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Magnesium in PDB 5fgd: Yeast 20S Proteasome BETA5-H(-2)L-T1A Double Mutant in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome BETA5-H(-2)L-T1A Double Mutant in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome BETA5-H(-2)L-T1A Double Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-H(-2)L-T1A Double Mutant in Complex with Carfilzomib, PDB code: 5fgd 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 (°) 136.790, 300.870, 145.840, 90.00, 113.11, 90.00
R / Rfree (%) 18.2 / 20.8

Other elements in 5fgd:

The structure of Yeast 20S Proteasome BETA5-H(-2)L-T1A Double Mutant in Complex with Carfilzomib also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome BETA5-H(-2)L-T1A Double Mutant in Complex with Carfilzomib (pdb code 5fgd). 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-H(-2)L-T1A Double Mutant in Complex with Carfilzomib, PDB code: 5fgd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5fgd

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome BETA5-H(-2)L-T1A Double 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-H(-2)L-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:54.3
occ:1.00
 O G:MET125 2.3 56.0 1.0
OG1 G:THR8 2.6 42.3 1.0
O G:ARG122 2.7 44.3 1.0
O G:TYR119 2.9 41.3 1.0
CG2 G:THR8 3.2 46.3 1.0
O G:ALA123 3.2 55.2 1.0
C G:MET125 3.4 52.5 1.0
CB G:THR8 3.5 45.4 1.0
C G:ALA123 3.6 49.8 1.0
CA G:ALA123 3.7 48.7 1.0
C G:ARG122 3.8 47.4 1.0
N G:THR8 4.1 48.6 1.0
C G:TYR119 4.1 41.8 1.0
CA G:ARG126 4.2 44.9 1.0
N G:ARG126 4.2 49.0 1.0
N G:ALA123 4.2 48.9 1.0
N G:MET125 4.3 52.1 1.0
CA G:THR8 4.4 47.4 1.0
CA G:MET125 4.5 54.0 1.0
CD G:PRO127 4.5 41.1 1.0
N G:TYR124 4.6 50.0 1.0
CA G:TYR119 4.8 40.6 1.0
C G:ARG126 4.8 44.1 1.0
C G:TYR124 5.0 51.1 1.0

Magnesium binding site 2 out of 7 in 5fgd

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome BETA5-H(-2)L-T1A Double 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-H(-2)L-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:74.1
occ:1.00
 O I:ASP177 2.7 52.7 1.0
O I:SER180 2.8 50.2 1.0
O I:ALA174 3.1 53.4 1.0
OXT I:ASP204 3.4 83.2 1.0
C I:ASP177 3.8 51.1 1.0
C I:SER180 4.0 53.1 1.0
O I:ALA178 4.1 53.7 1.0
C I:ALA174 4.1 54.6 1.0
NH1 Y:ARG19 4.2 66.1 1.0
CA I:ASP175 4.2 56.1 1.0
CA I:ALA178 4.3 50.9 1.0
C I:ASP204 4.3 74.8 1.0
C I:ALA178 4.4 51.8 1.0
O I:ASP204 4.4 76.6 1.0
N I:ALA178 4.5 49.5 1.0
O I:ASP175 4.5 61.0 1.0
NH2 Y:ARG19 4.5 67.6 1.0
C I:ASP175 4.5 56.3 1.0
N I:ASP175 4.7 55.0 1.0
CA I:GLY181 4.7 52.5 1.0
CZ Y:ARG19 4.7 65.7 1.0
N I:ASP177 4.8 49.8 1.0
N I:SER180 4.8 49.6 1.0
N I:GLY181 4.8 52.7 1.0
CA I:ASP177 4.9 50.0 1.0
OD1 I:ASP175 4.9 62.6 1.0

