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Magnesium in PDB 5d0s: Yeast 20S Proteasome BETA5-D166N Mutant in Complex with Carfilzomib

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-D166N Mutant in Complex with Carfilzomib, PDB code: 5d0s 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 (°) 135.020, 300.640, 144.310, 90.00, 113.02, 90.00
R / Rfree (%) 21.6 / 23.7

Other elements in 5d0s:

The structure of Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant in Complex with Carfilzomib (pdb code 5d0s). 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-D166N Mutant in Complex with Carfilzomib, PDB code: 5d0s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5d0s

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:49.1
occ:1.00
 O G:MET125 2.2 38.3 1.0
O G:ARG122 2.6 41.9 1.0
OG1 G:THR8 2.7 35.8 1.0
O G:TYR119 2.9 35.7 1.0
O G:ALA123 3.2 44.7 1.0
CG2 G:THR8 3.3 38.2 1.0
C G:MET125 3.4 38.8 1.0
O G:HOH438 3.4 50.7 1.0
C G:ALA123 3.5 42.4 1.0
CB G:THR8 3.6 38.2 1.0
CA G:ALA123 3.6 41.2 1.0
C G:ARG122 3.7 42.0 1.0
N G:ALA123 4.1 41.3 1.0
N G:THR8 4.1 39.7 1.0
C G:TYR119 4.1 33.9 1.0
CA G:ARG126 4.1 34.4 1.0
N G:ARG126 4.1 35.8 1.0
N G:MET125 4.2 40.8 1.0
CA G:MET125 4.4 41.9 1.0
CA G:THR8 4.5 40.1 1.0
N G:TYR124 4.5 42.6 1.0
CD G:PRO127 4.5 31.9 1.0
C G:ARG126 4.8 33.6 1.0
CA G:TYR119 4.9 32.4 1.0
C G:TYR124 4.9 41.0 1.0
CB G:ALA123 4.9 40.3 1.0
CA G:ARG122 5.0 43.7 1.0
N G:PRO127 5.0 32.8 1.0

Magnesium binding site 2 out of 7 in 5d0s

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:48.0
occ:1.00
 O I:ASP177 2.3 35.9 1.0
O I:ALA174 2.6 40.6 1.0
O I:SER180 2.6 39.2 1.0
C I:ASP177 3.4 36.3 1.0
C I:ALA174 3.7 40.1 1.0
C I:SER180 3.8 38.3 1.0
OXT I:ASP204 3.9 50.7 1.0
CA I:ASP175 4.1 41.2 1.0
CA I:ALA178 4.2 36.2 1.0
O I:ALA178 4.2 38.7 1.0
N I:ALA178 4.2 35.8 1.0
N I:ASP177 4.2 35.0 1.0
C I:ALA178 4.3 37.3 1.0
C I:ASP175 4.3 39.6 1.0
N I:ASP175 4.3 40.0 1.0
CA I:ASP177 4.4 36.1 1.0
O I:ASP175 4.4 41.5 1.0
N I:SER180 4.5 36.3 1.0
O I:HOH403 4.6 29.1 1.0
CA I:SER180 4.7 37.8 1.0
NH1 Y:ARG19 4.7 53.9 1.0
C I:ASP204 4.8 53.2 1.0
N I:GLY181 4.8 37.2 1.0
O I:ASP204 4.8 49.7 1.0
CA I:ALA174 4.8 39.0 1.0
CA I:GLY181 4.8 37.9 1.0
NH2 Y:ARG19 4.9 52.1 1.0
N I:ARG176 4.9 37.4 1.0
CG2 Y:VAL26 5.0 45.0 1.0
CB I:ASP177 5.0 37.5 1.0
OD1 I:ASP175 5.0 46.7 1.0

