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Magnesium in PDB 5cz7: Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis

Enzymatic activity of Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis

All present enzymatic activity of Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis, PDB code: 5cz7 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.090, 301.660, 145.510, 90.00, 113.44, 90.00
R / Rfree (%) 19.7 / 21.5

Other elements in 5cz7:

The structure of Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis 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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis (pdb code 5cz7). 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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis, PDB code: 5cz7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 5cz7

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Magnesium binding site 1 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:40.1
occ:1.00
 O G:MET125 2.1 42.1 1.0
O G:HOH432 2.3 34.3 1.0
O G:ARG122 2.3 40.3 1.0
O G:TYR119 2.4 34.2 1.0
OG1 G:THR8 2.6 37.1 1.0
CG2 G:THR8 3.3 38.5 1.0
C G:MET125 3.4 41.5 1.0
C G:ARG122 3.5 40.5 1.0
CB G:THR8 3.5 38.1 1.0
C G:TYR119 3.6 33.1 1.0
O G:ALA123 3.6 42.8 1.0
CA G:ALA123 3.8 40.9 1.0
C G:ALA123 3.8 42.2 1.0
N G:ALA123 4.1 40.4 1.0
N G:MET125 4.2 44.0 1.0
N G:ARG126 4.2 37.6 1.0
CA G:ARG126 4.2 36.5 1.0
CA G:MET125 4.3 45.2 1.0
CA G:TYR119 4.3 32.2 1.0
N G:THR8 4.4 39.0 1.0
CD G:PRO127 4.5 33.8 1.0
N G:THR120 4.6 33.3 1.0
CA G:THR8 4.6 38.9 1.0
CA G:ARG122 4.7 41.9 1.0
N G:ARG122 4.7 39.3 1.0
N G:TYR124 4.7 42.3 1.0
CA G:THR120 4.7 33.3 1.0
C G:ARG126 4.8 35.6 1.0
CB G:MET125 4.8 50.0 1.0
C G:THR120 4.8 34.4 1.0
CB G:TYR119 4.9 32.1 1.0
O G:HOH442 4.9 45.4 1.0
N G:PRO127 4.9 34.5 1.0

Magnesium binding site 2 out of 11 in 5cz7

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Magnesium binding site 2 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.2
occ:1.00
 O I:SER180 2.5 39.5 1.0
O I:ASP177 2.5 37.7 1.0
O I:ALA174 2.8 36.6 1.0
C I:ASP177 3.6 37.4 1.0
C I:SER180 3.7 39.3 1.0
OXT I:ASP204 3.9 47.0 1.0
C I:ALA174 3.9 37.7 1.0
O I:ALA178 4.1 40.7 1.0
CA I:ASP175 4.2 40.5 1.0
CA I:ALA178 4.3 37.5 1.0
C I:ALA178 4.3 39.2 1.0
N I:ALA178 4.4 36.9 1.0
N I:SER180 4.4 38.2 1.0
N I:ASP177 4.4 38.0 1.0
N I:ASP175 4.5 39.0 1.0
C I:ASP175 4.5 40.6 1.0
N I:GLY181 4.5 39.5 1.0
CA I:GLY181 4.6 40.7 1.0
CA I:ASP177 4.6 37.8 1.0
CA I:SER180 4.6 39.0 1.0
NH1 Y:ARG19 4.6 51.0 1.0
O I:ASP175 4.6 43.0 1.0
O I:ASP204 4.7 43.6 1.0
C I:ASP204 4.7 46.1 1.0
NH2 Y:ARG19 4.8 50.3 1.0
OD1 I:ASP175 5.0 45.0 1.0
CA I:ALA174 5.0 36.6 1.0

