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Magnesium in PDB 5d0v: Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-T1C Mutant in Complex with Carfilzomib, PDB code: 5d0v 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 (°) 135.170, 299.940, 144.940, 90.00, 112.56, 90.00
R / Rfree (%) 19.3 / 22

Other elements in 5d0v:

The structure of Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib (pdb code 5d0v). 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-T1C Mutant in Complex with Carfilzomib, PDB code: 5d0v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5d0v

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:54.2
occ:1.00
 O G:MET125 2.1 52.8 1.0
OG1 G:THR8 2.7 48.1 1.0
O G:TYR119 2.8 44.0 1.0
O G:ARG122 2.8 47.8 1.0
C G:MET125 3.2 51.4 1.0
CG2 G:THR8 3.3 49.6 1.0
O G:ALA123 3.3 51.4 1.0
CB G:THR8 3.5 48.6 1.0
C G:ALA123 3.7 51.8 1.0
CA G:ALA123 3.9 50.5 1.0
C G:ARG122 3.9 50.1 1.0
CA G:ARG126 3.9 45.6 1.0
N G:ARG126 4.0 48.5 1.0
C G:TYR119 4.0 43.9 1.0
N G:THR8 4.2 49.9 1.0
N G:MET125 4.2 54.2 1.0
CA G:MET125 4.3 55.1 1.0
N G:ALA123 4.4 50.2 1.0
CD G:PRO127 4.4 42.6 1.0
CA G:THR8 4.5 49.4 1.0
C G:ARG126 4.6 44.2 1.0
N G:TYR124 4.7 53.4 1.0
CA G:TYR119 4.7 42.4 1.0
N G:PRO127 4.8 43.5 1.0
C G:TYR124 4.9 53.3 1.0
CB G:MET125 5.0 58.7 1.0

Magnesium binding site 2 out of 8 in 5d0v

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg303

b:38.1
occ:1.00
 OD1 N:ASP51 2.6 27.5 1.0
O N:ASN92 2.7 52.1 1.0
OE1 H:GLN91 2.8 56.2 1.0
OD2 N:ASP51 3.3 39.6 1.0
CG N:ASP51 3.3 23.4 1.0
NE2 H:GLN91 3.4 58.6 1.0
CD H:GLN91 3.5 52.9 1.0
C N:ASN92 4.0 50.8 1.0
CZ H:PHE88 4.4 35.0 1.0
CE1 H:PHE88 4.5 35.1 1.0
CD2 N:LEU93 4.6 48.5 1.0
CB N:ASP51 4.7 28.3 1.0
CA N:LEU93 4.8 47.3 1.0
N N:LEU93 4.8 49.0 1.0
CB N:ASN92 4.9 56.4 1.0
CA N:ASN92 4.9 52.3 1.0

Magnesium binding site 3 out of 8 in 5d0v

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:58.2
occ:1.00
 O I:ASP177 2.6 54.7 1.0
O I:SER180 2.7 55.0 1.0
O I:ALA174 2.8 56.4 1.0
OXT I:ASP204 3.5 77.8 1.0
C I:ASP177 3.7 52.9 1.0
C I:ALA174 3.8 56.7 1.0
C I:SER180 3.9 54.7 1.0
CA I:ASP175 4.0 58.1 1.0
O I:ALA178 4.2 59.4 1.0
NH1 Y:ARG19 4.2 71.0 1.0
C I:ASP175 4.3 56.3 1.0
N I:ASP175 4.4 56.5 1.0
O I:ASP175 4.4 59.0 1.0
CA I:ALA178 4.4 52.6 1.0
C I:ASP204 4.4 73.8 1.0
NH2 Y:ARG19 4.4 70.8 1.0
O I:ASP204 4.5 73.3 1.0
C I:ALA178 4.5 55.6 1.0
N I:ALA178 4.5 51.0 1.0
N I:ASP177 4.6 51.2 1.0
CA I:GLY181 4.7 55.8 1.0
CZ Y:ARG19 4.7 68.0 1.0
OD1 I:ASP175 4.7 61.0 1.0
CA I:ASP177 4.7 52.4 1.0
N I:GLY181 4.7 55.6 1.0
N I:SER180 4.8 51.5 1.0
CA I:SER180 4.9 53.3 1.0

