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Magnesium in PDB 5d0z: Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib, PDB code: 5d0z 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 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.270, 300.740, 144.380, 90.00, 112.88, 90.00
R / Rfree (%) 17.8 / 20.7

Other elements in 5d0z:

The structure of Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib 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 Carfilzomib (pdb code 5d0z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib, PDB code: 5d0z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5d0z

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib


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

b:60.0
occ:1.00
 O G:MET125 2.4 50.4 1.0
OG1 G:THR8 2.6 52.2 1.0
O G:ARG122 2.8 57.2 1.0
O G:ALA123 3.0 54.0 1.0
O G:TYR119 3.2 45.8 1.0
CG2 G:THR8 3.3 52.9 1.0
C G:ALA123 3.5 56.0 1.0
CB G:THR8 3.5 52.4 1.0
C G:MET125 3.5 53.4 1.0
CA G:ALA123 3.6 54.7 1.0
N G:THR8 3.8 56.2 1.0
C G:ARG122 3.9 57.4 1.0
N G:ALA123 4.2 55.4 1.0
CA G:ARG126 4.2 50.2 1.0
N G:ARG126 4.3 51.3 1.0
CA G:THR8 4.3 53.6 1.0
N G:MET125 4.3 58.9 1.0
C G:TYR119 4.5 47.7 1.0
N G:TYR124 4.5 58.1 1.0
CA G:MET125 4.5 59.0 1.0
CD G:PRO127 4.7 46.0 1.0
CB G:ALA123 4.8 52.9 1.0
C G:ILE7 4.9 58.9 1.0
C G:TYR124 4.9 58.0 1.0
CA G:ILE7 5.0 58.7 1.0

Magnesium binding site 2 out of 7 in 5d0z

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:47.7
occ:1.00
 O I:ASP177 2.3 48.6 1.0
O I:SER180 2.7 46.9 1.0
O I:ALA174 2.7 54.2 1.0
C I:ASP177 3.4 48.4 1.0
OXT I:ASP204 3.7 55.4 1.0
C I:ALA174 3.8 55.1 1.0
C I:SER180 3.9 49.6 1.0
CA I:ALA178 4.1 49.5 1.0
N I:ALA178 4.2 48.7 1.0
O I:ALA178 4.2 56.1 1.0
CA I:ASP175 4.3 55.1 1.0
C I:ALA178 4.3 50.1 1.0
N I:ASP177 4.4 48.0 1.0
C I:ASP175 4.5 52.3 1.0
CA I:ASP177 4.5 49.6 1.0
N I:ASP175 4.5 54.0 1.0
N I:SER180 4.5 45.3 1.0
C I:ASP204 4.6 65.7 1.0
O I:ASP175 4.6 49.1 1.0
O I:ASP204 4.6 66.9 1.0
NH1 Y:ARG19 4.7 65.0 1.0
CA I:SER180 4.7 48.9 1.0
N I:GLY181 4.8 49.8 1.0
CA I:GLY181 4.8 50.9 1.0
CA I:ALA174 5.0 54.7 1.0
CG2 Y:VAL26 5.0 58.2 1.0
NH2 Y:ARG19 5.0 69.1 1.0
N I:LEU179 5.0 49.6 1.0

Magnesium binding site 3 out of 7 in 5d0z

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:56.7
occ:1.00
 O I:ASP204 2.2 66.9 1.0
O Y:ASP168 2.3 51.6 1.0
O Y:ALA165 2.6 48.8 1.0
O Y:SER171 2.7 56.3 1.0
C I:ASP204 3.1 65.7 1.0
C Y:ASP168 3.3 50.7 1.0
CA Y:ALA169 3.5 50.7 1.0
CA I:ASP204 3.6 67.1 1.0
O Y:ALA169 3.7 48.0 1.0
NH1 Y:ARG19 3.7 65.0 1.0
C Y:ALA169 3.7 48.8 1.0
C Y:ALA165 3.8 54.9 1.0
N Y:ALA169 3.8 51.8 1.0
C Y:SER171 3.9 55.5 1.0
O Y:HIS166 3.9 47.6 1.0
OXT I:ASP204 4.0 55.4 1.0
CB I:ASP204 4.0 70.7 1.0
N Y:SER171 4.3 51.2 1.0
CZ Y:ARG19 4.3 65.0 1.0
C Y:HIS166 4.4 52.1 1.0
NH2 Y:ARG19 4.5 69.1 1.0
N Y:TYR170 4.5 49.4 1.0
CA Y:ASP168 4.6 49.9 1.0
CA Y:ALA165 4.6 53.9 1.0
N Y:ASP168 4.7 51.0 1.0
CA Y:SER171 4.7 52.2 1.0
N Y:HIS166 4.7 57.3 1.0
CA Y:HIS166 4.8 53.1 1.0
CB Y:ALA169 4.8 50.8 1.0
O Y:ALA164 4.9 56.3 1.0
N Y:GLY172 4.9 58.7 1.0
C Y:ARG167 5.0 51.5 1.0
N I:ASP204 5.0 64.7 1.0

