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Magnesium in PDB 5cz8: Yeast 20S Proteasome BETA5-L(-49)S-K33A Mutant in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome BETA5-L(-49)S-K33A Mutant in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome BETA5-L(-49)S-K33A Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-L(-49)S-K33A Mutant in Complex with Carfilzomib, PDB code: 5cz8 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 (°) 136.440, 299.270, 144.460, 90.00, 113.12, 90.00
R / Rfree (%) 19.1 / 21.5

Other elements in 5cz8:

The structure of Yeast 20S Proteasome BETA5-L(-49)S-K33A 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-L(-49)S-K33A Mutant in Complex with Carfilzomib (pdb code 5cz8). 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-L(-49)S-K33A Mutant in Complex with Carfilzomib, PDB code: 5cz8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5cz8

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-L(-49)S-K33A 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-L(-49)S-K33A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.3
occ:1.00
 O G:MET125 2.2 59.7 1.0
OG1 G:THR8 2.7 49.4 1.0
O G:ARG122 2.9 51.2 1.0
O G:TYR119 3.0 50.1 1.0
O G:ALA123 3.1 59.8 1.0
CG2 G:THR8 3.3 54.4 1.0
C G:MET125 3.3 60.2 1.0
CB G:THR8 3.6 53.2 1.0
C G:ALA123 3.7 58.2 1.0
CA G:ALA123 3.8 56.9 1.0
CA G:ARG126 3.9 54.1 1.0
C G:ARG122 4.0 55.1 1.0
N G:ARG126 4.0 57.2 1.0
N G:THR8 4.1 58.2 1.0
C G:TYR119 4.2 50.4 1.0
N G:MET125 4.3 62.6 1.0
N G:ALA123 4.4 55.0 1.0
CD G:PRO127 4.4 51.3 1.0
CA G:MET125 4.4 64.2 1.0
CA G:THR8 4.4 55.5 1.0
C G:ARG126 4.6 52.4 1.0
N G:TYR124 4.7 61.6 1.0
N G:PRO127 4.8 51.4 1.0
CA G:TYR119 4.9 50.4 1.0
C G:TYR124 4.9 61.2 1.0

Magnesium binding site 2 out of 8 in 5cz8

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-L(-49)S-K33A 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-L(-49)S-K33A 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 3.5 57.0 1.0
CA G:PHE64 3.8 56.1 1.0
NZ G:LYS89 3.8 58.8 1.0
CD1 G:PHE64 4.1 51.7 1.0
C G:PHE64 4.2 55.0 1.0
CB G:PHE64 4.2 54.5 1.0
CA G:CYS65 4.4 58.5 1.0
CB G:CYS65 4.5 60.4 1.0
O G:ILE63 4.5 62.6 1.0
CE G:LYS89 4.5 56.3 1.0
O G:CYS65 4.5 63.2 1.0
CG G:PHE64 4.6 52.1 1.0
O N:SER68 4.6 71.6 1.0
C G:CYS65 4.8 59.4 1.0
SG G:CYS65 4.9 61.3 1.0
N G:PHE64 5.0 60.5 1.0

Magnesium binding site 3 out of 8 in 5cz8

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-L(-49)S-K33A 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-L(-49)S-K33A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:66.4
occ:1.00
 O I:ASP204 2.1 83.4 1.0
O Y:ASP168 2.3 61.8 1.0
O Y:ALA165 2.5 61.8 1.0
O Y:SER171 2.7 62.1 1.0
C I:ASP204 3.1 79.1 1.0
C Y:ASP168 3.3 66.2 1.0
CA Y:ALA169 3.6 66.6 1.0
CA I:ASP204 3.6 78.5 1.0
O Y:ALA169 3.6 62.1 1.0
C Y:ALA165 3.7 61.7 1.0
C Y:ALA169 3.8 64.3 1.0
O Y:HIS166 3.8 57.6 1.0
N Y:ALA169 3.8 67.3 1.0
CB I:ASP204 3.9 80.2 1.0
C Y:SER171 3.9 64.7 1.0
NH1 Y:ARG19 4.0 75.7 1.0
OXT I:ASP204 4.0 73.2 1.0
C Y:HIS166 4.2 60.9 1.0
N Y:SER171 4.4 66.9 1.0
CA Y:ASP168 4.5 66.3 1.0
CA Y:ALA165 4.6 62.4 1.0
N Y:HIS166 4.6 61.1 1.0
N Y:ASP168 4.6 66.4 1.0
CA Y:HIS166 4.6 61.8 1.0
N Y:TYR170 4.6 66.2 1.0
CZ Y:ARG19 4.7 76.6 1.0
CA Y:SER171 4.7 64.6 1.0
C Y:ARG167 4.8 65.3 1.0
O Y:ALA164 4.8 60.0 1.0
CB Y:ALA169 4.9 68.3 1.0
N Y:GLY172 4.9 66.5 1.0
N I:ASP204 4.9 76.0 1.0
N Y:ARG167 4.9 61.0 1.0
O Y:ARG167 5.0 68.9 1.0
NH2 Y:ARG19 5.0 80.6 1.0
CG I:ASP204 5.0 81.5 1.0

