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Magnesium in PDB 5fgf: Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple Mutant in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple Mutant in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple Mutant in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple Mutant in Complex with Carfilzomib, PDB code: 5fgf 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 (°) 136.080, 300.970, 144.890, 90.00, 113.11, 90.00
R / Rfree (%) 19.2 / 21.4

Other elements in 5fgf:

The structure of Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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)A-T1A-K81R Triple Mutant in Complex with Carfilzomib (pdb code 5fgf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple Mutant in Complex with Carfilzomib, PDB code: 5fgf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5fgf

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:52.6
occ:1.00
 O G:MET125 2.2 49.4 1.0
O G:ARG122 2.4 42.3 1.0
O G:TYR119 2.6 40.7 1.0
OG1 G:THR8 2.6 43.0 1.0
CG2 G:THR8 3.3 43.7 1.0
O G:ALA123 3.4 51.0 1.0
C G:MET125 3.4 47.1 1.0
CB G:THR8 3.5 43.0 1.0
C G:ARG122 3.5 44.5 1.0
C G:ALA123 3.7 47.3 1.0
CA G:ALA123 3.7 45.2 1.0
C G:TYR119 3.8 39.1 1.0
N G:ALA123 4.1 44.7 1.0
CA G:ARG126 4.2 41.5 1.0
N G:ARG126 4.2 43.6 1.0
N G:MET125 4.2 48.4 1.0
N G:THR8 4.3 44.6 1.0
CA G:MET125 4.4 50.0 1.0
CA G:TYR119 4.5 37.6 1.0
CA G:THR8 4.5 44.3 1.0
CD G:PRO127 4.6 38.1 1.0
N G:TYR124 4.6 47.9 1.0
CA G:ARG122 4.8 48.6 1.0
N G:THR120 4.8 37.9 1.0
C G:ARG126 4.8 40.1 1.0
N G:ARG122 4.8 45.7 1.0
CA G:THR120 4.9 38.9 1.0
CB G:MET125 4.9 55.2 1.0
C G:THR120 5.0 40.3 1.0
N G:PRO127 5.0 38.7 1.0
C G:TYR124 5.0 47.6 1.0

Magnesium binding site 2 out of 9 in 5fgf

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:65.3
occ:1.00
 O I:ASP177 2.5 45.5 1.0
O I:SER180 2.5 48.5 1.0
O I:ALA174 2.9 46.5 1.0
OXT I:ASP204 3.6 63.0 1.0
C I:ASP177 3.7 44.9 1.0
C I:SER180 3.8 47.1 1.0
O I:ALA178 4.0 52.3 1.0
C I:ALA174 4.0 48.0 1.0
C I:ALA178 4.2 47.8 1.0
CA I:ALA178 4.2 45.7 1.0
CA I:ASP175 4.3 49.5 1.0
NH1 Y:ARG19 4.3 57.6 1.0
N I:ALA178 4.4 44.6 1.0
C I:ASP204 4.5 63.3 1.0
N I:SER180 4.5 44.5 1.0
O I:ASP204 4.6 61.5 1.0
CA I:GLY181 4.6 46.7 1.0
N I:GLY181 4.6 46.5 1.0
N I:ASP175 4.6 48.7 1.0
C I:ASP175 4.7 50.7 1.0
N I:ASP177 4.7 44.2 1.0
O I:ASP175 4.7 57.1 1.0
CA I:SER180 4.7 46.0 1.0
CA I:ASP177 4.8 44.5 1.0
NH2 Y:ARG19 4.8 57.7 1.0
CZ Y:ARG19 5.0 56.4 1.0
OD1 I:ASP175 5.0 53.4 1.0

