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

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

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

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-H(-2)T-T1A Double Mutant in Complex with Carfilzomib, PDB code: 5fge 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 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.160, 301.550, 145.790, 90.00, 113.20, 90.00
R / Rfree (%) 19 / 21.4

Other elements in 5fge:

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

Magnesium binding site 1 out of 7 in 5fge

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

b:58.5
occ:1.00
 O G:MET125 2.2 49.4 1.0
O G:ARG122 2.5 43.7 1.0
OG1 G:THR8 2.6 46.1 1.0
O G:TYR119 2.6 40.9 1.0
CG2 G:THR8 3.3 46.4 1.0
O G:ALA123 3.4 52.4 1.0
C G:MET125 3.4 49.0 1.0
CB G:THR8 3.5 46.0 1.0
C G:ARG122 3.6 47.5 1.0
C G:ALA123 3.7 49.0 1.0
CA G:ALA123 3.7 48.0 1.0
C G:TYR119 3.8 42.0 1.0
N G:ALA123 4.1 48.3 1.0
CA G:ARG126 4.2 44.0 1.0
N G:ARG126 4.2 45.8 1.0
N G:MET125 4.2 50.3 1.0
N G:THR8 4.3 47.5 1.0
CA G:MET125 4.4 52.6 1.0
CA G:THR8 4.5 47.3 1.0
CA G:TYR119 4.6 40.5 1.0
CD G:PRO127 4.6 41.3 1.0
N G:TYR124 4.6 49.7 1.0
CA G:ARG122 4.8 51.5 1.0
N G:THR120 4.8 41.8 1.0
C G:ARG126 4.8 42.6 1.0
N G:ARG122 4.9 48.8 1.0
C G:TYR124 5.0 49.6 1.0
CB G:MET125 5.0 57.5 1.0
CA G:THR120 5.0 42.0 1.0

Magnesium binding site 2 out of 7 in 5fge

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

b:74.4
occ:1.00
 O I:SER180 2.5 55.7 1.0
O I:ASP177 2.7 49.4 1.0
O I:ALA174 3.2 50.0 1.0
OXT I:ASP204 3.3 73.0 1.0
C I:SER180 3.8 51.5 1.0
O I:ALA178 3.8 49.8 1.0
C I:ASP177 3.8 47.8 1.0
C I:ALA178 4.2 49.0 1.0
NH1 Y:ARG19 4.2 60.7 1.0
C I:ASP204 4.2 69.0 1.0
CA I:ALA178 4.2 47.9 1.0
O I:ASP204 4.3 66.6 1.0
C I:ALA174 4.3 51.5 1.0
N I:ALA178 4.5 46.9 1.0
CA I:GLY181 4.5 49.9 1.0
N I:SER180 4.6 46.9 1.0
CA I:ASP175 4.6 52.1 1.0
N I:GLY181 4.6 50.2 1.0
NH2 Y:ARG19 4.7 62.3 1.0
CA I:SER180 4.8 49.5 1.0
O I:ASP175 4.8 56.0 1.0
C I:ASP175 4.9 52.6 1.0
CZ Y:ARG19 4.9 59.9 1.0
N I:ASP175 4.9 51.3 1.0
N I:ASP177 5.0 46.9 1.0
CA I:ASP177 5.0 47.3 1.0

