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Magnesium in PDB 5d0x: Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib

Enzymatic activity of Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib

All present enzymatic activity of Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib, PDB code: 5d0x 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 (°) 136.810, 300.230, 145.290, 90.00, 113.10, 90.00
R / Rfree (%) 20.4 / 22.4

Other elements in 5d0x:

The structure of Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib 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-T1S Mutant in Complex with Bortezomib (pdb code 5d0x). 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-T1S Mutant in Complex with Bortezomib, PDB code: 5d0x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5d0x

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:49.8
occ:1.00
 O G:MET125 2.1 48.2 1.0
O G:ARG122 2.4 45.4 1.0
O G:TYR119 2.6 41.6 1.0
OG1 G:THR8 2.6 45.8 1.0
CG2 G:THR8 3.2 47.3 1.0
C G:MET125 3.3 49.0 1.0
O G:ALA123 3.5 49.4 1.0
CB G:THR8 3.5 46.2 1.0
C G:ARG122 3.6 46.7 1.0
C G:ALA123 3.8 49.2 1.0
C G:TYR119 3.8 40.7 1.0
CA G:ALA123 3.8 47.9 1.0
N G:ALA123 4.1 47.0 1.0
N G:ARG126 4.2 45.7 1.0
CA G:ARG126 4.2 44.1 1.0
N G:MET125 4.2 49.3 1.0
N G:THR8 4.3 46.8 1.0
CA G:MET125 4.3 52.1 1.0
CA G:TYR119 4.5 40.2 1.0
CA G:THR8 4.5 46.6 1.0
CD G:PRO127 4.5 40.5 1.0
N G:TYR124 4.7 49.9 1.0
C G:ARG126 4.8 42.5 1.0
N G:THR120 4.8 39.9 1.0
CA G:ARG122 4.8 48.5 1.0
CB G:MET125 4.8 57.9 1.0
N G:ARG122 4.8 45.8 1.0
CA G:THR120 4.9 40.2 1.0
N G:PRO127 4.9 40.5 1.0
CB G:TYR119 5.0 40.5 1.0

Magnesium binding site 2 out of 8 in 5d0x

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib


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-T1S Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:55.1
occ:1.00
 O Y:ASP168 2.3 45.1 1.0
O I:ASP204 2.3 54.6 1.0
O Y:ALA165 2.5 48.4 1.0
O Y:SER171 2.6 49.2 1.0
C I:ASP204 3.2 57.5 1.0
C Y:ASP168 3.3 46.1 1.0
NH1 Y:ARG19 3.6 65.8 1.0
CA Y:ALA169 3.6 47.6 1.0
CA I:ASP204 3.6 58.3 1.0
C Y:ALA165 3.7 46.3 1.0
O Y:ALA169 3.8 49.9 1.0
C Y:SER171 3.8 45.0 1.0
C Y:ALA169 3.8 48.0 1.0
N Y:ALA169 3.8 47.7 1.0
CB I:ASP204 3.9 59.8 1.0
O Y:HIS166 4.0 45.8 1.0
OXT I:ASP204 4.1 59.7 1.0
N Y:SER171 4.3 44.2 1.0
CZ Y:ARG19 4.3 62.7 1.0
CA Y:ALA165 4.5 46.6 1.0
C Y:HIS166 4.5 46.9 1.0
CA Y:ASP168 4.5 45.5 1.0
N Y:ASP168 4.5 48.4 1.0
CA Y:SER171 4.6 43.1 1.0
NH2 Y:ARG19 4.6 67.6 1.0
N Y:TYR170 4.6 46.9 1.0
N Y:HIS166 4.7 46.8 1.0
O Y:ALA164 4.7 49.1 1.0
N Y:GLY172 4.7 46.2 1.0
CA Y:GLY172 4.9 48.3 1.0
CA Y:HIS166 4.9 47.2 1.0
CG I:ASP204 4.9 60.0 1.0
C Y:ARG167 4.9 48.7 1.0
CB Y:ALA169 4.9 47.4 1.0
CB Y:SER171 5.0 42.0 1.0

