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Magnesium in PDB 5cz5: Yeast 20S Proteasome BETA1-T1A Mutant in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome BETA1-T1A Mutant in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome BETA1-T1A Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA1-T1A Mutant in Complex with Carfilzomib, PDB code: 5cz5 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 (°) 136.770, 300.420, 145.340, 90.00, 113.14, 90.00
R / Rfree (%) 20.1 / 22.2

Other elements in 5cz5:

The structure of Yeast 20S Proteasome BETA1-T1A 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 BETA1-T1A Mutant in Complex with Carfilzomib (pdb code 5cz5). 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 BETA1-T1A Mutant in Complex with Carfilzomib, PDB code: 5cz5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cz5

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA1-T1A 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 BETA1-T1A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.7
occ:1.00
 O G:MET125 2.3 50.6 1.0
OG1 G:THR8 2.6 42.9 1.0
O G:ARG122 2.8 47.1 1.0
O G:TYR119 2.9 39.8 1.0
O G:ALA123 3.2 49.4 1.0
CG2 G:THR8 3.2 46.6 1.0
C G:MET125 3.4 49.9 1.0
CB G:THR8 3.5 45.9 1.0
C G:ALA123 3.7 49.9 1.0
CA G:ALA123 3.8 48.7 1.0
C G:ARG122 3.9 48.5 1.0
CA G:ARG126 4.1 44.6 1.0
N G:THR8 4.1 50.2 1.0
C G:TYR119 4.1 41.0 1.0
N G:ARG126 4.1 46.7 1.0
N G:ALA123 4.3 47.2 1.0
N G:MET125 4.3 51.0 1.0
CA G:THR8 4.4 48.1 1.0
CD G:PRO127 4.4 41.9 1.0
CA G:MET125 4.5 53.2 1.0
N G:TYR124 4.7 51.9 1.0
C G:ARG126 4.7 44.2 1.0
CA G:TYR119 4.8 40.9 1.0
N G:PRO127 4.9 42.7 1.0

Magnesium binding site 2 out of 8 in 5cz5

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA1-T1A 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 BETA1-T1A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg302

b:30.0
occ:1.00
 N G:CYS65 3.1 47.7 1.0
CA G:PHE64 3.6 46.3 1.0
C G:PHE64 3.9 46.4 1.0
NZ G:LYS89 4.0 45.2 1.0
CB G:PHE64 4.1 45.2 1.0
CA G:CYS65 4.1 48.6 1.0
CD1 G:PHE64 4.2 45.4 1.0
CB G:CYS65 4.2 50.6 1.0
O G:ILE63 4.3 48.6 1.0
O G:CYS65 4.4 54.0 1.0
CG G:PHE64 4.5 45.2 1.0
CE G:LYS89 4.5 44.3 1.0
C G:CYS65 4.6 49.4 1.0
SG G:CYS65 4.7 53.2 1.0
N G:PHE64 4.8 48.6 1.0
O N:SER68 4.8 80.0 1.0
C G:ILE63 5.0 49.5 1.0

Magnesium binding site 3 out of 8 in 5cz5

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA1-T1A 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 BETA1-T1A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:51.9
occ:1.00
 O I:ASP177 2.3 46.7 1.0
O I:SER180 2.7 46.6 1.0
O I:ALA174 2.8 53.8 1.0
C I:ASP177 3.4 46.3 1.0
OXT I:ASP204 3.7 62.2 1.0
C I:ALA174 3.9 52.8 1.0
C I:SER180 4.0 47.3 1.0
CA I:ALA178 4.1 45.9 1.0
O I:ALA178 4.2 50.6 1.0
N I:ALA178 4.2 45.3 1.0
CA I:ASP175 4.2 53.3 1.0
C I:ALA178 4.3 47.4 1.0
N I:ASP177 4.3 46.3 1.0
C I:ASP175 4.4 50.7 1.0
CA I:ASP177 4.5 46.5 1.0
NH1 Y:ARG19 4.5 66.5 1.0
N I:ASP175 4.5 53.2 1.0
O I:ASP204 4.5 67.0 1.0
O I:ASP175 4.5 49.6 1.0
C I:ASP204 4.6 63.5 1.0
N I:SER180 4.6 44.9 1.0
NH2 Y:ARG19 4.7 66.6 1.0
CA I:SER180 4.8 47.1 1.0
N I:GLY181 4.9 47.6 1.0
CA I:GLY181 4.9 48.8 1.0
CG2 Y:VAL26 4.9 54.0 1.0

