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Magnesium in PDB 6h39: Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5

Enzymatic activity of Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5

All present enzymatic activity of Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5, PDB code: 6h39 was solved by M.Groll, F.K.Hansen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 137.140, 300.780, 145.080, 90.00, 113.48, 90.00
R / Rfree (%) 18.7 / 21.7

Other elements in 6h39:

The structure of Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 (pdb code 6h39). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5, PDB code: 6h39:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6h39

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Magnesium binding site 1 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:76.1
occ:1.00
 O G:MET125 2.3 54.5 1.0
O G:ARG122 2.6 49.0 1.0
OG1 G:THR8 2.7 48.0 1.0
O G:TYR119 3.0 45.9 1.0
O G:ALA123 3.0 54.6 1.0
CG2 G:THR8 3.3 49.4 1.0
C G:MET125 3.5 53.4 1.0
C G:ALA123 3.5 53.8 1.0
CB G:THR8 3.5 48.7 1.0
CA G:ALA123 3.6 50.8 1.0
C G:ARG122 3.7 49.5 1.0
N G:THR8 4.1 53.4 1.0
N G:ALA123 4.1 48.1 1.0
C G:TYR119 4.2 45.3 1.0
N G:MET125 4.2 51.4 1.0
N G:ARG126 4.2 49.3 1.0
CA G:ARG126 4.3 48.5 1.0
O G:HOH433 4.3 75.5 1.0
CA G:THR8 4.4 51.1 1.0
CA G:MET125 4.4 56.8 1.0
N G:TYR124 4.5 55.6 1.0
CD G:PRO127 4.7 47.4 1.0
C G:TYR124 4.9 52.1 1.0
CB G:ALA123 4.9 50.1 1.0
C G:ARG126 4.9 49.0 1.0
CA G:TYR119 4.9 42.3 1.0
CA G:ARG122 5.0 55.4 1.0

Magnesium binding site 2 out of 10 in 6h39

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Magnesium binding site 2 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:89.5
occ:1.00
 O I:SER180 2.7 58.4 1.0
O I:ASP177 2.8 55.2 1.0
O I:ALA174 2.9 56.1 1.0
OXT I:ASP204 3.3 75.6 1.0
C I:SER180 3.9 56.2 1.0
C I:ALA174 3.9 59.0 1.0
C I:ASP177 4.0 54.3 1.0
CA I:ASP175 4.1 59.9 1.0
C I:ASP204 4.3 76.1 1.0
O I:ASP204 4.4 78.5 1.0
N I:ASP175 4.4 58.6 1.0
NH2 Y:ARG19 4.4 71.9 1.0
CA I:GLY181 4.5 57.3 1.0
C I:ASP175 4.5 58.6 1.0
O I:ALA178 4.6 57.1 1.0
OD1 I:ASP175 4.6 64.9 1.0
N I:GLY181 4.6 55.9 1.0
O I:ASP175 4.6 61.9 1.0
N I:ASP177 4.8 52.3 1.0
CA I:ALA178 4.8 52.7 1.0
C I:ALA178 4.8 54.7 1.0
NH1 Y:ARG19 4.8 72.9 1.0
N I:ALA178 4.8 52.6 1.0
N I:SER180 4.9 53.0 1.0
CA I:SER180 4.9 54.7 1.0
CA I:ASP177 5.0 54.1 1.0

Magnesium binding site 3 out of 10 in 6h39

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Magnesium binding site 3 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg802