Magnesium binding site 3 out of 7 in 5fge

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

b:52.8
occ:1.00
 O I:ASP204 2.2 66.6 1.0
O Y:ASP168 2.2 47.4 1.0
O Y:ALA165 2.4 51.3 1.0
O Y:SER171 2.4 50.3 1.0
O Y:HOH403 2.7 53.1 1.0
C I:ASP204 3.1 69.0 1.0
C Y:ASP168 3.3 47.3 1.0
C Y:ALA165 3.5 48.8 1.0
O Y:ALA169 3.5 50.9 1.0
CA Y:ALA169 3.6 49.3 1.0
C Y:SER171 3.6 49.9 1.0
C Y:ALA169 3.6 50.5 1.0
NH1 Y:ARG19 3.7 60.7 1.0
CA I:ASP204 3.8 66.0 1.0
N Y:ALA169 3.8 47.9 1.0
OXT I:ASP204 4.1 73.0 1.0
CB I:ASP204 4.1 64.4 1.0
N Y:SER171 4.1 48.3 1.0
CA Y:ALA165 4.2 48.4 1.0
O Y:HIS166 4.3 49.2 1.0
CA Y:SER171 4.4 48.4 1.0
CZ Y:ARG19 4.5 59.9 1.0
N Y:TYR170 4.5 49.4 1.0
CA Y:ASP168 4.5 47.3 1.0
C Y:HIS166 4.6 49.5 1.0
N Y:HIS166 4.6 48.0 1.0
N Y:ASP168 4.6 48.9 1.0
O Y:ALA164 4.6 47.1 1.0
N Y:GLY172 4.6 50.4 1.0
CA Y:GLY172 4.8 50.3 1.0
NH2 Y:ARG19 4.9 62.3 1.0
CA Y:HIS166 4.9 48.8 1.0
CB Y:SER171 4.9 48.1 1.0
CB Y:ALA169 4.9 50.2 1.0
C Y:ARG167 5.0 51.6 1.0

Magnesium binding site 4 out of 7 in 5fge

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

b:65.8
occ:1.00
 O K:ALA165 2.2 49.6 1.0
O K:ASP168 2.2 52.2 1.0
O W:ASP204 2.3 69.2 1.0
O K:SER171 2.6 52.6 1.0
C W:ASP204 3.1 67.3 1.0
C K:ASP168 3.2 50.3 1.0
C K:ALA165 3.3 49.6 1.0
CA W:ASP204 3.6 63.7 1.0
CA K:ALA169 3.6 51.9 1.0
O K:ALA169 3.8 52.5 1.0
C K:SER171 3.8 50.1 1.0
C K:ALA169 3.8 52.7 1.0
N K:ALA169 3.8 50.0 1.0
O K:HIS166 4.0 52.9 1.0
NH1 K:ARG19 4.0 62.6 1.0
CB W:ASP204 4.0 62.3 1.0
OXT W:ASP204 4.0 73.3 1.0
CA K:ALA165 4.1 48.7 1.0
N K:SER171 4.2 49.8 1.0
C K:HIS166 4.3 50.8 1.0
N K:HIS166 4.4 48.6 1.0
N K:ASP168 4.4 50.5 1.0
CA K:ASP168 4.4 48.8 1.0
O K:ALA164 4.4 49.3 1.0
CA K:SER171 4.5 49.3 1.0
CA K:HIS166 4.6 50.1 1.0
N K:TYR170 4.6 52.3 1.0
CZ K:ARG19 4.7 59.9 1.0
C K:ARG167 4.7 52.3 1.0
N K:GLY172 4.8 50.5 1.0
N K:ARG167 4.9 49.3 1.0
CA K:GLY172 4.9 51.3 1.0
CB K:SER171 4.9 49.4 1.0
CB K:ALA165 4.9 48.8 1.0
N W:ASP204 5.0 64.3 1.0