Magnesium binding site 3 out of 7 in 5fgd

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome BETA5-H(-2)L-T1A Double 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-H(-2)L-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:66.8
occ:1.00
 O I:ASP204 2.1 76.6 1.0
O Y:ASP168 2.3 51.6 1.0
O Y:ALA165 2.4 52.0 1.0
O Y:SER171 2.7 58.1 1.0
C I:ASP204 3.1 74.8 1.0
C Y:ASP168 3.3 50.7 1.0
CA Y:ALA169 3.5 53.5 1.0
O Y:ALA169 3.5 58.4 1.0
C Y:ALA165 3.6 51.1 1.0
C Y:ALA169 3.7 54.7 1.0
CA I:ASP204 3.7 69.7 1.0
NH1 Y:ARG19 3.8 66.1 1.0
N Y:ALA169 3.8 52.0 1.0
C Y:SER171 3.9 53.6 1.0
OXT I:ASP204 3.9 83.2 1.0
O Y:HIS166 4.0 50.9 1.0
CB I:ASP204 4.1 69.4 1.0
N Y:SER171 4.3 51.3 1.0
CA Y:ALA165 4.3 51.4 1.0
C Y:HIS166 4.4 52.4 1.0
CA Y:ASP168 4.5 50.7 1.0
N Y:ASP168 4.6 51.8 1.0
N Y:HIS166 4.6 51.0 1.0
CZ Y:ARG19 4.6 65.7 1.0
N Y:TYR170 4.6 54.3 1.0
CA Y:SER171 4.7 51.8 1.0
O Y:ALA164 4.7 50.3 1.0
CA Y:HIS166 4.8 52.0 1.0
C Y:ARG167 4.9 54.9 1.0
CB Y:ALA169 4.9 53.6 1.0
N Y:GLY172 4.9 54.3 1.0
NH2 Y:ARG19 4.9 67.6 1.0

Magnesium binding site 4 out of 7 in 5fgd

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome BETA5-H(-2)L-T1A Double 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-H(-2)L-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:60.9
occ:1.00
 O K:ASP168 2.1 54.7 1.0
O W:ASP204 2.2 74.3 1.0
O K:ALA165 2.3 50.2 1.0
O K:SER171 2.8 55.4 1.0
C W:ASP204 3.1 71.6 1.0
C K:ASP168 3.1 53.3 1.0
C K:ALA165 3.4 50.9 1.0
CA K:ALA169 3.5 55.9 1.0
O K:ALA169 3.7 59.1 1.0
CA W:ASP204 3.7 66.3 1.0
N K:ALA169 3.7 52.6 1.0
C K:ALA169 3.7 57.3 1.0
O K:HIS166 3.8 54.6 1.0
C K:SER171 4.0 53.1 1.0
OXT W:ASP204 4.0 78.1 1.0
NH1 K:ARG19 4.0 68.5 1.0
CB W:ASP204 4.1 64.6 1.0
C K:HIS166 4.2 53.5 1.0
CA K:ALA165 4.2 52.1 1.0
CA K:ASP168 4.3 52.9 1.0
N K:ASP168 4.3 53.3 1.0
N K:SER171 4.4 52.6 1.0
N K:HIS166 4.4 50.2 1.0
O K:ALA164 4.5 55.2 1.0
N K:TYR170 4.6 57.2 1.0
CA K:HIS166 4.6 52.7 1.0
C K:ARG167 4.6 54.8 1.0
CA K:SER171 4.7 52.6 1.0
CZ K:ARG19 4.8 65.0 1.0
N K:ARG167 4.8 52.8 1.0
O K:ARG167 4.9 57.9 1.0
CB K:ALA169 4.9 56.0 1.0

