.5 1.0
OD1 J:ASP120 4.6 66.6 1.0
C J:THR124 4.7 51.7 1.0
CG1 I:VAL35 4.8 57.9 1.0
C J:ILE119 4.8 48.3 1.0
OG I:SER30 4.9 65.6 1.0
C J:GLN118 4.9 46.7 1.0
CD2 I:LEU28 4.9 56.7 1.0
CA J:ILE119 5.0 46.1 1.0

Magnesium binding site 5 out of 8 in 5fgh

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) 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-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:86.7
occ:1.00
 O K:ASP168 2.2 64.1 1.0
O K:ALA165 2.3 59.0 1.0
O W:ASP204 2.4 80.3 1.0
O K:SER171 3.1 60.8 1.0
C K:ASP168 3.1 60.6 1.0
C W:ASP204 3.2 73.8 1.0
C K:ALA165 3.5 58.6 1.0
O K:HIS166 3.5 62.0 1.0
CA K:ALA169 3.6 62.1 1.0
CA W:ASP204 3.6 68.9 1.0
N K:ALA169 3.7 61.2 1.0
C K:HIS166 3.9 58.7 1.0
C K:ALA169 4.0 62.1 1.0
O K:ALA169 4.0 61.0 1.0
CB W:ASP204 4.1 68.0 1.0
OXT W:ASP204 4.1 78.0 1.0
N K:ASP168 4.2 57.1 1.0
C K:SER171 4.2 59.5 1.0
CA K:ASP168 4.2 57.5 1.0
NH1 K:ARG19 4.3 73.0 1.0
N K:HIS166 4.3 56.4 1.0
C K:ARG167 4.4 58.8 1.0
CA K:HIS166 4.4 58.1 1.0
CA K:ALA165 4.4 60.1 1.0
N K:ARG167 4.5 58.6 1.0
O K:ALA164 4.6 57.5 1.0
O K:ARG167 4.6 65.0 1.0
N K:SER171 4.7 62.3 1.0
N K:TYR170 4.9 63.4 1.0
CB K:ALA169 4.9 61.6 1.0
CA K:SER171 5.0 59.3 1.0
CA K:ARG167 5.0 58.7 1.0
N W:ASP204 5.0 68.1 1.0

Magnesium binding site 6 out of 8 in 5fgh

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) 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-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:76.3
occ:1.00
 OXT L:ASP222 2.2 82.6 1.0
O V:ILE163 2.2 53.0 1.0
O V:ASP166 2.3 53.0 1.0
C L:ASP222 3.0 82.0 1.0
C V:ASP166 3.1 54.9 1.0
O V:SER169 3.2 56.4 1.0
C V:ILE163 3.3 55.0 1.0
O V:TRP164 3.4 64.2 1.0
C V:TRP164 3.6 57.5 1.0
N V:ASP166 3.7 51.4 1.0
CA L:ASP222 3.7 79.3 1.0
N V:LEU167 3.8 54.4 1.0
O L:ASP222 3.9 89.4 1.0
CA V:LEU167 3.9 54.1 1.0
O V:GLY162 3.9 51.8 1.0
CA V:ASP166 4.0 53.9 1.0
CA V:TRP164 4.0 56.5 1.0
N V:TRP164 4.0 54.4 1.0
N V:ASN165 4.1 56.1 1.0
C V:ASN165 4.2 52.6 1.0
C V:SER169 4.3 52.7 1.0
CA V:ILE163 4.4 54.6 1.0
CB L:ASP222 4.4 78.0 1.0
NH1 V:ARG19 4.5 66.9 1.0
CD2 V:LEU167 4.5 52.5 1.0
C V:LEU167 4.6 55.6 1.0
O L:ARG221 4.6 75.3 1.0
CA V:ASN165 4.6 54.7 1.0
N L:ASP222 4.9 76.1 1.0
O V:ASN165 4.9 54.0 1.0
O V:LEU167 4.9 57.9 1.0
C V:GLY162 4.9 53.1 1.0
N V:SER169 5.0 52.1 1.0
CB V:ASP166 5.0 53.2 1.0

Magnesium binding site 7 out of 8 in 5fgh

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) 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-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:52.9
occ:1.00
 O N:SER169 2.5 47.0 1.0
O N:ILE163 2.7 44.7 1.0
O N:ASP166 2.9 49.6 1.0
NH1 N:ARG19 3.4 52.3 1.0
C N:SER169 3.7 45.2 1.0
CD1 a:LEU34 3.7 50.7 1.0
C N:ILE163 3.8 46.1 1.0
CG2 N:ILE163 4.0 45.7 1.0
C N:ASP166 4.0 47.3 1.0
CZ N:ARG19 4.1 50.6 1.0
CA N:GLY167 4.3 46.5 1.0
CA N:GLY170 4.3 45.8 1.0
O N:GLY167 4.3 46.9 1.0
NH2 N:ARG19 4.4 51.9 1.0
N N:GLY170 4.4 45.1 1.0
CA N:ILE163 4.5 45.8 1.0
C N:GLY167 4.5 46.3 1.0
N N:GLY167 4.6 45.4 1.0
CA N:SER169 4.7 43.1 1.0
N N:SER169 4.7 44.8 1.0
CB N:ILE163 4.8 45.2 1.0
N N:LYS164 4.9 46.5 1.0
NE N:ARG19 5.0 49.9 1.0

Magnesium binding site 8 out of 8 in 5fgh

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-K33A Mutant (Propeptide Expressed in Trans) 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-K33A Mutant (Propeptide Expressed in Trans) in Complex with MG132 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:74.8
occ:1.00
 O Z:VAL198 2.4 59.6 1.0
O Z:THR192 2.9 63.9 1.0
O Z:HIS195 3.3 53.4 1.0
O Z:ASP222 3.4 80.6 1.0
NH2 Z:ARG28 3.5 72.1 1.0
CG2 Z:THR192 3.6 70.0 1.0
C Z:VAL198 3.6 61.3 1.0
C Z:THR192 3.8 66.9 1.0
O Z:ILE196 4.0 62.9 1.0
OD1 Z:ASP222 4.2 79.3 1.0
CA Z:THR192 4.2 68.3 1.0
CA Z:ILE196 4.3 57.2 1.0
NH2 H:ARG19 4.3 75.2 1.0
C Z:ILE196 4.3 56.8 1.0
C Z:HIS195 4.4 56.6 1.0
CA Z:GLY199 4.4 62.4 1.0
C Z:ASP222 4.4 80.1 1.0
CZ Z:ARG28 4.4 67.2 1.0
N Z:GLY199 4.5 60.2 1.0
CB Z:THR192 4.5 68.0 1.0
N Z:VAL198 4.5 56.9 1.0
NH1 Z:ARG28 4.6 69.7 1.0
CA Z:VAL198 4.6 59.4 1.0
O Z:LYS220 4.7 67.9 1.0
N Z:ILE196 4.8 55.2 1.0
OXT Z:ASP222 5.0 85.2 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: Sun Sep 29 04:11:52 2024

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