Magnesium binding site 3 out of 9 in 5fgf

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:65.7
occ:1.00
 O I:ASP204 2.2 61.5 1.0
O Y:ASP168 2.2 46.1 1.0
O Y:ALA165 2.4 46.8 1.0
O Y:SER171 2.5 46.4 1.0
C I:ASP204 3.1 63.3 1.0
C Y:ASP168 3.3 44.3 1.0
C Y:ALA165 3.5 45.9 1.0
O Y:ALA169 3.5 47.7 1.0
CA Y:ALA169 3.5 46.0 1.0
C Y:ALA169 3.6 47.4 1.0
C Y:SER171 3.7 46.2 1.0
NH1 Y:ARG19 3.7 57.6 1.0
CA I:ASP204 3.8 61.4 1.0
N Y:ALA169 3.8 44.0 1.0
OXT I:ASP204 4.1 63.0 1.0
CB I:ASP204 4.1 61.2 1.0
N Y:SER171 4.1 44.5 1.0
CA Y:ALA165 4.2 45.4 1.0
O Y:HIS166 4.2 46.6 1.0
CZ Y:ARG19 4.4 56.4 1.0
CA Y:SER171 4.4 45.0 1.0
N Y:TYR170 4.5 46.8 1.0
CA Y:ASP168 4.5 44.3 1.0
C Y:HIS166 4.5 46.3 1.0
N Y:HIS166 4.6 46.0 1.0
N Y:ASP168 4.6 46.2 1.0
O Y:ALA164 4.6 44.6 1.0
N Y:GLY172 4.7 47.1 1.0
NH2 Y:ARG19 4.8 57.7 1.0
CA Y:GLY172 4.8 47.9 1.0
CA Y:HIS166 4.8 46.5 1.0
CB Y:ALA169 4.9 46.1 1.0
C Y:ARG167 5.0 48.4 1.0
CB Y:SER171 5.0 44.3 1.0

Magnesium binding site 4 out of 9 in 5fgf

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:56.4
occ:1.00
 O W:ASP204 2.2 61.9 1.0
O K:ASP168 2.2 48.9 1.0
O K:ALA165 2.3 44.8 1.0
O K:SER171 2.5 48.5 1.0
C W:ASP204 3.1 61.3 1.0
C K:ASP168 3.2 46.8 1.0
C K:ALA165 3.4 45.4 1.0
CA K:ALA169 3.6 47.8 1.0
CA W:ASP204 3.7 59.5 1.0
O K:ALA169 3.7 49.0 1.0
C K:SER171 3.7 46.5 1.0
C K:ALA169 3.7 49.3 1.0
N K:ALA169 3.8 46.3 1.0
NH1 K:ARG19 3.9 57.3 1.0
OXT W:ASP204 4.0 61.3 1.0
CB W:ASP204 4.0 58.9 1.0
O K:HIS166 4.1 49.0 1.0
CA K:ALA165 4.1 45.2 1.0
N K:SER171 4.2 45.7 1.0
C K:HIS166 4.4 47.3 1.0
CA K:ASP168 4.4 45.8 1.0
N K:HIS166 4.4 44.9 1.0
N K:ASP168 4.5 47.8 1.0
CA K:SER171 4.5 45.7 1.0
O K:ALA164 4.5 45.9 1.0
CZ K:ARG19 4.6 55.2 1.0
N K:TYR170 4.6 49.3 1.0
CA K:HIS166 4.7 46.5 1.0
N K:GLY172 4.7 47.3 1.0
C K:ARG167 4.8 48.8 1.0
CA K:GLY172 4.9 47.8 1.0
NH2 K:ARG19 4.9 57.0 1.0
CB K:SER171 5.0 46.4 1.0
N K:ARG167 5.0 46.5 1.0
CB K:ALA169 5.0 47.0 1.0
CB K:ALA165 5.0 45.4 1.0