Magnesium binding site 4 out of 8 in 5d0v

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:59.2
occ:1.00
 O I:ASP204 2.2 73.3 1.0
O Y:ASP168 2.4 54.7 1.0
O Y:ALA165 2.5 51.1 1.0
O Y:SER171 2.8 56.9 1.0
C I:ASP204 3.1 73.8 1.0
C Y:ASP168 3.3 53.8 1.0
CA Y:ALA169 3.4 55.9 1.0
CA I:ASP204 3.5 71.9 1.0
O Y:ALA169 3.6 55.2 1.0
C Y:ALA169 3.7 54.1 1.0
C Y:ALA165 3.7 50.6 1.0
N Y:ALA169 3.7 56.4 1.0
O Y:HIS166 3.8 51.4 1.0
NH1 Y:ARG19 3.8 71.0 1.0
CB I:ASP204 4.0 71.0 1.0
C Y:SER171 4.0 52.5 1.0
OXT I:ASP204 4.1 77.8 1.0
N Y:SER171 4.3 50.8 1.0
C Y:HIS166 4.3 53.2 1.0
CA Y:ASP168 4.5 52.6 1.0
CA Y:ALA165 4.5 50.2 1.0
N Y:ASP168 4.5 53.5 1.0
CZ Y:ARG19 4.5 68.0 1.0
N Y:TYR170 4.6 52.9 1.0
N Y:HIS166 4.7 51.4 1.0
CA Y:SER171 4.7 50.3 1.0
CA Y:HIS166 4.8 52.0 1.0
C Y:ARG167 4.8 55.0 1.0
CB Y:ALA169 4.8 57.8 1.0
O Y:ALA164 4.8 51.4 1.0
NH2 Y:ARG19 4.9 70.8 1.0
N I:ASP204 4.9 70.5 1.0
O Y:ARG167 5.0 58.0 1.0
N Y:GLY172 5.0 53.4 1.0

Magnesium binding site 5 out of 8 in 5d0v

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:59.0
occ:1.00
 O K:ASP168 2.3 54.6 1.0
O K:ALA165 2.3 60.6 1.0
O W:ASP204 2.4 72.8 1.0
C K:ASP168 3.1 55.7 1.0
C W:ASP204 3.1 72.3 1.0
O K:SER171 3.2 53.4 1.0
O K:HIS166 3.2 61.4 1.0
CA K:ALA169 3.5 58.2 1.0
C K:ALA165 3.5 56.8 1.0
CA W:ASP204 3.5 69.2 1.0
N K:ALA169 3.6 57.4 1.0
C K:HIS166 3.8 57.8 1.0
C K:ALA169 3.9 59.5 1.0
O K:ALA169 4.0 62.5 1.0
CB W:ASP204 4.1 68.4 1.0
OXT W:ASP204 4.1 75.3 1.0
N K:ASP168 4.2 55.2 1.0
CA K:ASP168 4.2 54.8 1.0
NH1 K:ARG19 4.3 70.6 1.0
C K:ARG167 4.3 56.9 1.0
N K:HIS166 4.4 55.3 1.0
C K:SER171 4.4 54.6 1.0
CA K:HIS166 4.4 56.7 1.0
CA K:ALA165 4.5 56.4 1.0
O K:ARG167 4.5 60.7 1.0
N K:ARG167 4.6 56.0 1.0
O K:ALA164 4.6 62.2 1.0
N K:SER171 4.7 55.6 1.0
N K:TYR170 4.8 58.1 1.0
CB K:ALA169 4.8 58.5 1.0
N W:ASP204 4.8 66.7 1.0
NE1 W:TRP182 4.8 61.2 1.0
CA K:ARG167 5.0 55.8 1.0