Magnesium binding site 5 out of 7 in 5fgd

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome BETA5-H(-2)L-T1A Double 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-H(-2)L-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:74.1
occ:1.00
 OXT L:ASP222 2.1 80.5 1.0
O V:ASP166 2.1 50.7 1.0
O V:ILE163 2.2 55.1 1.0
O V:SER169 2.5 53.5 1.0
C L:ASP222 3.1 79.0 1.0
C V:ASP166 3.1 51.6 1.0
C V:ILE163 3.2 54.5 1.0
CA L:ASP222 3.6 76.5 1.0
C V:SER169 3.7 48.6 1.0
O V:GLY162 3.8 49.0 1.0
N V:LEU167 3.9 51.4 1.0
CA V:LEU167 3.9 51.7 1.0
O V:TRP164 3.9 60.3 1.0
N V:ASP166 4.0 51.8 1.0
O L:ASP222 4.0 83.7 1.0
C V:TRP164 4.1 55.4 1.0
CA V:ILE163 4.1 54.3 1.0
NH1 V:ARG19 4.1 64.1 1.0
N V:TRP164 4.2 52.3 1.0
CA V:ASP166 4.2 51.4 1.0
CB L:ASP222 4.2 75.0 1.0
CA V:TRP164 4.3 53.9 1.0
C V:LEU167 4.4 51.4 1.0
N V:SER169 4.5 47.5 1.0
N V:ASN165 4.6 55.0 1.0
N V:GLY170 4.6 48.7 1.0
CA V:GLY170 4.6 51.4 1.0
CA V:SER169 4.6 47.1 1.0
O V:LEU167 4.6 53.5 1.0
CZ V:ARG19 4.7 59.9 1.0
C V:ASN165 4.7 51.8 1.0
NH2 V:ARG19 4.8 64.7 1.0
C V:GLY162 4.8 52.9 1.0
O L:ARG221 4.9 75.2 1.0
N V:ILE163 4.9 53.1 1.0
CB V:SER169 4.9 47.6 1.0
N L:ASP222 4.9 74.4 1.0
CB V:ASP166 5.0 50.1 1.0
CD2 V:LEU167 5.0 49.9 1.0

Magnesium binding site 6 out of 7 in 5fgd

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome BETA5-H(-2)L-T1A Double 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-H(-2)L-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:53.2
occ:1.00
 O N:SER169 2.4 45.1 1.0
O N:ILE163 2.9 43.7 1.0
O N:ASP166 2.9 48.7 1.0
NH1 N:ARG19 3.3 48.5 1.0
C N:SER169 3.7 43.9 1.0
CD1 a:LEU34 3.8 48.5 1.0
C N:ASP166 4.0 45.9 1.0
C N:ILE163 4.0 45.5 1.0
CZ N:ARG19 4.0 48.9 1.0
CA N:GLY167 4.1 45.7 1.0
CG2 N:ILE163 4.1 45.1 1.0
O N:GLY167 4.2 47.6 1.0
NH2 N:ARG19 4.3 50.5 1.0
CA N:GLY170 4.3 44.5 1.0
C N:GLY167 4.3 46.3 1.0
N N:GLY170 4.5 43.9 1.0
N N:GLY167 4.5 44.2 1.0
N N:SER169 4.6 42.9 1.0
CA N:ILE163 4.6 45.0 1.0
CA N:SER169 4.7 41.8 1.0
NE N:ARG19 5.0 47.3 1.0
CB N:ILE163 5.0 44.8 1.0

Magnesium binding site 7 out of 7 in 5fgd

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome BETA5-H(-2)L-T1A Double 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-H(-2)L-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:62.8
occ:1.00
 O Z:VAL198 2.4 55.4 1.0
O Z:THR192 2.7 63.4 1.0
O Z:HIS195 3.0 51.0 1.0
O Z:ASP222 3.4 81.7 1.0
NH2 Z:ARG28 3.6 69.6 1.0
C Z:VAL198 3.6 56.9 1.0
C Z:THR192 3.7 63.5 1.0
CG2 Z:THR192 3.7 65.6 1.0
O Z:ILE196 3.9 53.9 1.0
C Z:HIS195 4.0 52.5 1.0
CA Z:THR192 4.0 62.9 1.0
CA Z:ILE196 4.1 52.3 1.0
C Z:ILE196 4.2 50.2 1.0
OD1 Z:ASP222 4.3 74.8 1.0
N Z:VAL198 4.4 53.0 1.0
NH2 H:ARG19 4.4 67.4 1.0
C Z:ASP222 4.5 79.8 1.0
CB Z:THR192 4.5 63.1 1.0
N Z:GLY199 4.5 57.4 1.0
N Z:ILE196 4.5 50.8 1.0
CA Z:GLY199 4.5 58.9 1.0
CA Z:VAL198 4.6 55.4 1.0
CZ Z:ARG28 4.7 66.2 1.0
N Z:GLU193 4.9 62.6 1.0
NH1 Z:ARG28 4.9 67.0 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 04:10:31 2024

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