Magnesium binding site 5 out of 9 in 5fgf

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:56.9
occ:1.00
 OXT L:ASP222 2.1 65.9 1.0
O V:ASP166 2.2 44.2 1.0
O V:ILE163 2.2 48.2 1.0
O V:SER169 2.4 48.5 1.0
C L:ASP222 3.1 68.5 1.0
C V:ASP166 3.2 45.3 1.0
C V:ILE163 3.3 49.0 1.0
C V:SER169 3.6 44.2 1.0
CA L:ASP222 3.7 67.9 1.0
O V:GLY162 3.8 47.0 1.0
CA V:LEU167 3.8 46.4 1.0
N V:LEU167 3.9 46.3 1.0
NH1 V:ARG19 4.0 55.9 1.0
N V:ASP166 4.0 45.0 1.0
O L:ASP222 4.1 68.0 1.0
CA V:ILE163 4.1 49.4 1.0
O V:TRP164 4.1 52.9 1.0
C V:TRP164 4.2 49.5 1.0
CA V:ASP166 4.2 45.4 1.0
N V:TRP164 4.2 48.9 1.0
CB L:ASP222 4.2 67.9 1.0
C V:LEU167 4.3 46.9 1.0
N V:SER169 4.3 42.7 1.0
CA V:TRP164 4.4 49.4 1.0
N V:GLY170 4.5 44.7 1.0
CA V:SER169 4.5 43.0 1.0
CA V:GLY170 4.5 47.0 1.0
O V:LEU167 4.5 46.6 1.0
CZ V:ARG19 4.6 52.7 1.0
N V:ASN165 4.6 48.7 1.0
NH2 V:ARG19 4.7 54.7 1.0
C V:GLY162 4.7 47.7 1.0
C V:ASN165 4.8 45.5 1.0
CB V:SER169 4.9 43.0 1.0
N V:ILE163 4.9 48.1 1.0
O L:ARG221 4.9 64.7 1.0
CD2 V:LEU167 5.0 45.2 1.0
N V:GLY168 5.0 45.6 1.0
N L:ASP222 5.0 64.9 1.0
CB V:ASP166 5.0 45.0 1.0

Magnesium binding site 6 out of 9 in 5fgf

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:54.1
occ:1.00
 O N:SER169 2.4 40.6 1.0
O N:ILE163 2.6 41.9 1.0
O N:ASP166 2.8 44.8 1.0
NH1 N:ARG19 3.5 46.2 1.0
C N:SER169 3.6 39.6 1.0
CD1 a:LEU34 3.7 45.4 1.0
C N:ILE163 3.7 42.6 1.0
CG2 N:ILE163 3.9 40.9 1.0
C N:ASP166 3.9 42.3 1.0
CZ N:ARG19 4.2 45.4 1.0
CA N:GLY167 4.2 41.9 1.0
CA N:GLY170 4.3 40.7 1.0
CA N:ILE163 4.4 41.5 1.0
O N:GLY167 4.4 40.9 1.0
NH2 N:ARG19 4.4 46.6 1.0
N N:GLY170 4.4 39.8 1.0
N N:GLY167 4.5 41.3 1.0
C N:GLY167 4.5 41.5 1.0
N N:SER169 4.6 38.2 1.0
CA N:SER169 4.7 37.4 1.0
CB N:ILE163 4.7 41.0 1.0
N N:LYS164 4.8 43.4 1.0

Magnesium binding site 7 out of 9 in 5fgf

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:63.3
occ:1.00
 O Z:HOH407 2.4 40.3 1.0
O Z:THR192 2.5 57.6 1.0
O Z:VAL198 2.6 46.8 1.0
O Z:HIS195 2.6 46.3 1.0
C Z:THR192 3.6 58.1 1.0
C Z:HIS195 3.6 46.9 1.0
O Z:ASP222 3.7 70.1 1.0
C Z:VAL198 3.8 50.8 1.0
CA Z:ILE196 3.8 47.3 1.0
NH2 Z:ARG28 3.8 62.5 1.0
O Z:ILE196 3.9 47.8 1.0
CG2 Z:THR192 4.0 57.6 1.0
CA Z:THR192 4.0 57.6 1.0
C Z:ILE196 4.0 45.6 1.0
N Z:ILE196 4.1 46.0 1.0
NH2 H:ARG19 4.3 61.4 1.0
N Z:VAL198 4.4 47.1 1.0
CA Z:VAL198 4.6 49.6 1.0
OD1 Z:ASP222 4.6 70.5 1.0
CB Z:THR192 4.6 57.2 1.0
N Z:HIS195 4.7 49.3 1.0
N Z:GLU193 4.8 57.5 1.0
N Z:GLY199 4.8 52.7 1.0
CA Z:HIS195 4.8 47.8 1.0
C Z:ASP222 4.8 71.2 1.0
N Z:GLN197 4.9 45.1 1.0
CA Z:GLY199 4.9 53.5 1.0
O Z:ALA191 4.9 57.3 1.0
CZ Z:ARG28 5.0 61.7 1.0
CB Z:VAL198 5.0 51.4 1.0
NH1 H:ARG19 5.0 55.4 1.0
CZ H:ARG19 5.0 55.7 1.0