Magnesium binding site 4 out of 8 in 5cz8

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-L(-49)S-K33A 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-L(-49)S-K33A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:70.5
occ:1.00
 O K:ASP168 2.1 65.6 1.0
O K:ALA165 2.4 59.4 1.0
O W:ASP204 2.4 78.8 1.0
O K:SER171 2.9 60.5 1.0
C K:ASP168 3.1 65.0 1.0
C W:ASP204 3.2 76.1 1.0
C K:ALA165 3.5 60.1 1.0
CA K:ALA169 3.5 65.4 1.0
O K:HIS166 3.5 64.0 1.0
CA W:ASP204 3.6 73.8 1.0
N K:ALA169 3.7 65.6 1.0
O K:ALA169 3.8 60.2 1.0
C K:ALA169 3.8 64.5 1.0
C K:HIS166 4.0 61.4 1.0
CB W:ASP204 4.0 72.8 1.0
C K:SER171 4.0 63.2 1.0
OXT W:ASP204 4.2 77.6 1.0
N K:ASP168 4.3 65.6 1.0
NH1 K:ARG19 4.3 71.9 1.0
CA K:ASP168 4.3 65.0 1.0
N K:HIS166 4.4 59.4 1.0
CA K:HIS166 4.4 61.0 1.0
N K:SER171 4.4 63.7 1.0
CA K:ALA165 4.4 60.7 1.0
C K:ARG167 4.5 62.9 1.0
O K:ALA164 4.5 62.0 1.0
N K:ARG167 4.6 60.8 1.0
N K:TYR170 4.7 65.6 1.0
O K:ARG167 4.7 63.0 1.0
CA K:SER171 4.7 62.6 1.0
CB K:ALA169 4.9 66.6 1.0
N W:ASP204 4.9 72.4 1.0
CZ K:ARG19 5.0 74.7 1.0

Magnesium binding site 5 out of 8 in 5cz8

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-L(-49)S-K33A 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-L(-49)S-K33A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:76.9
occ:1.00
 OXT L:ASP222 2.3 75.7 1.0
O V:ASP166 2.3 57.5 1.0
O V:ILE163 2.4 69.6 1.0
C V:ASP166 3.1 57.5 1.0
C L:ASP222 3.1 79.6 1.0
O V:TRP164 3.2 68.5 1.0
O V:SER169 3.3 58.6 1.0
C V:ILE163 3.4 66.4 1.0
C V:TRP164 3.5 64.0 1.0
N V:ASP166 3.7 56.6 1.0
CA L:ASP222 3.7 79.8 1.0
N V:LEU167 3.7 56.8 1.0
CA V:LEU167 3.8 57.4 1.0
O V:GLY162 4.0 65.6 1.0
O L:ASP222 4.0 79.2 1.0
CA V:TRP164 4.0 64.0 1.0
N V:ASN165 4.0 63.2 1.0
CA V:ASP166 4.0 57.4 1.0
N V:TRP164 4.1 64.1 1.0
C V:ASN165 4.2 58.3 1.0
O L:ARG221 4.3 74.1 1.0
C V:SER169 4.5 59.3 1.0
CA V:ILE163 4.5 65.9 1.0
CA V:ASN165 4.5 60.8 1.0
NH1 V:ARG19 4.5 73.3 1.0
CD2 V:LEU167 4.6 57.8 1.0
CB L:ASP222 4.6 77.6 1.0
CD1 L:ILE35 4.6 69.7 1.0
C V:LEU167 4.6 57.5 1.0
O V:ASN165 4.8 54.2 1.0
N L:ASP222 4.8 78.5 1.0
O V:LEU167 4.9 56.9 1.0
C V:GLY162 5.0 65.2 1.0