Magnesium binding site 3 out of 11 in 5cz7

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Magnesium binding site 3 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:65.7
occ:1.00
 MG I:MG303 2.7 43.2 1.0
O Y:HIS166 3.1 41.0 1.0
O I:ASP204 3.3 43.6 1.0
C I:ASP204 3.5 46.1 1.0
O Y:ASP168 3.7 39.4 1.0
OXT I:ASP204 3.7 47.0 1.0
CA Y:ALA169 3.7 41.3 1.0
NE1 I:TRP182 3.7 42.7 1.0
O Y:ALA165 3.8 38.4 1.0
C Y:ASP168 3.9 39.3 1.0
N Y:ALA169 3.9 40.0 1.0
C Y:HIS166 4.0 39.4 1.0
CA I:ASP204 4.1 46.5 1.0
CD1 I:TRP182 4.2 42.5 1.0
O Y:ARG167 4.2 38.5 1.0
C Y:ARG167 4.3 39.1 1.0
CE2 I:TRP182 4.3 43.3 1.0
CB Y:ALA169 4.5 41.5 1.0
NE I:ARG27 4.6 36.0 1.0
N Y:ASP168 4.6 38.9 1.0
C Y:ALA169 4.6 42.7 1.0
N Y:ARG167 4.7 38.6 1.0
O Y:ALA169 4.7 43.6 1.0
CZ2 I:TRP182 4.8 44.7 1.0
CA Y:ARG167 4.8 39.0 1.0
O I:ALA178 4.8 40.7 1.0
CA Y:HIS166 4.8 39.3 1.0
CA Y:ASP168 4.9 39.3 1.0
C Y:ALA165 4.9 38.4 1.0

Magnesium binding site 4 out of 11 in 5cz7

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Magnesium binding site 4 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg303

b:43.2
occ:1.00
 O Y:ASP168 2.3 39.4 1.0
O I:ASP204 2.4 43.6 1.0
O Y:ALA165 2.4 38.4 1.0
O Y:SER171 2.5 41.3 1.0
MG I:MG302 2.7 65.7 1.0
C I:ASP204 3.2 46.1 1.0
C Y:ASP168 3.3 39.3 1.0
C Y:ALA165 3.5 38.4 1.0
O Y:ALA169 3.6 43.6 1.0
NH1 Y:ARG19 3.6 51.0 1.0
CA Y:ALA169 3.6 41.3 1.0
C Y:SER171 3.7 40.5 1.0
C Y:ALA169 3.7 42.7 1.0
CA I:ASP204 3.7 46.5 1.0
N Y:ALA169 3.9 40.0 1.0
CB I:ASP204 4.0 46.4 1.0
N Y:SER171 4.1 39.8 1.0
OXT I:ASP204 4.1 47.0 1.0
CA Y:ALA165 4.2 38.1 1.0
O Y:HIS166 4.3 41.0 1.0
CZ Y:ARG19 4.4 49.9 1.0
CA Y:SER171 4.4 39.9 1.0
CA Y:ASP168 4.5 39.3 1.0
N Y:ASP168 4.5 38.9 1.0
C Y:HIS166 4.5 39.4 1.0
N Y:TYR170 4.5 42.9 1.0
N Y:HIS166 4.6 39.1 1.0
N Y:GLY172 4.7 41.1 1.0
O Y:ALA164 4.7 38.4 1.0
NH2 Y:ARG19 4.8 50.3 1.0
CA Y:HIS166 4.8 39.3 1.0
CA Y:GLY172 4.8 42.3 1.0
CB Y:SER171 4.9 39.4 1.0
CG I:ASP204 4.9 45.4 1.0
C Y:ARG167 5.0 39.1 1.0

Magnesium binding site 5 out of 11 in 5cz7

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Magnesium binding site 5 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:53.2
occ:1.00
 O I:HOH442 2.2 48.0 1.0
OE1 J:GLN118 3.2 36.2 1.0
O J:THR124 3.3 33.0 1.0
N J:ASP120 3.6 31.5 1.0
CB J:ASP120 3.7 33.2 1.0
CG J:ASP120 3.8 34.9 1.0
OD2 J:ASP120 3.9 38.1 1.0
CG J:GLN118 4.0 31.8 1.0
CD J:GLN118 4.0 33.4 1.0
CE1 J:HIS133 4.1 32.3 1.0
O J:GLN118 4.1 29.6 1.0
CB J:THR124 4.2 33.9 1.0
CA J:ASP120 4.2 32.1 1.0
C J:ILE119 4.3 30.4 1.0
C J:THR124 4.3 33.6 1.0
C J:GLN118 4.4 29.5 1.0
CG2 J:THR124 4.4 33.5 1.0
CA J:ILE119 4.4 28.8 1.0
OD1 J:ASP120 4.6 36.4 1.0
N J:ILE119 4.6 28.8 1.0
CB J:GLN118 4.7 30.7 1.0
ND1 J:HIS133 4.9 32.7 1.0
CG1 I:VAL35 4.9 44.7 1.0
CA J:THR124 4.9 34.1 1.0
NE2 J:HIS133 5.0 31.6 1.0

