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Magnesium in PDB 5fgg: Yeast 20S Proteasome BETA5-L(-49S)_D17N Double Mutant in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome BETA5-L(-49S)_D17N Double Mutant in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome BETA5-L(-49S)_D17N Double Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-L(-49S)_D17N Double Mutant in Complex with Carfilzomib, PDB code: 5fgg 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 134.330, 300.470, 144.290, 90.00, 112.69, 90.00
R / Rfree (%) 18.9 / 20.8

Other elements in 5fgg:

The structure of Yeast 20S Proteasome BETA5-L(-49S)_D17N Double 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(-49S)_D17N Double Mutant in Complex with Carfilzomib (pdb code 5fgg). 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(-49S)_D17N Double Mutant in Complex with Carfilzomib, PDB code: 5fgg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5fgg

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome BETA5-L(-49S)_D17N 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-L(-49S)_D17N Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:51.1
occ:1.00
 O G:MET125 2.3 45.8 1.0
O G:ARG122 2.5 45.5 1.0
OG1 G:THR8 2.6 40.3 1.0
O G:TYR119 2.7 40.6 1.0
O G:ALA123 3.2 50.8 1.0
CG2 G:THR8 3.3 44.6 1.0
C G:MET125 3.5 46.1 1.0
CB G:THR8 3.5 43.9 1.0
C G:ALA123 3.5 48.6 1.0
C G:ARG122 3.5 46.1 1.0
CA G:ALA123 3.6 46.5 1.0
C G:TYR119 3.9 38.7 1.0
N G:ALA123 4.0 45.4 1.0
N G:THR8 4.1 47.8 1.0
N G:MET125 4.2 48.1 1.0
N G:ARG126 4.3 42.9 1.0
CA G:ARG126 4.3 41.1 1.0
CA G:THR8 4.4 45.8 1.0
CA G:MET125 4.4 49.7 1.0
N G:TYR124 4.5 49.5 1.0
CD G:PRO127 4.7 38.1 1.0
CA G:TYR119 4.7 38.1 1.0
CA G:ARG122 4.8 48.5 1.0
CB G:ALA123 4.9 46.5 1.0
N G:THR120 4.9 38.1 1.0
N G:ARG122 4.9 45.4 1.0
C G:ARG126 4.9 39.5 1.0
C G:TYR124 4.9 47.6 1.0

Magnesium binding site 2 out of 8 in 5fgg

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome BETA5-L(-49S)_D17N 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-L(-49S)_D17N Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:65.2
occ:1.00
 O I:ASP177 2.5 55.9 1.0
O I:SER180 2.8 56.6 1.0
O I:ALA174 3.0 53.5 1.0
OXT I:ASP204 3.5 69.6 1.0
C I:ASP177 3.6 53.2 1.0
C I:SER180 4.0 53.3 1.0
O I:ALA178 4.1 56.5 1.0
C I:ALA174 4.1 54.2 1.0
CA I:ALA178 4.1 53.2 1.0
C I:ALA178 4.2 54.3 1.0
N I:ALA178 4.3 52.0 1.0
CA I:ASP175 4.4 56.8 1.0
C I:ASP204 4.4 74.5 1.0
O I:ASP204 4.4 74.9 1.0
NH2 Y:ARG19 4.5 81.6 1.0
C I:ASP175 4.6 55.3 1.0
O I:ASP175 4.6 56.3 1.0
N I:ASP177 4.6 52.0 1.0
N I:SER180 4.7 49.5 1.0
N I:ASP175 4.7 54.2 1.0
CA I:ASP177 4.7 52.6 1.0
NH1 Y:ARG19 4.8 83.1 1.0
CA I:GLY181 4.9 51.1 1.0
N I:GLY181 4.9 51.6 1.0
CA I:SER180 4.9 52.0 1.0