Magnesium binding site 3 out of 8 in 5d0x

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib


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-T1S Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg201

b:54.7
occ:1.00
 OE1 J:GLN118 3.4 44.2 1.0
O J:THR124 3.7 43.2 1.0
CB J:ASP120 3.9 39.0 1.0
CG J:ASP120 4.0 40.5 1.0
OD2 J:ASP120 4.1 43.5 1.0
N J:ASP120 4.1 37.3 1.0
CD J:GLN118 4.2 41.7 1.0
CB J:THR124 4.2 42.5 1.0
CG J:GLN118 4.3 39.0 1.0
CG2 J:THR124 4.3 42.8 1.0
O J:GLN118 4.4 36.1 1.0
CE1 J:HIS133 4.4 38.3 1.0
CG1 I:VAL35 4.6 50.7 1.0
C J:THR124 4.6 42.0 1.0
CA J:ASP120 4.6 37.8 1.0
OD1 J:ASP120 4.7 42.5 1.0
C J:ILE119 4.8 37.2 1.0
CD2 I:LEU28 4.8 47.9 1.0
C J:GLN118 4.8 36.4 1.0
OG I:SER30 4.9 58.5 1.0
CA J:ILE119 4.9 35.7 1.0

Magnesium binding site 4 out of 8 in 5d0x

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib


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-T1S Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:49.8
occ:1.00
 O K:ASP168 2.2 49.2 1.0
O K:ALA165 2.4 46.6 1.0
O W:ASP204 2.4 53.1 1.0
O K:SER171 2.6 48.7 1.0
C K:ASP168 3.2 48.0 1.0
C W:ASP204 3.3 54.0 1.0
C K:ALA165 3.6 48.6 1.0
CA K:ALA169 3.6 50.0 1.0
CA W:ASP204 3.7 54.7 1.0
NH1 K:ARG19 3.7 62.9 1.0
C K:SER171 3.8 47.5 1.0
N K:ALA169 3.8 49.3 1.0
C K:ALA169 3.8 51.7 1.0
O K:ALA169 3.9 52.8 1.0
CB W:ASP204 3.9 54.9 1.0
O K:HIS166 3.9 49.5 1.0
OXT W:ASP204 4.2 55.4 1.0
N K:SER171 4.3 46.1 1.0
C K:HIS166 4.3 49.7 1.0
CA K:ALA165 4.3 50.8 1.0
CA K:ASP168 4.4 47.2 1.0
N K:ASP168 4.4 48.7 1.0
CZ K:ARG19 4.4 62.6 1.0
CA K:SER171 4.5 45.9 1.0
N K:HIS166 4.6 49.1 1.0
O K:ALA164 4.6 51.5 1.0
N K:TYR170 4.6 50.2 1.0
CA K:HIS166 4.7 50.4 1.0
C K:ARG167 4.8 49.5 1.0
N K:GLY172 4.8 49.0 1.0
NH2 K:ARG19 4.8 68.2 1.0
CA K:GLY172 4.9 50.7 1.0
CB K:SER171 4.9 45.3 1.0
N K:ARG167 4.9 48.8 1.0
CG W:ASP204 4.9 54.5 1.0
CB K:ALA169 5.0 49.4 1.0

Magnesium binding site 5 out of 8 in 5d0x

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib


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-T1S Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:48.2
occ:1.00
 O K:ILE82 2.8 37.7 1.0
N K:LEU86 3.7 33.3 1.0
C K:ILE82 3.7 37.0 1.0
CA K:ILE82 3.8 36.5 1.0
CB K:ASN85 3.8 33.0 1.0
CG2 K:ILE82 3.9 37.6 1.0
CB K:LEU86 4.0 34.4 1.0
CA K:LEU86 4.0 34.2 1.0
C K:ASN85 4.2 33.0 1.0
CH2 K:TRP58 4.3 36.0 1.0
CB K:ILE82 4.4 37.5 1.0
CA K:ASN85 4.5 32.6 1.0
O K:LYS81 4.8 36.3 1.0
O K:ASN85 4.8 33.1 1.0
CG1 K:ILE82 4.8 38.9 1.0
CG K:LEU86 4.9 35.0 1.0
N K:LEU83 4.9 36.6 1.0