Magnesium binding site 4 out of 8 in 5cz5

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA1-T1A 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 BETA1-T1A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:43.0
occ:1.00
 O I:ASP204 2.3 67.0 1.0
O Y:ASP168 2.3 47.4 1.0
O Y:ALA165 2.5 44.7 1.0
O Y:SER171 2.9 50.3 1.0
C I:ASP204 3.1 63.5 1.0
C Y:ASP168 3.3 46.9 1.0
CA Y:ALA169 3.5 45.6 1.0
CA I:ASP204 3.6 64.3 1.0
C Y:ALA165 3.7 46.7 1.0
O Y:HIS166 3.7 47.3 1.0
O Y:ALA169 3.8 45.3 1.0
N Y:ALA169 3.8 46.5 1.0
C Y:ALA169 3.8 45.6 1.0
NH1 Y:ARG19 4.0 66.5 1.0
OXT I:ASP204 4.0 62.2 1.0
C Y:SER171 4.1 48.6 1.0
CB I:ASP204 4.1 65.6 1.0
C Y:HIS166 4.2 47.3 1.0
N Y:SER171 4.4 45.9 1.0
CA Y:ASP168 4.5 46.3 1.0
N Y:ASP168 4.5 46.5 1.0
N Y:HIS166 4.6 47.6 1.0
CZ Y:ARG19 4.6 63.6 1.0
CA Y:ALA165 4.6 47.4 1.0
CA Y:HIS166 4.6 47.6 1.0
N Y:TYR170 4.7 46.3 1.0
C Y:ARG167 4.8 46.4 1.0
NH2 Y:ARG19 4.8 66.6 1.0
O Y:ALA164 4.8 46.1 1.0
CA Y:SER171 4.8 46.2 1.0
CB Y:ALA169 4.9 45.9 1.0
N Y:ARG167 4.9 45.3 1.0
O Y:ARG167 5.0 44.8 1.0
N I:ASP204 5.0 62.4 1.0

Magnesium binding site 5 out of 8 in 5cz5

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA1-T1A 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 BETA1-T1A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:52.9
occ:1.00
 O K:ASP168 2.1 48.9 1.0
O K:ALA165 2.4 46.5 1.0
O W:ASP204 2.4 65.6 1.0
O K:SER171 2.8 43.8 1.0
C W:ASP204 3.1 60.3 1.0
C K:ASP168 3.2 48.7 1.0
CA W:ASP204 3.5 59.9 1.0
C K:ALA165 3.5 47.4 1.0
CA K:ALA169 3.6 48.4 1.0
O K:HIS166 3.7 51.2 1.0
N K:ALA169 3.8 49.2 1.0
C K:ALA169 3.8 50.0 1.0
O K:ALA169 3.9 50.3 1.0
CB W:ASP204 3.9 59.2 1.0
C K:SER171 4.0 46.6 1.0
C K:HIS166 4.1 48.0 1.0
OXT W:ASP204 4.1 64.0 1.0
NH1 K:ARG19 4.1 57.8 1.0
N K:SER171 4.3 48.1 1.0
N K:ASP168 4.3 49.5 1.0
CA K:ASP168 4.3 48.0 1.0
CA K:ALA165 4.4 48.8 1.0
N K:HIS166 4.4 47.2 1.0
CA K:HIS166 4.5 48.2 1.0
O K:ALA164 4.5 51.8 1.0
C K:ARG167 4.6 49.5 1.0
N K:TYR170 4.6 49.6 1.0
CA K:SER171 4.7 46.3 1.0
CZ K:ARG19 4.7 59.0 1.0
N K:ARG167 4.8 47.3 1.0
N W:ASP204 4.9 59.4 1.0
NH2 K:ARG19 4.9 63.9 1.0
O K:ARG167 4.9 50.8 1.0
CB K:ALA169 4.9 47.1 1.0
N K:GLY172 5.0 47.9 1.0