Magnesium binding site 6 out of 8 in 5cz8

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-L(-49)S-K33A 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-L(-49)S-K33A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:67.4
occ:1.00
 O N:SER169 2.5 55.9 1.0
O N:ILE163 2.8 54.0 1.0
O N:ASP166 3.1 56.7 1.0
NH1 N:ARG19 3.3 61.6 1.0
C N:SER169 3.7 54.2 1.0
CD1 a:LEU34 3.8 57.5 1.0
C N:ILE163 3.9 56.0 1.0
CG2 N:ILE163 4.0 56.9 1.0
CZ N:ARG19 4.1 58.9 1.0
C N:ASP166 4.1 54.8 1.0
CA N:GLY167 4.2 54.4 1.0
O N:GLY167 4.3 55.6 1.0
NH2 N:ARG19 4.3 58.8 1.0
CA N:GLY170 4.3 57.4 1.0
C N:GLY167 4.5 54.8 1.0
N N:GLY170 4.5 55.4 1.0
CA N:ILE163 4.6 56.0 1.0
N N:GLY167 4.6 53.5 1.0
N N:SER169 4.7 51.4 1.0
CA N:SER169 4.8 50.2 1.0
CB N:ILE163 4.9 56.4 1.0
N N:LYS164 4.9 56.6 1.0

Magnesium binding site 7 out of 8 in 5cz8

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-L(-49)S-K33A 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-L(-49)S-K33A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg301

b:30.0
occ:1.00
 N U:CYS65 3.4 59.1 1.0
CA U:PHE64 3.8 57.0 1.0
NZ U:LYS89 4.0 65.2 1.0
C U:PHE64 4.1 57.3 1.0
CB U:CYS65 4.3 61.5 1.0
CD1 U:PHE64 4.3 50.8 1.0
CA U:CYS65 4.3 60.9 1.0
CB U:PHE64 4.3 54.6 1.0
O U:CYS65 4.5 66.5 1.0
O U:ILE63 4.5 62.4 1.0
CE U:LYS89 4.6 61.5 1.0
SG U:CYS65 4.7 64.6 1.0
CG U:PHE64 4.7 51.0 1.0
C U:CYS65 4.8 63.8 1.0
O b:SER68 4.9 70.6 1.0
N U:PHE64 5.0 58.7 1.0

Magnesium binding site 8 out of 8 in 5cz8

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-L(-49)S-K33A 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 BETA5-L(-49)S-K33A Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:72.2
occ:1.00
 O Z:THR192 2.5 72.6 1.0
O Z:VAL198 2.6 63.5 1.0
O Z:HIS195 3.0 57.9 1.0
C Z:THR192 3.5 73.5 1.0
CG2 Z:THR192 3.6 74.3 1.0
O Z:ASP222 3.6 79.4 1.0
NH2 Z:ARG28 3.7 80.7 1.0
C Z:VAL198 3.8 65.6 1.0
CA Z:THR192 3.9 72.6 1.0
C Z:HIS195 4.0 60.9 1.0
O Z:ILE196 4.0 64.9 1.0
CA Z:ILE196 4.1 62.5 1.0
OD1 Z:ASP222 4.3 78.1 1.0
C Z:ILE196 4.3 60.5 1.0
CB Z:THR192 4.4 73.7 1.0
NH2 H:ARG19 4.4 73.0 1.0
N Z:ILE196 4.5 61.7 1.0
N Z:VAL198 4.5 63.2 1.0
CA Z:GLY199 4.6 68.8 1.0
N Z:GLY199 4.6 66.4 1.0
C Z:ASP222 4.7 80.7 1.0
CA Z:VAL198 4.7 65.2 1.0
N Z:GLU193 4.7 71.6 1.0
CZ Z:ARG28 4.7 77.0 1.0
NH1 Z:ARG28 5.0 78.1 1.0
O Z:LYS220 5.0 67.4 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 02:21:11 2024

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