Magnesium binding site 3 out of 7 in 5d0s

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:48.0
occ:1.00
 O Y:ASN168 2.2 38.2 1.0
O Y:ALA165 2.3 38.8 1.0
O I:ASP204 2.3 49.7 1.0
O Y:SER171 2.4 40.9 1.0
O Y:HOH407 2.7 44.5 1.0
C I:ASP204 3.2 53.2 1.0
C Y:ASN168 3.2 38.4 1.0
C Y:ALA165 3.4 39.3 1.0
CA Y:ALA169 3.6 36.7 1.0
C Y:SER171 3.6 40.1 1.0
CA I:ASP204 3.6 53.5 1.0
C Y:ALA169 3.7 34.5 1.0
O Y:ALA169 3.8 35.0 1.0
N Y:ALA169 3.8 38.2 1.0
NH1 Y:ARG19 3.9 53.9 1.0
CB I:ASP204 3.9 54.3 1.0
O Y:HIS166 4.0 38.6 1.0
N Y:SER171 4.1 37.6 1.0
OXT I:ASP204 4.2 50.7 1.0
CA Y:ALA165 4.2 38.5 1.0
C Y:HIS166 4.4 39.4 1.0
CZ Y:ARG19 4.4 52.3 1.0
CA Y:ASN168 4.4 37.6 1.0
CA Y:SER171 4.4 38.3 1.0
N Y:HIS166 4.4 39.7 1.0
N Y:ASN168 4.5 37.8 1.0
O Y:ALA164 4.5 36.6 1.0
N Y:TYR170 4.5 36.8 1.0
CA Y:HIS166 4.6 39.5 1.0
N Y:GLY172 4.6 42.0 1.0
NH2 Y:ARG19 4.6 52.1 1.0
CA Y:GLY172 4.8 42.5 1.0
CB Y:SER171 4.9 37.9 1.0
CB Y:ALA169 4.9 37.1 1.0
C Y:ARG167 5.0 38.4 1.0

Magnesium binding site 4 out of 7 in 5d0s

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:32.0
occ:1.00
 O W:ASP204 2.3 49.8 1.0
O K:SER171 2.4 36.3 1.0
O K:ALA165 2.4 38.7 1.0
O K:ASN168 2.4 39.6 1.0
O K:HOH418 2.5 40.4 1.0
C W:ASP204 3.2 49.6 1.0
C K:ASN168 3.4 37.7 1.0
C K:ALA165 3.5 37.9 1.0
C K:SER171 3.6 36.7 1.0
CA K:ALA169 3.6 37.1 1.0
CA W:ASP204 3.6 48.1 1.0
O K:ALA169 3.7 37.4 1.0
C K:ALA169 3.7 37.5 1.0
NH1 K:ARG19 3.7 45.8 1.0
N K:ALA169 3.9 37.3 1.0
CB W:ASP204 3.9 47.6 1.0
N K:SER171 4.1 36.0 1.0
OXT W:ASP204 4.2 50.6 1.0
O K:HIS166 4.2 39.2 1.0
CA K:ALA165 4.3 38.2 1.0
CZ K:ARG19 4.3 45.0 1.0
CA K:SER171 4.4 35.8 1.0
N K:TYR170 4.5 37.2 1.0
C K:HIS166 4.5 37.7 1.0
N K:HIS166 4.5 36.8 1.0
NH2 K:ARG19 4.5 46.7 1.0
N K:GLY172 4.6 37.7 1.0
CA K:ASN168 4.6 37.4 1.0
O K:ALA164 4.6 37.1 1.0
N K:ASN168 4.6 38.1 1.0
CA K:GLY172 4.7 38.8 1.0
CA K:HIS166 4.7 37.2 1.0
CB K:SER171 4.9 35.3 1.0
CB K:ALA169 4.9 36.2 1.0
CG W:ASP204 5.0 47.6 1.0