Magnesium binding site 3 out of 8 in 5fgg

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome BETA5-L(-49S)_D17N 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-L(-49S)_D17N Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:62.9
occ:1.00
 O Y:ASP168 2.2 58.2 1.0
O I:ASP204 2.4 74.9 1.0
O Y:ALA165 2.4 51.2 1.0
O Y:SER171 2.8 62.2 1.0
C I:ASP204 3.1 74.5 1.0
C Y:ASP168 3.2 58.1 1.0
O Y:HIS166 3.6 54.4 1.0
C Y:ALA165 3.6 55.3 1.0
CA Y:ALA169 3.6 58.8 1.0
CA I:ASP204 3.6 74.7 1.0
N Y:ALA169 3.8 59.0 1.0
NH1 Y:ARG19 3.8 83.1 1.0
O Y:ALA169 3.8 58.2 1.0
C Y:ALA169 3.9 58.6 1.0
OXT I:ASP204 3.9 69.6 1.0
C Y:HIS166 4.0 56.5 1.0
C Y:SER171 4.0 60.0 1.0
CB I:ASP204 4.1 75.7 1.0
N Y:ASP168 4.4 56.9 1.0
N Y:HIS166 4.4 55.0 1.0
CA Y:ASP168 4.4 56.8 1.0
CA Y:HIS166 4.4 56.5 1.0
N Y:SER171 4.5 57.8 1.0
CA Y:ALA165 4.5 57.2 1.0
C Y:ARG167 4.6 57.3 1.0
O Y:ALA164 4.7 52.4 1.0
N Y:ARG167 4.7 56.3 1.0
N Y:TYR170 4.8 59.4 1.0
O Y:ARG167 4.8 57.0 1.0
CA Y:SER171 4.8 58.5 1.0
CZ Y:ARG19 4.9 80.6 1.0
CB Y:ALA169 4.9 59.8 1.0
N I:ASP204 5.0 72.9 1.0

Magnesium binding site 4 out of 8 in 5fgg

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome BETA5-L(-49S)_D17N 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-L(-49S)_D17N Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:60.9
occ:1.00
 O K:ASP168 2.1 56.3 1.0
O K:ALA165 2.3 51.4 1.0
O W:ASP204 2.4 73.8 1.0
O K:SER171 2.5 55.0 1.0
C W:ASP204 3.2 70.0 1.0
C K:ASP168 3.2 57.5 1.0
C K:ALA165 3.5 55.9 1.0
CA K:ALA169 3.6 60.0 1.0
CA W:ASP204 3.6 67.7 1.0
NH1 K:ARG19 3.7 77.4 1.0
O K:ALA169 3.7 59.2 1.0
C K:SER171 3.7 58.4 1.0
O K:HIS166 3.7 56.1 1.0
C K:ALA169 3.8 60.2 1.0
N K:ALA169 3.8 58.6 1.0
OXT W:ASP204 4.1 73.9 1.0
CB W:ASP204 4.1 67.8 1.0
C K:HIS166 4.1 56.2 1.0
N K:SER171 4.3 58.1 1.0
CA K:ALA165 4.3 56.8 1.0
CA K:ASP168 4.4 57.3 1.0
N K:HIS166 4.4 56.0 1.0
N K:ASP168 4.4 56.3 1.0
CA K:HIS166 4.5 56.1 1.0
CA K:SER171 4.5 57.5 1.0
O K:ALA164 4.6 54.8 1.0
N K:TYR170 4.7 60.8 1.0
C K:ARG167 4.7 55.8 1.0
CZ K:ARG19 4.7 75.3 1.0
N K:GLY172 4.7 59.8 1.0
N K:ARG167 4.8 54.7 1.0
CA K:GLY172 4.9 61.7 1.0
CB K:SER171 4.9 56.2 1.0
O K:ARG167 4.9 55.8 1.0
CB K:ALA169 5.0 61.1 1.0
N W:ASP204 5.0 67.3 1.0

Magnesium binding site 5 out of 8 in 5fgg

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome BETA5-L(-49S)_D17N 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-L(-49S)_D17N Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:62.6
occ:1.00
 OXT L:ASP222 2.2 76.4 1.0
O V:ILE163 2.4 50.0 1.0
O V:ASP166 2.5 43.3 1.0
C L:ASP222 3.0 75.9 1.0
O V:TRP164 3.2 54.4 1.0
C V:ASP166 3.2 45.5 1.0
O V:SER169 3.4 44.0 1.0
C V:ILE163 3.5 51.9 1.0
CA L:ASP222 3.5 72.1 1.0
C V:TRP164 3.5 52.1 1.0
O L:ASP222 3.8 75.8 1.0
N V:LEU167 3.8 46.0 1.0
N V:ASP166 3.8 46.4 1.0
CA V:LEU167 3.9 46.7 1.0
CA V:TRP164 4.0 52.0 1.0
O L:ARG221 4.1 64.0 1.0
N V:TRP164 4.2 50.5 1.0
CA V:ASP166 4.2 45.4 1.0
O V:GLY162 4.2 50.4 1.0
N V:ASN165 4.2 50.2 1.0
C V:ASN165 4.3 46.9 1.0
CD2 V:LEU167 4.4 46.8 1.0
CB L:ASP222 4.4 69.4 1.0
CD1 L:ILE35 4.6 56.3 1.0
NH1 V:ARG19 4.6 58.6 1.0
C V:SER169 4.6 45.7 1.0
CA V:ILE163 4.6 52.2 1.0
N L:ASP222 4.6 69.0 1.0
C V:LEU167 4.6 46.5 1.0
CA V:ASN165 4.7 48.6 1.0
C L:ARG221 4.8 65.7 1.0
O V:ASN165 4.9 45.2 1.0
O V:LEU167 5.0 46.8 1.0