Magnesium binding site 8 out of 9 in 5fgf

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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-H(-2)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg302

b:41.7
occ:1.00
 O Z:PRO127 2.5 42.2 1.0
O Z:LEU97 2.7 38.9 1.0
N Z:TYR105 3.1 39.3 1.0
C Z:LEU97 3.4 38.9 1.0
CA Z:LEU97 3.5 36.7 1.0
CD2 Z:TYR105 3.6 40.5 1.0
CA Z:PRO104 3.7 38.9 1.0
C Z:PRO127 3.7 41.2 1.0
CB Z:LEU97 3.7 35.7 1.0
CB Z:TYR105 3.8 38.9 1.0
CD2 Z:LEU97 3.8 35.6 1.0
C Z:PRO104 3.9 38.6 1.0
O Z:LYS100 3.9 45.1 1.0
CA Z:TYR105 4.0 39.0 1.0
CB Z:PRO104 4.0 39.5 1.0
CA Z:VAL128 4.0 42.1 1.0
CG Z:TYR105 4.1 40.6 1.0
O Z:TYR105 4.2 41.5 1.0
CB Z:LYS100 4.2 44.0 1.0
C Z:LYS100 4.3 44.7 1.0
N Z:VAL128 4.3 41.6 1.0
CG Z:LEU97 4.4 35.2 1.0
C Z:TYR105 4.6 41.0 1.0
N Z:TYR98 4.6 39.0 1.0
CE2 Z:TYR105 4.6 42.4 1.0
CG1 Z:VAL128 4.7 43.9 1.0
CA Z:LYS100 4.7 43.6 1.0
C Z:VAL128 4.7 41.7 1.0
CA Z:PRO127 4.8 40.6 1.0
N Z:LEU97 4.9 38.4 1.0
N Z:LYS100 4.9 42.5 1.0
N Z:PRO104 4.9 39.6 1.0
N Z:ARG101 5.0 44.7 1.0
CB Z:VAL128 5.0 43.3 1.0

Magnesium binding site 9 out of 9 in 5fgf

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple 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 9 of Yeast 20S Proteasome BETA5-H(-2)A-T1A-K81R Triple Mutant in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg202

b:42.2
occ:1.00
 O b:SER169 2.5 39.8 1.0
O b:ILE163 2.7 41.7 1.0
O b:ASP166 2.9 41.3 1.0
NH1 b:ARG19 3.6 47.4 1.0
CD1 M:LEU34 3.6 45.2 1.0
C b:SER169 3.8 40.6 1.0
C b:ILE163 3.8 41.7 1.0
C b:ASP166 3.9 41.6 1.0
CG2 b:ILE163 4.0 41.2 1.0
CA b:GLY167 4.2 42.1 1.0
CZ b:ARG19 4.2 46.3 1.0
O b:GLY167 4.4 43.1 1.0
NH2 b:ARG19 4.4 46.7 1.0
CA b:GLY170 4.4 42.7 1.0
CA b:ILE163 4.4 40.8 1.0
N b:GLY167 4.5 41.1 1.0
C b:GLY167 4.5 42.7 1.0
N b:GLY170 4.6 41.5 1.0
N b:SER169 4.7 41.5 1.0
CA b:SER169 4.8 40.0 1.0
CB b:ILE163 4.8 40.8 1.0
N b:LYS164 4.8 42.9 1.0
CG M:LEU34 4.9 46.0 1.0
O b:LYS164 5.0 46.8 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 04:11:09 2024

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