Magnesium binding site 6 out of 8 in 5d0x

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib


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-T1S Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:46.2
occ:1.00
 OXT L:ASP222 2.2 63.1 1.0
O V:ASP166 2.2 46.2 1.0
O V:ILE163 2.3 50.1 1.0
O V:SER169 2.3 46.3 1.0
C L:ASP222 3.1 67.2 1.0
C V:ASP166 3.2 44.3 1.0
C V:ILE163 3.3 48.4 1.0
C V:SER169 3.4 44.9 1.0
CA L:ASP222 3.8 68.7 1.0
NH1 V:ARG19 3.8 53.8 1.0
CA V:LEU167 3.9 43.4 1.0
O V:GLY162 3.9 44.3 1.0
N V:LEU167 3.9 44.2 1.0
O L:ASP222 4.0 69.4 1.0
CA V:ILE163 4.1 47.5 1.0
N V:ASP166 4.2 43.7 1.0
C V:TRP164 4.3 50.0 1.0
O V:TRP164 4.3 52.0 1.0
N V:SER169 4.3 41.4 1.0
C V:LEU167 4.3 44.4 1.0
CA V:ASP166 4.3 44.0 1.0
N V:TRP164 4.3 48.8 1.0
CB L:ASP222 4.3 67.9 1.0
N V:GLY170 4.3 46.9 1.0
CA V:GLY170 4.3 49.0 1.0
CA V:SER169 4.4 42.3 1.0
CZ V:ARG19 4.4 53.7 1.0
O V:LEU167 4.5 45.6 1.0
CA V:TRP164 4.5 50.4 1.0
NH2 V:ARG19 4.6 56.6 1.0
N V:ASN165 4.7 47.8 1.0
CB V:SER169 4.8 42.0 1.0
C V:GLY162 4.9 45.5 1.0
C V:ASN165 4.9 44.7 1.0
CD2 V:LEU167 5.0 42.5 1.0

Magnesium binding site 7 out of 8 in 5d0x

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib


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-T1S Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:42.4
occ:1.00
 O N:SER169 2.5 38.7 1.0
O N:ILE163 2.6 40.7 1.0
O N:ASP166 2.9 45.9 1.0
NH1 N:ARG19 3.5 45.0 1.0
C N:SER169 3.7 38.3 1.0
C N:ILE163 3.7 42.6 1.0
CD1 a:LEU34 3.7 48.6 1.0
CG2 N:ILE163 3.9 40.5 1.0
C N:ASP166 3.9 42.1 1.0
CZ N:ARG19 4.2 44.1 1.0
CA N:GLY167 4.2 40.8 1.0
CA N:GLY170 4.3 40.6 1.0
CA N:ILE163 4.4 41.6 1.0
O N:GLY167 4.4 41.2 1.0
N N:GLY170 4.5 38.9 1.0
N N:GLY167 4.5 40.4 1.0
NH2 N:ARG19 4.5 46.2 1.0
C N:GLY167 4.5 40.1 1.0
N N:SER169 4.7 38.8 1.0
CA N:SER169 4.7 37.3 1.0
CB N:ILE163 4.8 40.9 1.0
N N:LYS164 4.8 44.8 1.0
O N:LYS164 4.9 47.5 1.0
C N:LYS164 5.0 46.1 1.0
N N:ASP166 5.0 40.6 1.0
CG a:LEU34 5.0 48.5 1.0

Magnesium binding site 8 out of 8 in 5d0x

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Bortezomib


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-T1S Mutant in Complex with Bortezomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:55.6
occ:1.00
 O Z:VAL198 2.5 51.7 1.0
O Z:THR192 2.9 52.9 1.0
O Z:HIS195 3.0 49.0 1.0
NH2 Z:ARG28 3.6 61.4 1.0
C Z:VAL198 3.7 53.1 1.0
O Z:ASP222 3.7 72.6 1.0
CG2 Z:THR192 3.8 59.1 1.0
O Z:ILE196 3.9 50.5 1.0
C Z:THR192 3.9 56.6 1.0
CA Z:ILE196 4.0 48.7 1.0
C Z:HIS195 4.0 48.3 1.0
C Z:ILE196 4.1 48.1 1.0
CA Z:THR192 4.2 57.4 1.0
NH2 H:ARG19 4.3 59.5 1.0
OD1 Z:ASP222 4.4 61.5 1.0
N Z:VAL198 4.4 49.2 1.0
N Z:ILE196 4.4 47.8 1.0
CZ Z:ARG28 4.6 59.7 1.0
CA Z:VAL198 4.6 51.3 1.0
C Z:ASP222 4.6 68.8 1.0
N Z:GLY199 4.6 54.1 1.0
CB Z:THR192 4.6 58.4 1.0
CA Z:GLY199 4.7 54.9 1.0
NH1 Z:ARG28 4.8 60.4 1.0
NH1 H:ARG19 4.9 55.7 1.0
N Z:GLN197 4.9 46.5 1.0
OXT Z:ASP222 5.0 68.7 1.0
CZ H:ARG19 5.0 56.7 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 02:25:58 2024

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