Magnesium binding site 6 out of 11 in 5cz7

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Magnesium binding site 6 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:48.1
occ:1.00
 O K:SER171 2.3 44.7 1.0
O K:ALA165 2.3 41.2 1.0
O K:ASP168 2.3 42.3 1.0
O W:ASP204 2.4 47.5 1.0
C W:ASP204 3.2 47.7 1.0
C K:ASP168 3.4 41.5 1.0
C K:ALA165 3.4 41.5 1.0
C K:SER171 3.5 43.9 1.0
NH1 K:ARG19 3.6 52.1 1.0
CA W:ASP204 3.7 47.5 1.0
O K:ALA169 3.7 44.1 1.0
C K:ALA169 3.8 43.7 1.0
CA K:ALA169 3.8 42.8 1.0
CB W:ASP204 3.8 47.2 1.0
N K:ALA169 4.0 41.6 1.0
N K:SER171 4.0 42.5 1.0
CA K:ALA165 4.1 41.3 1.0
OXT W:ASP204 4.2 50.0 1.0
CA K:SER171 4.3 42.4 1.0
CZ K:ARG19 4.3 50.6 1.0
O K:HIS166 4.3 42.4 1.0
O W:HOH314 4.4 49.6 1.0
N K:GLY172 4.5 44.4 1.0
N K:HIS166 4.5 41.7 1.0
CA K:ASP168 4.6 40.8 1.0
C K:HIS166 4.6 41.6 1.0
N K:TYR170 4.6 44.2 1.0
N K:ASP168 4.6 40.9 1.0
CA K:GLY172 4.6 45.7 1.0
O K:ALA164 4.6 40.2 1.0
NH2 K:ARG19 4.7 51.2 1.0
CB K:SER171 4.7 41.9 1.0
CG W:ASP204 4.8 48.3 1.0
CA K:HIS166 4.8 41.8 1.0
CB K:ALA165 4.9 41.8 1.0

Magnesium binding site 7 out of 11 in 5cz7

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Magnesium binding site 7 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:48.4
occ:1.00
 O K:ILE82 2.7 35.1 1.0
O K:HOH423 3.0 44.5 1.0
C K:ILE82 3.6 34.3 1.0
CG2 K:ILE82 3.7 33.8 1.0
CA K:ILE82 3.7 34.5 1.0
N K:LEU86 3.8 33.0 1.0
CB K:ASN85 3.9 34.7 1.0
CB K:LEU86 4.0 33.4 1.0
CA K:LEU86 4.2 33.2 1.0
CH2 K:TRP58 4.2 30.9 1.0
CB K:ILE82 4.2 34.2 1.0
C K:ASN85 4.3 33.3 1.0
CA K:ASN85 4.6 34.1 1.0
CG1 K:ILE82 4.7 34.4 1.0
O K:ARG81 4.8 38.8 1.0
O K:HOH435 4.8 42.5 1.0
CZ3 K:TRP58 4.9 31.0 1.0
N K:LEU83 4.9 33.7 1.0
O K:ASN85 5.0 33.6 1.0
N K:ILE82 5.0 35.5 1.0
CG K:LEU86 5.0 33.8 1.0

