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Magnesium in PDB 5fgi: Yeast 20S Proteasome BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib, PDB code: 5fgi 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 (°) 136.810, 301.160, 145.900, 90.00, 113.30, 90.00
R / Rfree (%) 18.6 / 21

Other elements in 5fgi:

The structure of Yeast 20S Proteasome BETA1-T1A BETA2-T1A 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 BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib (pdb code 5fgi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib, PDB code: 5fgi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5fgi

Go back to Magnesium Binding Sites List in 5fgi
Magnesium binding site 1 out of 6 in the Yeast 20S Proteasome BETA1-T1A BETA2-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 BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:56.5
occ:1.00
 O G:MET125 2.3 52.0 1.0
OG1 G:THR8 2.8 44.8 1.0
O G:ALA123 3.0 56.0 1.0
O G:ARG122 3.1 48.4 1.0
O G:TYR119 3.2 41.8 1.0
CG2 G:THR8 3.3 48.0 1.0
C G:MET125 3.4 51.7 1.0
C G:ALA123 3.6 54.1 1.0
CB G:THR8 3.6 47.0 1.0
CA G:ALA123 3.8 52.8 1.0
N G:THR8 4.0 51.3 1.0
CA G:ARG126 4.0 46.1 1.0
N G:ARG126 4.1 48.0 1.0
C G:ARG122 4.1 51.2 1.0
N G:MET125 4.3 52.3 1.0
C G:TYR119 4.4 42.3 1.0
CA G:THR8 4.4 49.0 1.0
CA G:MET125 4.4 55.8 1.0
CD G:PRO127 4.4 43.5 1.0
N G:ALA123 4.5 50.9 1.0
N G:TYR124 4.6 55.3 1.0
C G:ARG126 4.8 44.7 1.0
C G:TYR124 4.9 51.8 1.0
N G:PRO127 4.9 43.5 1.0
C G:ILE7 5.0 54.2 1.0

Magnesium binding site 2 out of 6 in 5fgi

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Magnesium binding site 2 out of 6 in the Yeast 20S Proteasome BETA1-T1A BETA2-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 BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:55.4
occ:1.00
 O I:ALA174 2.6 50.9 1.0
O I:SER180 2.7 47.4 1.0
O I:ASP177 2.7 47.9 1.0
OXT I:ASP204 3.5 63.4 1.0
C I:ALA174 3.6 50.8 1.0
C I:ASP177 3.8 48.3 1.0
CA I:ASP175 3.9 53.8 1.0
C I:SER180 3.9 47.3 1.0
N I:ASP175 4.1 52.3 1.0
C I:ASP175 4.2 52.2 1.0
O I:ASP175 4.4 53.2 1.0
N I:ASP177 4.5 47.7 1.0
C I:ASP204 4.5 64.2 1.0
OD1 I:ASP175 4.5 56.2 1.0
CA I:GLY181 4.6 48.2 1.0
O I:ALA178 4.6 52.0 1.0
CA I:ALA178 4.7 47.5 1.0
N I:GLY181 4.7 47.8 1.0
N I:ALA178 4.7 47.6 1.0
O I:ASP204 4.7 66.0 1.0
CA I:ASP177 4.8 47.9 1.0
C I:ALA178 4.8 48.5 1.0
CA I:ALA174 4.8 47.8 1.0
NH2 Y:ARG19 4.8 63.5 1.0
N I:SER180 4.8 45.4 1.0
NH1 Y:ARG19 4.9 62.7 1.0
CA I:SER180 4.9 46.9 1.0
N I:ARG176 5.0 50.1 1.0

Magnesium binding site 3 out of 6 in 5fgi

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Magnesium binding site 3 out of 6 in the Yeast 20S Proteasome BETA1-T1A BETA2-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 BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:44.4
occ:1.00
 O I:ASP204 2.1 66.0 1.0
O Y:ASP168 2.3 46.0 1.0
O Y:ALA165 2.5 43.5 1.0
O Y:SER171 2.9 48.2 1.0
C I:ASP204 3.1 64.2 1.0
C Y:ASP168 3.3 45.9 1.0
CA Y:ALA169 3.5 45.1 1.0
CA I:ASP204 3.6 62.5 1.0
C Y:ALA165 3.7 45.7 1.0
O Y:ALA169 3.7 44.9 1.0
C Y:ALA169 3.8 45.2 1.0
O Y:HIS166 3.8 45.9 1.0
N Y:ALA169 3.8 45.6 1.0
NH1 Y:ARG19 3.9 62.7 1.0
CB I:ASP204 4.0 62.8 1.0
OXT I:ASP204 4.0 63.4 1.0
C Y:SER171 4.1 46.3 1.0
O Y:HOH402 4.3 53.1 1.0
C Y:HIS166 4.3 46.2 1.0
N Y:SER171 4.4 44.1 1.0
CA Y:ASP168 4.5 45.3 1.0
CZ Y:ARG19 4.5 60.7 1.0
N Y:ASP168 4.5 45.1 1.0
CA Y:ALA165 4.6 46.5 1.0
N Y:HIS166 4.6 46.3 1.0
N Y:TYR170 4.6 46.3 1.0
CA Y:HIS166 4.7 46.7 1.0
NH2 Y:ARG19 4.7 63.5 1.0
C Y:ARG167 4.8 46.0 1.0
CA Y:SER171 4.8 44.5 1.0
O Y:ALA164 4.9 47.3 1.0
CB Y:ALA169 4.9 45.4 1.0
O Y:ARG167 5.0 46.6 1.0
N I:ASP204 5.0 59.0 1.0