Magnesium binding site 4 out of 7 in 5d0z

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:41.5
occ:1.00
 O K:ASP168 2.2 51.7 1.0
O K:ALA165 2.3 51.6 1.0
O W:ASP204 2.4 66.3 1.0
O K:SER171 2.8 48.8 1.0
C W:ASP204 3.2 63.5 1.0
C K:ASP168 3.2 49.4 1.0
C K:ALA165 3.5 50.3 1.0
CA K:ALA169 3.6 49.9 1.0
CA W:ASP204 3.6 61.8 1.0
O K:HIS166 3.6 47.0 1.0
N K:ALA169 3.8 50.7 1.0
C K:ALA169 3.9 50.4 1.0
O K:ALA169 3.9 52.3 1.0
C K:SER171 4.0 49.5 1.0
CB W:ASP204 4.0 60.9 1.0
NH1 K:ARG19 4.0 63.9 1.0
C K:HIS166 4.1 47.7 1.0
OXT W:ASP204 4.2 62.0 1.0
N K:SER171 4.3 45.8 1.0
N K:HIS166 4.4 47.5 1.0
CA K:ASP168 4.4 48.0 1.0
CA K:ALA165 4.4 51.6 1.0
N K:ASP168 4.4 48.8 1.0
CA K:HIS166 4.5 48.6 1.0
O K:ALA164 4.6 53.5 1.0
CZ K:ARG19 4.6 64.8 1.0
N K:TYR170 4.6 47.9 1.0
C K:ARG167 4.7 49.5 1.0
CA K:SER171 4.7 47.0 1.0
NH2 K:ARG19 4.8 72.0 1.0
N K:ARG167 4.8 46.1 1.0
O K:ARG167 4.9 50.6 1.0
CB K:ALA169 4.9 48.3 1.0
N K:GLY172 5.0 52.2 1.0
N W:ASP204 5.0 60.9 1.0

Magnesium binding site 5 out of 7 in 5d0z

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:45.9
occ:1.00
 O N:SER169 2.5 43.3 1.0
O N:ILE163 2.6 47.0 1.0
O N:ASP166 3.0 45.4 1.0
NH1 N:ARG19 3.5 46.0 1.0
CD1 a:LEU34 3.7 53.8 1.0
C N:SER169 3.7 45.2 1.0
C N:ILE163 3.7 50.7 1.0
CG2 N:ILE163 3.9 47.7 1.0
C N:ASP166 4.1 46.4 1.0
CZ N:ARG19 4.2 45.6 1.0
CA N:GLY167 4.3 46.3 1.0
CA N:GLY170 4.3 48.5 1.0
CA N:ILE163 4.4 50.6 1.0
NH2 N:ARG19 4.5 45.5 1.0
O N:GLY167 4.5 48.9 1.0
N N:GLY170 4.5 45.9 1.0
C N:GLY167 4.6 46.8 1.0
N N:GLY167 4.6 46.0 1.0
N N:SER169 4.7 44.8 1.0
N N:LYS164 4.8 52.0 1.0
CA N:SER169 4.8 43.7 1.0
CB N:ILE163 4.8 48.8 1.0
O N:LYS164 4.9 55.1 1.0
CG a:LEU34 5.0 55.0 1.0
CA N:LYS164 5.0 52.8 1.0
C N:LYS164 5.0 53.0 1.0

Magnesium binding site 6 out of 7 in 5d0z

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA5-T1S Mutant in Complex with Carfilzomib


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:68.2
occ:1.00
 O Z:HIS195 2.8 51.6 1.0
O Z:VAL198 2.8 51.9 1.0
O Z:THR192 2.8 61.6 1.0
O Z:ASP222 3.5 77.5 1.0
NH2 Z:ARG28 3.6 64.0 1.0
CA Z:ILE196 3.7 51.6 1.0
O Z:ILE196 3.7 53.8 1.0
C Z:HIS195 3.7 54.6 1.0
C Z:ILE196 3.9 52.0 1.0
C Z:THR192 3.9 61.5 1.0
C Z:VAL198 4.0 54.7 1.0
CG2 Z:THR192 4.1 63.6 1.0
N Z:ILE196 4.2 52.2 1.0
NH2 H:ARG19 4.2 70.5 1.0
CA Z:THR192 4.3 61.0 1.0
N Z:VAL198 4.5 53.3 1.0
C Z:ASP222 4.5 75.2 1.0
OD1 Z:ASP222 4.5 71.3 1.0
CZ Z:ARG28 4.7 65.0 1.0
NH1 H:ARG19 4.7 63.1 1.0
CA Z:VAL198 4.8 54.8 1.0
CZ H:ARG19 4.8 63.0 1.0
N Z:GLN197 4.8 51.3 1.0
CB Z:THR192 4.9 61.2 1.0
OXT Z:ASP222 4.9 78.9 1.0
N Z:GLY199 4.9 54.4 1.0
CB Z:ILE196 4.9 51.7 1.0
NH1 Z:ARG28 5.0 66.9 1.0
CA Z:GLY199 5.0 59.2 1.0
CA Z:HIS195 5.0 53.4 1.0

Magnesium binding site 7 out of 7 in 5d0z

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


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 Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg202

b:30.0
occ:1.00
 O b:SER169 2.4 44.9 1.0
O b:ILE163 2.6 42.8 1.0
O b:ASP166 2.8 45.6 1.0
NH1 b:ARG19 3.5 55.7 1.0
C b:SER169 3.6 49.4 1.0
C b:ILE163 3.7 49.3 1.0
CD1 M:LEU34 3.8 54.9 1.0
C b:ASP166 3.9 48.6 1.0
CG2 b:ILE163 4.0 52.9 1.0
CA b:GLY167 4.2 50.0 1.0
CZ b:ARG19 4.2 55.2 1.0
CA b:GLY170 4.3 54.8 1.0
O b:GLY167 4.3 48.8 1.0
CA b:ILE163 4.4 51.0 1.0
N b:GLY170 4.4 52.5 1.0
C b:GLY167 4.4 49.7 1.0
N b:GLY167 4.5 49.7 1.0
NH2 b:ARG19 4.5 55.9 1.0
N b:SER169 4.6 46.2 1.0
CA b:SER169 4.6 46.6 1.0
N b:LYS164 4.8 52.1 1.0
CB b:ILE163 4.8 51.4 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 02:26:00 2024

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