b:69.3
occ:1.00
 O K:ASP168 2.2 50.7 1.0
O W:ASP204 2.3 66.6 1.0
O K:ALA165 2.4 50.0 1.0
O K:SER171 2.9 52.9 1.0
C W:ASP204 3.1 67.0 1.0
C K:ASP168 3.3 48.8 1.0
C K:ALA165 3.6 54.6 1.0
CA W:ASP204 3.6 65.5 1.0
CA K:ALA169 3.6 52.6 1.0
NH1 K:ARG19 3.7 70.0 1.0
O K:HIS166 3.8 51.1 1.0
O K:ALA169 3.8 50.3 1.0
N K:ALA169 3.8 47.8 1.0
C K:ALA169 3.8 54.3 1.0
CB W:ASP204 4.0 65.1 1.0
C K:SER171 4.0 51.3 1.0
OXT W:ASP204 4.1 68.4 1.0
C K:HIS166 4.2 52.9 1.0
N K:ASP168 4.4 53.6 1.0
N K:SER171 4.4 50.8 1.0
O W:HOH312 4.4 78.0 1.0
CA K:ASP168 4.5 51.1 1.0
CA K:ALA165 4.5 54.8 1.0
N K:HIS166 4.5 52.0 1.0
CZ K:ARG19 4.6 67.3 1.0
CA K:HIS166 4.6 53.0 1.0
O K:ALA164 4.7 53.9 1.0
N K:TYR170 4.7 53.2 1.0
C K:ARG167 4.7 54.5 1.0
CA K:SER171 4.8 50.1 1.0
N K:ARG167 4.9 53.0 1.0
NH2 K:ARG19 4.9 70.5 1.0
CB K:ALA169 5.0 52.4 1.0
N W:ASP204 5.0 65.8 1.0

Magnesium binding site 4 out of 10 in 6h39

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Magnesium binding site 4 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg803

b:0.2
occ:1.00
 OG1 K:THR21 2.4 60.1 1.0
O24 K:FGY801 3.3 55.1 1.0
O K:TYR170 3.4 52.0 1.0
CB K:THR21 3.5 55.6 1.0
CG2 K:THR21 3.6 57.2 1.0
N K:THR21 3.7 51.0 1.0
C8 K:MES804 3.7 96.5 1.0
C15 K:FGY801 3.8 53.7 1.0
CB K:TYR170 3.9 50.5 1.0
C25 K:FGY801 3.9 54.5 1.0
N K:THR1 4.0 35.7 1.0
CA K:THR21 4.1 51.8 1.0
C K:TYR170 4.3 50.3 1.0
N16 K:FGY801 4.4 54.5 1.0
O K:ARG19 4.4 46.8 1.0
CA K:TYR170 4.5 50.6 1.0
C14 K:FGY801 4.5 54.3 1.0
OG1 K:THR1 4.5 40.3 1.0
O2S K:MES804 4.5 79.4 1.0
C5 K:MES804 4.5 97.0 1.0
C K:ALA20 4.5 50.1 1.0
C17 K:FGY801 4.6 53.7 1.0
N4 K:MES804 4.7 97.0 1.0
CG K:TYR170 4.7 51.0 1.0
O K:THR21 4.7 52.9 1.0
CA K:ALA20 4.7 50.9 1.0
S K:MES804 4.8 91.8 1.0
CD1 K:TYR170 4.8 50.9 1.0
C7 K:MES804 4.8 98.2 1.0
C K:THR21 4.8 50.7 1.0
C6 K:MES804 5.0 97.1 1.0

Magnesium binding site 5 out of 10 in 6h39

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Magnesium binding site 5 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:52.0
occ:1.00
 O N:ILE163 2.5 48.7 1.0
O N:SER169 2.6 56.8 1.0
O N:ASP166 2.9 52.5 1.0
NH1 N:ARG19 3.6 57.0 1.0
C N:ILE163 3.7 54.3 1.0
CD1 a:LEU34 3.7 53.2 1.0
C N:SER169 3.8 53.0 1.0
C N:ASP166 3.9 51.3 1.0
CG2 N:ILE163 4.0 52.5 1.0
CZ N:ARG19 4.2 54.0 1.0
CA N:GLY167 4.2 50.1 1.0
CA N:ILE163 4.4 53.0 1.0
O N:GLY167 4.4 51.3 1.0
NH2 N:ARG19 4.4 52.8 1.0
CA N:GLY170 4.4 53.9 1.0
N N:GLY167 4.5 49.5 1.0
C N:GLY167 4.5 50.4 1.0
N N:GLY170 4.6 54.6 1.0
N N:LYS164 4.7 54.9 1.0
CB N:ILE163 4.8 52.4 1.0
N N:SER169 4.8 49.6 1.0
CA N:SER169 4.8 49.0 1.0
O N:LYS164 4.9 56.5 1.0
C N:LYS164 4.9 56.8 1.0
CA N:LYS164 4.9 55.9 1.0
CG a:LEU34 5.0 55.9 1.0