Magnesium binding site 5 out of 7 in 5fge

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

b:60.2
occ:1.00
 O V:ILE163 2.1 51.4 1.0
O V:ASP166 2.2 47.9 1.0
OXT L:ASP222 2.2 67.3 1.0
O V:SER169 2.3 49.3 1.0
O V:HOH406 2.5 50.0 1.0
C L:ASP222 3.2 73.1 1.0
C V:ASP166 3.2 49.4 1.0
C V:ILE163 3.2 52.1 1.0
C V:SER169 3.5 46.9 1.0
CA L:ASP222 3.7 72.7 1.0
O V:GLY162 3.7 50.5 1.0
N V:LEU167 3.9 50.1 1.0
CA V:LEU167 3.9 49.8 1.0
CA V:ILE163 4.0 52.6 1.0
N V:ASP166 4.1 49.5 1.0
NH1 V:ARG19 4.1 61.3 1.0
N V:TRP164 4.1 51.6 1.0
O L:ASP222 4.2 77.1 1.0
C V:TRP164 4.2 52.0 1.0
O V:TRP164 4.2 53.3 1.0
CA V:ASP166 4.2 49.0 1.0
CB L:ASP222 4.2 72.5 1.0
N V:SER169 4.3 45.9 1.0
C V:LEU167 4.3 50.1 1.0
N V:GLY170 4.3 48.0 1.0
CA V:TRP164 4.4 52.4 1.0
CA V:SER169 4.4 45.9 1.0
CA V:GLY170 4.4 50.1 1.0
O V:LEU167 4.6 51.0 1.0
CZ V:ARG19 4.6 57.5 1.0
N V:ASN165 4.6 51.7 1.0
C V:GLY162 4.7 50.7 1.0
NH2 V:ARG19 4.7 59.9 1.0
CB V:SER169 4.8 46.2 1.0
C V:ASN165 4.8 49.5 1.0
N V:ILE163 4.8 51.4 1.0
O L:ARG221 4.9 67.7 1.0
CB V:ASP166 5.0 48.4 1.0
N V:GLY168 5.0 48.8 1.0

Magnesium binding site 6 out of 7 in 5fge

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

b:51.9
occ:1.00
 O N:SER169 2.4 45.0 1.0
O N:ILE163 2.7 44.9 1.0
O N:ASP166 2.8 46.7 1.0
NH1 N:ARG19 3.5 49.8 1.0
C N:SER169 3.7 42.5 1.0
CD1 a:LEU34 3.7 48.1 1.0
C N:ILE163 3.8 45.7 1.0
C N:ASP166 3.9 44.5 1.0
CG2 N:ILE163 4.0 44.5 1.0
CA N:GLY167 4.1 45.0 1.0
CZ N:ARG19 4.2 48.7 1.0
O N:GLY167 4.3 45.1 1.0
CA N:GLY170 4.4 44.2 1.0
C N:GLY167 4.4 45.0 1.0
N N:GLY167 4.4 43.7 1.0
NH2 N:ARG19 4.4 50.2 1.0
CA N:ILE163 4.4 44.7 1.0
N N:GLY170 4.5 41.7 1.0
N N:SER169 4.6 41.6 1.0
CA N:SER169 4.7 40.4 1.0
CB N:ILE163 4.8 44.0 1.0
N N:LYS164 4.9 46.0 1.0
CG a:LEU34 5.0 48.7 1.0

Magnesium binding site 7 out of 7 in 5fge

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

b:69.5
occ:1.00
 O Z:VAL198 2.5 51.7 1.0
O Z:THR192 2.7 57.2 1.0
O Z:HIS195 3.1 49.5 1.0
O Z:ASP222 3.4 74.2 1.0
NH2 Z:ARG28 3.6 64.4 1.0
CG2 Z:THR192 3.7 63.0 1.0
C Z:THR192 3.7 60.9 1.0
C Z:VAL198 3.7 55.0 1.0
O Z:ILE196 4.1 53.4 1.0
CA Z:THR192 4.1 61.2 1.0
C Z:HIS195 4.2 50.5 1.0
OD1 Z:ASP222 4.3 74.1 1.0
CA Z:ILE196 4.3 50.9 1.0
C Z:ILE196 4.3 49.3 1.0
NH2 H:ARG19 4.4 61.7 1.0
C Z:ASP222 4.5 75.6 1.0
CB Z:THR192 4.5 61.8 1.0
CA Z:GLY199 4.5 57.1 1.0
N Z:VAL198 4.5 50.6 1.0
N Z:GLY199 4.5 56.5 1.0
CZ Z:ARG28 4.6 64.3 1.0
CA Z:VAL198 4.7 53.8 1.0
N Z:ILE196 4.7 49.0 1.0
NH1 Z:ARG28 4.8 67.5 1.0
O Z:LYS220 4.8 65.4 1.0
N Z:GLU193 4.9 60.6 1.0
OXT Z:ASP222 5.0 71.6 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 04:10:38 2024

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