Magnesium binding site 6 out of 8 in 5d0v

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:69.9
occ:1.00
 OXT L:ASP222 2.1 66.2 1.0
O V:ASP166 2.3 50.1 1.0
O V:ILE163 2.4 56.9 1.0
C L:ASP222 2.9 67.8 1.0
C V:ASP166 3.1 50.2 1.0
O V:TRP164 3.1 54.4 1.0
O V:SER169 3.3 52.6 1.0
C V:ILE163 3.5 57.7 1.0
C V:TRP164 3.5 53.9 1.0
CA L:ASP222 3.6 67.3 1.0
N V:ASP166 3.7 48.4 1.0
O L:ASP222 3.8 65.7 1.0
N V:LEU167 3.8 50.8 1.0
CA V:LEU167 3.9 49.5 1.0
CA V:TRP164 4.0 55.1 1.0
CA V:ASP166 4.0 47.7 1.0
O V:GLY162 4.0 56.1 1.0
N V:TRP164 4.1 56.6 1.0
N V:ASN165 4.1 51.5 1.0
C V:ASN165 4.2 49.1 1.0
O L:ARG221 4.3 62.7 1.0
CB L:ASP222 4.4 66.2 1.0
CD2 V:LEU167 4.5 47.2 1.0
C V:SER169 4.5 50.9 1.0
CA V:ILE163 4.6 57.4 1.0
NH1 V:ARG19 4.6 62.1 1.0
CA V:ASN165 4.6 50.9 1.0
C V:LEU167 4.6 50.4 1.0
N L:ASP222 4.7 64.8 1.0
CD1 L:ILE35 4.7 56.9 1.0
O V:ASN165 4.9 45.6 1.0
C L:ARG221 5.0 63.5 1.0

Magnesium binding site 7 out of 8 in 5d0v

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:41.7
occ:1.00
 O N:SER169 2.6 45.0 1.0
O N:ILE163 2.8 45.5 1.0
O N:ASP166 3.0 46.6 1.0
NH1 N:ARG19 3.5 45.1 1.0
CD1 a:LEU34 3.6 50.7 1.0
C N:SER169 3.9 43.3 1.0
C N:ILE163 3.9 46.0 1.0
C N:ASP166 4.0 44.0 1.0
CG2 N:ILE163 4.1 45.6 1.0
CA N:GLY167 4.2 42.6 1.0
CZ N:ARG19 4.2 44.8 1.0
O N:GLY167 4.3 43.2 1.0
O a:HOH308 4.4 41.5 1.0
NH2 N:ARG19 4.5 46.5 1.0
CA N:GLY170 4.5 45.7 1.0
C N:GLY167 4.5 42.7 1.0
N N:GLY167 4.5 42.6 1.0
CA N:ILE163 4.6 45.4 1.0
N N:GLY170 4.7 43.9 1.0
N N:SER169 4.8 42.7 1.0
CG a:LEU34 4.8 50.7 1.0
CA N:SER169 4.9 40.8 1.0
N N:LYS164 4.9 47.0 1.0
O N:LYS164 4.9 52.3 1.0

Magnesium binding site 8 out of 8 in 5d0v

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-T1C 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-T1C Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:61.6
occ:1.00
 O Z:THR192 2.5 60.5 1.0
O Z:VAL198 2.7 57.3 1.0
O Z:HIS195 2.8 49.6 1.0
C Z:THR192 3.6 62.5 1.0
O Z:ASP222 3.7 60.5 1.0
C Z:HIS195 3.7 51.7 1.0
CG2 Z:THR192 3.8 61.7 1.0
NH2 Z:ARG28 3.8 65.8 1.0
CA Z:ILE196 3.9 51.6 1.0
O Z:ILE196 3.9 50.9 1.0
C Z:VAL198 3.9 57.1 1.0
CA Z:THR192 4.0 61.1 1.0
C Z:ILE196 4.1 50.4 1.0
NH2 H:ARG19 4.2 67.5 1.0
N Z:ILE196 4.2 51.6 1.0
OD1 Z:ASP222 4.4 73.3 1.0
N Z:VAL198 4.5 52.5 1.0
CB Z:THR192 4.6 59.8 1.0
C Z:ASP222 4.7 68.9 1.0
CA Z:VAL198 4.8 55.0 1.0
N Z:GLU193 4.8 62.1 1.0
NH1 H:ARG19 4.8 61.9 1.0
N Z:HIS195 4.8 53.3 1.0
N Z:GLY199 4.9 57.1 1.0
CZ H:ARG19 4.9 61.8 1.0
CZ Z:ARG28 4.9 60.6 1.0
CA Z:HIS195 4.9 51.7 1.0
CA Z:GLY199 4.9 56.3 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 02:25:52 2024

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