Magnesium binding site 6 out of 10 in 6h39

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Magnesium binding site 6 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:89.0
occ:1.00
 OXT L:ASP222 2.1 80.1 1.0
O V:ILE163 2.2 54.4 1.0
O V:ASP166 2.2 53.1 1.0
O V:SER169 2.9 62.5 1.0
C L:ASP222 3.0 77.7 1.0
C V:ASP166 3.2 57.4 1.0
C V:ILE163 3.3 63.3 1.0
O V:TRP164 3.6 62.0 1.0
CA L:ASP222 3.7 73.2 1.0
C V:TRP164 3.8 62.2 1.0
O L:ASP222 3.8 82.5 1.0
N V:LEU167 3.9 58.1 1.0
CA V:LEU167 3.9 58.7 1.0
N V:ASP166 4.0 57.8 1.0
O V:GLY162 4.0 56.4 1.0
C V:SER169 4.1 56.7 1.0
N V:TRP164 4.1 61.9 1.0
CA V:TRP164 4.2 62.5 1.0
CA V:ASP166 4.2 57.4 1.0
NH1 V:ARG19 4.2 72.1 1.0
CA V:ILE163 4.3 63.2 1.0
N V:ASN165 4.3 62.4 1.0
CB L:ASP222 4.4 73.2 1.0
C V:LEU167 4.5 57.4 1.0
C V:ASN165 4.5 59.5 1.0
O V:LEU167 4.7 59.6 1.0
O L:ARG221 4.7 63.8 1.0
CD2 V:LEU167 4.8 58.7 1.0
N V:SER169 4.8 54.4 1.0
CA V:GLY170 4.9 59.4 1.0
N L:ASP222 4.9 73.8 1.0
CA V:ASN165 4.9 60.9 1.0
CZ V:ARG19 4.9 68.2 1.0
C V:GLY162 4.9 59.4 1.0
N V:GLY170 5.0 57.1 1.0

Magnesium binding site 7 out of 10 in 6h39

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Magnesium binding site 7 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg201

b:56.1
occ:1.00
 OE1 X:GLN118 3.7 50.7 1.0
O X:THR124 3.7 54.1 1.0
CB X:ASP120 3.8 46.6 1.0
CG X:ASP120 4.0 49.8 1.0
N X:ASP120 4.0 41.3 1.0
OD2 X:ASP120 4.1 54.5 1.0
CB X:THR124 4.2 48.1 1.0
CG X:GLN118 4.3 45.9 1.0
CG2 X:THR124 4.3 49.1 1.0
CD X:GLN118 4.3 47.5 1.0
CE1 X:HIS133 4.4 48.5 1.0
O X:GLN118 4.5 44.6 1.0
CA X:ASP120 4.5 43.9 1.0
C X:THR124 4.6 50.7 1.0
OD1 X:ASP120 4.7 52.5 1.0
C X:ILE119 4.7 43.1 1.0
CG1 W:VAL35 4.7 54.2 1.0
C X:GLN118 4.9 44.9 1.0
CA X:ILE119 5.0 42.5 1.0
CD2 W:LEU28 5.0 54.6 1.0

Magnesium binding site 8 out of 10 in 6h39

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Magnesium binding site 8 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg802

b:70.5
occ:1.00
 O Y:ASP168 2.2 51.6 1.0
O I:ASP204 2.3 78.5 1.0
O Y:ALA165 2.4 50.8 1.0
O Y:SER171 2.6 59.8 1.0
O Y:HOH916 3.2 76.2 1.0
C I:ASP204 3.2 76.1 1.0
C Y:ASP168 3.3 49.7 1.0
C Y:ALA165 3.5 53.6 1.0
NH1 Y:ARG19 3.6 72.9 1.0
CA Y:ALA169 3.6 50.4 1.0
CA I:ASP204 3.7 73.7 1.0
O Y:ALA169 3.7 51.7 1.0
C Y:ALA169 3.8 51.9 1.0
C Y:SER171 3.8 53.2 1.0
N Y:ALA169 3.9 50.0 1.0
CB I:ASP204 4.0 73.5 1.0
O Y:HIS166 4.0 53.0 1.0
N Y:SER171 4.2 50.0 1.0
OXT I:ASP204 4.2 75.6 1.0
C Y:HIS166 4.3 54.4 1.0
CA Y:ALA165 4.4 53.0 1.0
CZ Y:ARG19 4.4 69.0 1.0
CA Y:ASP168 4.4 50.8 1.0
N Y:ASP168 4.5 51.8 1.0
N Y:HIS166 4.5 53.8 1.0
CA Y:SER171 4.6 48.7 1.0
N Y:TYR170 4.6 51.9 1.0
O Y:ALA164 4.6 48.0 1.0
CA Y:HIS166 4.7 53.4 1.0
N Y:GLY172 4.8 57.0 1.0
C Y:ARG167 4.8 53.8 1.0
NH2 Y:ARG19 4.9 71.9 1.0
CA Y:GLY172 4.9 57.5 1.0
N Y:ARG167 5.0 53.3 1.0