Magnesium binding site 4 out of 6 in 5fgi

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Magnesium binding site 4 out of 6 in the Yeast 20S Proteasome BETA1-T1A BETA2-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 BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:45.6
occ:1.00
 O K:ASP168 2.2 49.0 1.0
O W:ASP204 2.2 69.7 1.0
O K:ALA165 2.3 47.8 1.0
O K:SER171 2.7 47.4 1.0
C W:ASP204 3.2 65.2 1.0
C K:ASP168 3.2 47.8 1.0
C K:ALA165 3.5 48.1 1.0
CA W:ASP204 3.6 62.5 1.0
CA K:ALA169 3.6 49.1 1.0
O K:HIS166 3.7 44.9 1.0
N K:ALA169 3.8 49.7 1.0
O K:ALA169 3.9 49.0 1.0
C K:ALA169 3.9 49.4 1.0
C K:SER171 3.9 47.8 1.0
CB W:ASP204 4.0 60.0 1.0
NH1 K:ARG19 4.0 61.8 1.0
C K:HIS166 4.1 45.3 1.0
OXT W:ASP204 4.2 67.1 1.0
N K:SER171 4.3 46.8 1.0
CA K:ASP168 4.4 45.9 1.0
N K:ASP168 4.4 45.6 1.0
CA K:ALA165 4.4 47.8 1.0
N K:HIS166 4.4 47.0 1.0
CA K:HIS166 4.5 45.9 1.0
CZ K:ARG19 4.6 62.1 1.0
O K:ALA164 4.6 46.0 1.0
N K:TYR170 4.7 49.0 1.0
CA K:SER171 4.7 45.9 1.0
C K:ARG167 4.7 45.9 1.0
NH2 K:ARG19 4.8 65.1 1.0
N K:ARG167 4.9 45.0 1.0
O K:ARG167 4.9 46.7 1.0
N K:GLY172 4.9 47.9 1.0
N W:ASP204 5.0 60.8 1.0

Magnesium binding site 5 out of 6 in 5fgi

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Magnesium binding site 5 out of 6 in the Yeast 20S Proteasome BETA1-T1A BETA2-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 BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:48.2
occ:1.00
 O N:SER169 2.5 42.6 1.0
O N:ILE163 2.8 47.3 1.0
O N:ASP166 2.9 54.9 1.0
NH1 N:ARG19 3.5 49.6 1.0
C N:SER169 3.7 43.5 1.0
C N:ILE163 3.9 47.8 1.0
CG2 N:ILE163 4.0 46.3 1.0
CD1 a:LEU34 4.0 51.7 1.0
C N:ASP166 4.0 51.4 1.0
CZ N:ARG19 4.1 48.1 1.0
CA N:GLY167 4.2 51.1 1.0
CA N:GLY170 4.3 46.4 1.0
O N:GLY167 4.3 49.4 1.0
NH2 N:ARG19 4.3 48.7 1.0
N N:GLY170 4.4 44.8 1.0
C N:GLY167 4.5 49.3 1.0
CA N:ILE163 4.5 46.9 1.0
N N:GLY167 4.5 50.9 1.0
N N:SER169 4.7 44.5 1.0
CA N:SER169 4.7 43.0 1.0
CB N:ILE163 4.9 46.1 1.0
N N:LYS164 4.9 48.8 1.0
NE N:ARG19 5.0 47.0 1.0

Magnesium binding site 6 out of 6 in 5fgi

Go back to Magnesium Binding Sites List in 5fgi
Magnesium binding site 6 out of 6 in the Yeast 20S Proteasome BETA1-T1A BETA2-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 BETA1-T1A BETA2-T1A Double Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:52.7
occ:1.00
 O Z:VAL198 2.6 53.3 1.0
O Z:THR192 2.8 67.3 1.0
O Z:HIS195 3.2 49.8 1.0
O Z:ASP222 3.3 84.0 1.0
CG2 Z:THR192 3.6 67.1 1.0
NH2 Z:ARG28 3.7 69.2 1.0
C Z:THR192 3.8 65.7 1.0
C Z:VAL198 3.8 55.3 1.0
O Z:ILE196 3.9 55.3 1.0
CA Z:THR192 4.1 64.4 1.0
OD1 Z:ASP222 4.2 82.1 1.0
C Z:HIS195 4.3 54.0 1.0
CA Z:ILE196 4.3 54.5 1.0
C Z:ILE196 4.3 53.8 1.0
NH2 H:ARG19 4.4 61.0 1.0
C Z:ASP222 4.5 83.1 1.0
CB Z:THR192 4.5 66.5 1.0
CA Z:GLY199 4.5 58.9 1.0
N Z:GLY199 4.6 56.9 1.0
CZ Z:ARG28 4.6 65.1 1.0
N Z:VAL198 4.6 53.2 1.0
CA Z:VAL198 4.8 54.8 1.0
N Z:ILE196 4.8 54.1 1.0
NH1 Z:ARG28 4.8 65.0 1.0
O Z:LYS220 4.8 75.2 1.0
N Z:GLU193 5.0 65.7 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 04:14:41 2024

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