Magnesium binding site 5 out of 7 in 5d0s

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:39.4
occ:1.00
 OXT L:ASP222 2.2 57.9 1.0
O V:ILE163 2.2 44.3 1.0
O V:ASP166 2.3 39.6 1.0
O V:SER169 2.7 43.1 1.0
C L:ASP222 3.0 60.2 1.0
C V:ASP166 3.2 40.3 1.0
C V:ILE163 3.3 46.8 1.0
CA L:ASP222 3.7 60.2 1.0
O V:GLY162 3.8 42.5 1.0
N V:LEU167 3.8 39.8 1.0
O V:TRP164 3.8 47.1 1.0
C V:SER169 3.8 42.0 1.0
CA V:LEU167 3.9 39.9 1.0
O L:ASP222 3.9 56.3 1.0
C V:TRP164 3.9 46.0 1.0
N V:ASP166 3.9 41.3 1.0
N V:TRP164 4.1 46.5 1.0
CA V:ASP166 4.2 40.6 1.0
NH1 V:ARG19 4.2 48.0 1.0
CA V:ILE163 4.2 47.6 1.0
CA V:TRP164 4.2 47.2 1.0
O V:HOH402 4.3 39.1 1.0
CB L:ASP222 4.3 59.1 1.0
C V:LEU167 4.4 40.0 1.0
N V:ASN165 4.4 44.2 1.0
N V:SER169 4.6 40.7 1.0
C V:ASN165 4.6 41.9 1.0
O V:LEU167 4.7 41.0 1.0
CA V:GLY170 4.7 45.5 1.0
O L:ARG221 4.7 57.2 1.0
N V:GLY170 4.7 43.0 1.0
CA V:SER169 4.7 41.4 1.0
CZ V:ARG19 4.8 46.6 1.0
C V:GLY162 4.8 44.2 1.0
CD2 V:LEU167 4.9 39.6 1.0
NH2 V:ARG19 4.9 46.9 1.0
N L:ASP222 4.9 59.0 1.0

Magnesium binding site 6 out of 7 in 5d0s

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:37.4
occ:1.00
 O N:ILE163 2.5 34.1 1.0
O N:SER169 2.5 32.6 1.0
O N:ASP166 2.8 35.0 1.0
C N:ILE163 3.6 35.4 1.0
CD1 a:LEU34 3.6 38.9 1.0
NH1 N:ARG19 3.7 36.8 1.0
C N:SER169 3.7 32.4 1.0
C N:ASP166 3.9 34.3 1.0
CG2 N:ILE163 3.9 34.4 1.0
CA N:GLY167 4.2 34.5 1.0
CA N:ILE163 4.3 34.9 1.0
CA N:GLY170 4.4 34.6 1.0
CZ N:ARG19 4.4 35.9 1.0
O N:GLY167 4.4 34.3 1.0
N N:GLY167 4.5 34.2 1.0
N N:GLY170 4.5 33.2 1.0
C N:GLY167 4.5 34.0 1.0
N N:LYS164 4.6 35.9 1.0
NH2 N:ARG19 4.7 36.3 1.0
N N:SER169 4.7 32.1 1.0
CB N:ILE163 4.7 34.4 1.0
CA N:SER169 4.7 30.9 1.0
CG a:LEU34 4.8 39.1 1.0
C N:LYS164 4.9 37.2 1.0
O N:LYS164 4.9 37.4 1.0
CA N:LYS164 4.9 37.7 1.0
N N:ASP166 5.0 34.7 1.0

Magnesium binding site 7 out of 7 in 5d0s

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA5-D166N 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-D166N Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:58.6
occ:1.00
 O Z:THR192 2.5 50.9 1.0
O Z:VAL198 2.6 44.7 1.0
O Z:HIS195 2.8 39.7 1.0
C Z:THR192 3.6 49.9 1.0
CG2 Z:THR192 3.7 50.8 1.0
NH2 Z:ARG28 3.7 51.6 1.0
C Z:VAL198 3.8 43.9 1.0
O Z:ASP222 3.8 64.2 1.0
C Z:HIS195 3.9 40.6 1.0
CA Z:THR192 3.9 49.4 1.0
O Z:ILE196 4.0 40.7 1.0
CA Z:ILE196 4.0 39.5 1.0
C Z:ILE196 4.2 38.9 1.0
OD1 Z:ASP222 4.3 58.3 1.0
NH2 H:ARG19 4.4 51.2 1.0
N Z:ILE196 4.4 39.9 1.0
CB Z:THR192 4.4 50.0 1.0
N Z:VAL198 4.5 40.3 1.0
CA Z:VAL198 4.7 42.4 1.0
N Z:GLY199 4.7 45.8 1.0
CA Z:GLY199 4.7 46.4 1.0
C Z:ASP222 4.7 61.1 1.0
CZ Z:ARG28 4.8 51.9 1.0
N Z:GLU193 4.8 49.7 1.0
N Z:HIS195 5.0 41.5 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 02:23:30 2024

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