Magnesium binding site 9 out of 10 in 6h39

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Magnesium binding site 9 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


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 in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg803

b:96.9
occ:1.00
 OG1 Y:THR21 2.5 54.8 1.0
O Y:GLY23 2.9 61.6 1.0
O1 Y:MES804 3.1 96.2 1.0
N Y:GLY23 3.4 53.5 1.0
CB Y:THR21 3.4 53.9 1.0
C6 Y:MES804 3.4 96.5 1.0
C5 Y:MES804 3.5 95.3 1.0
C Y:THR21 3.7 52.1 1.0
C Y:GLY23 3.8 56.1 1.0
O Y:THR21 3.8 52.7 1.0
CA Y:GLY23 3.8 54.5 1.0
C25 Y:FGY801 4.0 56.6 1.0
N Y:ALA22 4.1 51.7 1.0
C2 Y:MES804 4.1 96.1 1.0
C3 Y:MES804 4.1 96.1 1.0
C Y:ALA22 4.2 52.8 1.0
CA Y:THR21 4.2 51.3 1.0
CD1 Y:TYR170 4.3 51.6 1.0
CA Y:ALA22 4.3 51.9 1.0
N4 Y:MES804 4.4 95.2 1.0
CE1 Y:TYR170 4.4 52.8 1.0
O Y:HOH925 4.6 73.4 1.0
CG2 Y:THR21 4.6 53.7 1.0
CG Y:TYR170 4.9 51.5 1.0

Magnesium binding site 10 out of 10 in 6h39

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Magnesium binding site 10 out of 10 in the Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Yeast 20S Proteasome in Complex with the Peptidic Non-Covalent Binding Inhibitor Rts-V5 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:73.1
occ:1.00
 O Z:VAL198 2.5 61.0 1.0
O Z:THR192 2.8 64.0 1.0
O Z:HIS195 3.0 50.2 1.0
NH2 Z:ARG28 3.4 70.6 1.0
O Z:ASP222 3.5 75.9 1.0
C Z:VAL198 3.7 57.5 1.0
CG2 Z:THR192 3.8 65.1 1.0
O Z:ILE196 3.9 59.1 1.0
C Z:THR192 3.9 65.4 1.0
C Z:HIS195 4.0 52.7 1.0
CA Z:ILE196 4.1 53.7 1.0
C Z:ILE196 4.1 53.9 1.0
CA Z:THR192 4.2 63.9 1.0
NH2 H:ARG19 4.3 68.6 1.0
OD1 Z:ASP222 4.3 71.9 1.0
CZ Z:ARG28 4.4 68.3 1.0
N Z:VAL198 4.4 53.5 1.0
N Z:ILE196 4.5 52.3 1.0
C Z:ASP222 4.5 78.5 1.0
N Z:GLY199 4.6 58.6 1.0
CA Z:GLY199 4.6 62.0 1.0
CB Z:THR192 4.6 63.4 1.0
CA Z:VAL198 4.6 55.0 1.0
NH1 Z:ARG28 4.7 70.5 1.0
O Z:LYS220 5.0 66.0 1.0
OXT Z:ASP222 5.0 77.1 1.0

Reference:

S.Bhatia, V.Krieger, M.Groll, J.D.Osko, N.ReßIng, H.Ahlert, A.Borkhardt, T.Kurz, D.W.Christianson, J.Hauer, F.K.Hansen. Discovery of the First-in-Class Dual Histone Deacetylase-Proteasome Inhibitor. J. Med. Chem. V. 61 10299 2018.
ISSN: ISSN 1520-4804
PubMed: 30365892
DOI: 10.1021/ACS.JMEDCHEM.8B01487
Page generated: Tue Oct 1 01:30:13 2024

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