Magnesium binding site 8 out of 11 in 5cz7

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Magnesium binding site 8 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:40.4
occ:1.00
 OXT L:ASP222 2.2 49.7 1.0
O V:SER169 2.2 37.5 1.0
O V:ILE163 2.2 38.3 1.0
O V:ASP166 2.2 38.4 1.0
O V:HOH427 2.5 37.4 1.0
C L:ASP222 3.1 53.5 1.0
C V:ASP166 3.2 37.7 1.0
C V:ILE163 3.3 39.1 1.0
C V:SER169 3.4 36.9 1.0
CA L:ASP222 3.7 54.6 1.0
NH1 V:ARG19 3.8 46.6 1.0
O V:GLY162 3.9 37.4 1.0
CA V:LEU167 3.9 36.3 1.0
N V:LEU167 3.9 37.2 1.0
O L:ASP222 4.0 55.9 1.0
CA V:ILE163 4.1 39.7 1.0
N V:ASP166 4.2 38.7 1.0
CB L:ASP222 4.2 53.9 1.0
N V:SER169 4.2 34.9 1.0
N V:GLY170 4.3 38.4 1.0
N V:TRP164 4.3 39.8 1.0
CA V:GLY170 4.3 40.0 1.0
CA V:ASP166 4.3 37.9 1.0
C V:LEU167 4.3 36.5 1.0
CA V:SER169 4.3 35.4 1.0
C V:TRP164 4.3 40.9 1.0
O V:TRP164 4.4 41.1 1.0
CZ V:ARG19 4.4 45.4 1.0
CA V:TRP164 4.5 41.7 1.0
O V:LEU167 4.5 36.9 1.0
NH2 V:ARG19 4.7 47.2 1.0
N V:ASN165 4.7 40.1 1.0
CB V:SER169 4.7 35.3 1.0
C V:GLY162 4.8 38.8 1.0
C V:ASN165 4.9 39.2 1.0
N V:ILE163 5.0 39.5 1.0
N V:GLY168 5.0 35.3 1.0

Magnesium binding site 9 out of 11 in 5cz7

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Magnesium binding site 9 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:38.9
occ:1.00
 O N:ILE163 2.5 35.8 1.0
O N:SER169 2.5 32.7 1.0
O N:ASP166 2.8 36.4 1.0
CD1 a:LEU34 3.6 43.0 1.0
C N:ILE163 3.6 36.3 1.0
NH1 N:ARG19 3.7 38.1 1.0
C N:SER169 3.7 32.4 1.0
C N:ASP166 3.8 35.4 1.0
CG2 N:ILE163 4.0 34.7 1.0
CA N:GLY167 4.2 35.1 1.0
CA N:ILE163 4.3 35.1 1.0
CZ N:ARG19 4.3 37.6 1.0
O N:GLY167 4.4 35.2 1.0
N N:GLY167 4.4 34.7 1.0
CA N:GLY170 4.5 33.7 1.0
C N:GLY167 4.5 34.9 1.0
N N:GLY170 4.6 32.6 1.0
NH2 N:ARG19 4.6 38.8 1.0
N N:LYS164 4.7 38.4 1.0
N N:SER169 4.7 32.9 1.0
CA N:SER169 4.7 31.5 1.0
CB N:ILE163 4.8 34.5 1.0
N N:ASP166 4.8 35.2 1.0
O N:LYS164 4.8 42.4 1.0
C N:LYS164 4.8 40.4 1.0
CG a:LEU34 4.8 42.5 1.0
CA N:ASP166 4.9 35.3 1.0
CA N:LYS164 4.9 40.8 1.0

Magnesium binding site 10 out of 11 in 5cz7

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Magnesium binding site 10 out of 11 in the Yeast 20S Proteasome BETA5-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis


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-T1A BETA5-K81R Double Mutant in Complex with Bortezomib, Propeptide Expressed in Cis within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg203

b:70.6
occ:1.00
 OD1 N:ASP51 2.7 33.2 1.0
O N:ASN92 2.9 46.0 1.0
OD2 N:ASP51 3.2 34.2 1.0
CG N:ASP51 3.3 30.1 1.0
NE2 H:GLN91 3.4 55.5 1.0
OE1 H:GLN91 4.1 61.1 1.0
C N:ASN92 4.1 46.2 1.0
CD H:GLN91 4.1 51.6 1.0
O N:HOH310 4.4 39.7 1.0
O H:HOH408 4.4 31.5 1.0
CA N:LEU93 4.7 42.5 1.0
CB N:ASP51 4.8 32.0 1.0
CE1 H:PHE88 4.8 31.4 1.0
N N:LEU93 4.9 44.6 1.0
O N:HOH313 4.9 33.5 1.0
CD2 N:LEU93 4.9 41.9 1.0
CZ H:PHE88 4.9 31.9 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 02:21:02 2024

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