Magnesium binding site 6 out of 8 in 5fgg

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome BETA5-L(-49S)_D17N 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-L(-49S)_D17N Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:52.0
occ:1.00
 O N:SER169 2.5 42.6 1.0
O N:ILE163 2.6 44.0 1.0
O N:ASP166 2.9 41.6 1.0
NH1 N:ARG19 3.5 46.7 1.0
C N:SER169 3.7 41.0 1.0
CD1 a:LEU34 3.7 48.0 1.0
C N:ILE163 3.8 44.4 1.0
C N:ASP166 3.9 42.9 1.0
CG2 N:ILE163 4.0 43.3 1.0
CA N:GLY167 4.1 43.4 1.0
CZ N:ARG19 4.2 44.8 1.0
CA N:GLY170 4.3 43.2 1.0
NH2 N:ARG19 4.4 45.0 1.0
O N:GLY167 4.4 41.9 1.0
CA N:ILE163 4.4 43.2 1.0
C N:GLY167 4.5 42.3 1.0
N N:GLY170 4.5 41.9 1.0
N N:GLY167 4.5 43.4 1.0
N N:SER169 4.7 40.0 1.0
CA N:SER169 4.7 39.0 1.0
N N:LYS164 4.8 45.3 1.0
CB N:ILE163 4.8 42.9 1.0
CG a:LEU34 5.0 47.7 1.0
O N:LYS164 5.0 47.8 1.0

Magnesium binding site 7 out of 8 in 5fgg

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome BETA5-L(-49S)_D17N 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-L(-49S)_D17N Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:62.2
occ:1.00
 O Z:VAL198 2.6 53.1 1.0
O Z:THR192 2.8 60.0 1.0
O Z:HIS195 2.9 48.3 1.0
O Z:ASP222 3.3 76.0 1.0
NH2 Z:ARG28 3.6 60.9 1.0
O Z:ILE196 3.8 50.9 1.0
C Z:THR192 3.8 60.0 1.0
C Z:VAL198 3.8 54.5 1.0
CA Z:ILE196 3.9 50.0 1.0
CG2 Z:THR192 3.9 60.7 1.0
C Z:HIS195 3.9 50.1 1.0
C Z:ILE196 4.0 49.2 1.0
CA Z:THR192 4.2 60.4 1.0
NH2 H:ARG19 4.3 61.8 1.0
OD1 Z:ASP222 4.3 68.2 1.0
N Z:ILE196 4.3 49.2 1.0
N Z:VAL198 4.4 51.8 1.0
C Z:ASP222 4.4 72.9 1.0
CZ Z:ARG28 4.6 60.7 1.0
CB Z:THR192 4.7 60.5 1.0
CA Z:VAL198 4.7 53.7 1.0
N Z:GLY199 4.7 55.3 1.0
CA Z:GLY199 4.8 55.1 1.0
NH1 Z:ARG28 4.9 64.3 1.0
NH1 H:ARG19 4.9 60.2 1.0
N Z:GLN197 4.9 48.5 1.0
CZ H:ARG19 4.9 58.7 1.0
OXT Z:ASP222 5.0 75.3 1.0

Magnesium binding site 8 out of 8 in 5fgg

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome BETA5-L(-49S)_D17N 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 8 of Yeast 20S Proteasome BETA5-L(-49S)_D17N Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg202

b:30.0
occ:1.00
 O b:SER169 2.2 40.5 1.0
O b:ILE163 2.6 41.2 1.0
O b:ASP166 2.6 39.6 1.0
C b:SER169 3.4 41.5 1.0
NH1 b:ARG19 3.5 48.1 1.0
C b:ILE163 3.7 42.8 1.0
C b:ASP166 3.7 41.4 1.0
CD1 M:LEU34 3.9 46.2 1.0
CG2 b:ILE163 4.0 42.0 1.0
CA b:GLY167 4.0 41.4 1.0
CZ b:ARG19 4.2 47.1 1.0
CA b:GLY170 4.2 44.1 1.0
N b:GLY170 4.2 42.9 1.0
CA b:ILE163 4.2 41.8 1.0
O b:GLY167 4.3 43.0 1.0
C b:GLY167 4.3 41.2 1.0
N b:GLY167 4.3 41.0 1.0
N b:SER169 4.4 40.4 1.0
CA b:SER169 4.4 39.4 1.0
NH2 b:ARG19 4.5 48.6 1.0
CB b:ILE163 4.7 41.6 1.0
N b:LYS164 4.8 44.1 1.0
CB b:SER169 4.9 38.5 1.0
CA b:ASP166 4.9 41.0 1.0
N b:ASP166 5.0 41.0 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 04:11:30 2024

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