Magnesium binding site 6 out of 8 in 5cz5

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA1-T1A 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 BETA1-T1A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:64.6
occ:1.00
 OXT L:ASP222 2.1 76.4 1.0
O V:ILE163 2.2 57.5 1.0
O V:ASP166 2.2 49.8 1.0
O V:SER169 2.7 49.5 1.0
C L:ASP222 3.1 74.4 1.0
C V:ASP166 3.2 48.3 1.0
C V:ILE163 3.3 55.4 1.0
CA L:ASP222 3.7 72.2 1.0
O V:TRP164 3.8 54.8 1.0
C V:SER169 3.9 49.0 1.0
O V:GLY162 3.9 52.5 1.0
N V:LEU167 3.9 48.0 1.0
CA V:LEU167 3.9 47.6 1.0
C V:TRP164 3.9 53.6 1.0
N V:ASP166 4.0 47.6 1.0
O L:ASP222 4.0 74.9 1.0
N V:TRP164 4.1 53.5 1.0
NH1 V:ARG19 4.1 62.8 1.0
CA V:ASP166 4.2 47.8 1.0
CA V:TRP164 4.2 54.1 1.0
CA V:ILE163 4.2 54.7 1.0
CB L:ASP222 4.4 70.0 1.0
N V:ASN165 4.4 53.0 1.0
C V:LEU167 4.4 47.9 1.0
C V:ASN165 4.6 48.5 1.0
N V:SER169 4.6 47.6 1.0
CA V:GLY170 4.7 53.0 1.0
O V:LEU167 4.7 49.5 1.0
CZ V:ARG19 4.7 59.4 1.0
N V:GLY170 4.7 49.4 1.0
O L:ARG221 4.7 64.7 1.0
CA V:SER169 4.8 47.7 1.0
NH2 V:ARG19 4.8 60.8 1.0
C V:GLY162 4.9 53.1 1.0
CD2 V:LEU167 4.9 46.6 1.0
N L:ASP222 4.9 71.6 1.0

Magnesium binding site 7 out of 8 in 5cz5

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA1-T1A 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 BETA1-T1A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:56.7
occ:1.00
 O N:SER169 2.7 48.0 1.0
O N:ASP166 2.7 58.4 1.0
O N:ILE163 2.8 45.9 1.0
NH1 N:ARG19 3.6 56.2 1.0
C N:ASP166 3.7 55.8 1.0
CA N:GLY167 3.8 57.4 1.0
CD1 a:LEU34 3.8 50.8 1.0
C N:SER169 3.9 47.0 1.0
C N:ILE163 3.9 49.0 1.0
O N:GLY167 4.1 57.5 1.0
N N:GLY167 4.1 55.8 1.0
C N:GLY167 4.2 54.6 1.0
CZ N:ARG19 4.2 56.6 1.0
CG2 N:ILE163 4.3 49.2 1.0
NH2 N:ARG19 4.4 60.7 1.0
CA N:ILE163 4.6 47.6 1.0
N N:SER169 4.7 46.5 1.0
CA N:GLY170 4.7 51.4 1.0
N N:GLY170 4.7 49.1 1.0
CA N:SER169 4.8 44.7 1.0
CA N:ASP166 4.9 53.1 1.0
N N:ASP166 4.9 53.2 1.0
O a:HOH311 4.9 42.0 1.0
N N:LYS164 4.9 50.6 1.0
O N:LYS164 5.0 57.2 1.0

Magnesium binding site 8 out of 8 in 5cz5

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA1-T1A 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 8 of Yeast 20S Proteasome BETA1-T1A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:61.9
occ:1.00
 O Z:VAL198 2.6 48.5 1.0
O Z:THR192 2.6 55.9 1.0
O Z:HIS195 3.2 47.4 1.0
O Z:ASP222 3.4 66.0 1.0
CG2 Z:THR192 3.5 58.1 1.0
C Z:THR192 3.6 57.6 1.0
NH2 Z:ARG28 3.7 60.7 1.0
C Z:VAL198 3.8 51.9 1.0
CA Z:THR192 4.0 57.4 1.0
OD1 Z:ASP222 4.0 66.7 1.0
O Z:ILE196 4.1 49.1 1.0
C Z:HIS195 4.3 47.5 1.0
CB Z:THR192 4.3 58.0 1.0
NH2 H:ARG19 4.4 60.5 1.0
CA Z:ILE196 4.4 46.9 1.0
C Z:ILE196 4.5 46.8 1.0
C Z:ASP222 4.5 67.5 1.0
CA Z:GLY199 4.5 53.9 1.0
N Z:GLY199 4.6 52.7 1.0
CZ Z:ARG28 4.7 58.1 1.0
N Z:VAL198 4.7 49.1 1.0
O Z:LYS220 4.8 60.1 1.0
N Z:GLU193 4.8 58.3 1.0
CA Z:VAL198 4.8 51.4 1.0
N Z:ILE196 4.8 47.0 1.0
NH1 Z:ARG28 4.9 60.3 1.0
CG Z:ASP222 5.0 63.9 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 02:20:31 2024

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