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Magnesium in PDB 9aw3: Yeast 20S Proteasome Soaked with MA9 Crude Extract

Enzymatic activity of Yeast 20S Proteasome Soaked with MA9 Crude Extract

All present enzymatic activity of Yeast 20S Proteasome Soaked with MA9 Crude Extract:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome Soaked with MA9 Crude Extract, PDB code: 9aw3 was solved by R.Meneghello, J.K.Rustiguel, A.Z.N.Fernandes, D.B.B.Trivella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.84 / 3.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 131.964, 301.458, 142.649, 90, 111.98, 90
R / Rfree (%) 21.5 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome Soaked with MA9 Crude Extract (pdb code 9aw3). 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 Soaked with MA9 Crude Extract, PDB code: 9aw3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 9aw3

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Magnesium binding site 1 out of 7 in the Yeast 20S Proteasome Soaked with MA9 Crude Extract


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 Soaked with MA9 Crude Extract within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:113.8
occ:1.00
 OXT Z:ASP222 1.9 111.6 1.0
O H:ASP166 1.9 97.7 1.0
C H:ASP166 2.6 99.3 1.0
O H:ILE163 2.7 91.7 1.0
C Z:ASP222 3.1 118.2 1.0
N H:LEU167 3.2 94.3 1.0
CA H:LEU167 3.2 101.4 1.0
O H:SER169 3.4 105.3 1.0
N H:ASP166 3.5 97.5 1.0
O H:TRP164 3.7 84.7 1.0
CA H:ASP166 3.7 102.5 1.0
C H:ILE163 3.8 92.0 1.0
O Z:ASP222 3.8 116.8 1.0
C H:TRP164 3.9 97.5 1.0
C H:LEU167 4.0 101.7 1.0
CD2 H:LEU167 4.1 84.2 1.0
CA Z:ASP222 4.2 118.4 1.0
C H:ASN165 4.2 88.5 1.0
O H:LEU167 4.4 97.8 1.0
CB H:LEU167 4.4 106.5 1.0
N H:ASN165 4.4 90.2 1.0
CA H:TRP164 4.4 108.4 1.0
N H:TRP164 4.5 104.5 1.0
O H:GLY162 4.6 80.4 1.0
CG H:LEU167 4.6 76.4 1.0
C H:SER169 4.6 96.0 1.0
NH1 H:ARG19 4.7 93.8 1.0
CB H:ASP166 4.8 108.6 1.0
CA H:ILE163 4.8 90.6 1.0
N H:GLY168 4.8 104.8 1.0
CD1 Z:ILE35 4.8 92.4 1.0
CA H:ASN165 4.8 82.9 1.0
O H:ASN165 4.9 105.5 1.0
O Z:ARG221 4.9 105.0 1.0
N H:SER169 4.9 95.1 1.0
CB Z:ASP222 4.9 117.4 1.0

Magnesium binding site 2 out of 7 in 9aw3

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Magnesium binding site 2 out of 7 in the Yeast 20S Proteasome Soaked with MA9 Crude Extract


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 Soaked with MA9 Crude Extract within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:87.4
occ:1.00
 OXT I:ASP204 2.8 128.0 1.0
O I:SER180 2.9 112.8 1.0
O I:ALA174 3.0 94.8 1.0
CA I:GLY181 3.7 103.3 1.0
O I:ASP177 3.8 73.9 1.0
C I:ALA174 3.8 103.5 1.0
C I:SER180 3.8 90.8 1.0
C I:ASP204 4.0 137.7 1.0
OD1 I:ASP175 4.0 105.9 1.0
CA I:ASP175 4.0 117.6 1.0
N I:GLY181 4.2 85.9 1.0
N I:ASP175 4.3 113.0 1.0
CE I:MET201 4.4 111.0 1.0
OD1 I:ASP204 4.4 123.2 1.0
O I:ASP204 4.4 144.1 1.0
NH2 Y:ARG19 4.5 107.8 1.0
CG I:ARG202 4.6 119.5 1.0
CB I:ALA174 4.8 86.4 1.0
C I:ASP175 4.8 113.7 1.0
O I:ARG202 4.8 105.9 1.0
CD I:ARG202 4.9 120.7 1.0
N I:TRP182 4.9 99.2 1.0
CA I:ALA174 4.9 97.4 1.0
C I:GLY181 4.9 106.4 1.0
N I:ASP204 4.9 114.4 1.0
CG I:ASP175 4.9 121.3 1.0

Magnesium binding site 3 out of 7 in 9aw3

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Magnesium binding site 3 out of 7 in the Yeast 20S Proteasome Soaked with MA9 Crude Extract


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 Soaked with MA9 Crude Extract within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:62.3
occ:1.00
 O L:VAL198 2.7 105.2 1.0
O L:THR192 2.8 89.1 1.0
O L:HIS195 2.9 71.3 1.0
O L:ASP222 3.0 110.5 1.0
NH1 L:ARG28 3.5 108.8 1.0
OD1 L:ASP222 3.6 136.4 1.0
CG2 L:THR192 3.7 85.5 1.0
O L:ILE196 3.8 95.4 1.0
C L:THR192 3.8 90.4 1.0
CA L:ILE196 3.9 70.6 1.0
C L:HIS195 3.9 83.1 1.0
C L:VAL198 3.9 88.8 1.0
C L:ILE196 4.0 88.9 1.0
CA L:THR192 4.1 84.7 1.0
C L:ASP222 4.2 116.8 1.0
NH1 V:ARG19 4.3 95.7 1.0
N L:ILE196 4.4 80.4 1.0
CG L:ASP222 4.4 124.2 1.0
CZ L:ARG28 4.5 106.3 1.0
CB L:THR192 4.6 86.4 1.0
CA L:GLY199 4.6 92.4 1.0
N L:VAL198 4.7 79.8 1.0
NH2 L:ARG28 4.7 104.2 1.0
O L:LYS220 4.7 93.7 1.0
N L:GLY199 4.8 87.3 1.0
CA L:VAL198 4.9 77.3 1.0
OD2 L:ASP222 5.0 118.5 1.0
OXT L:ASP222 5.0 110.5 1.0
N L:GLN197 5.0 97.8 1.0

Magnesium binding site 4 out of 7 in 9aw3

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Magnesium binding site 4 out of 7 in the Yeast 20S Proteasome Soaked with MA9 Crude Extract


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 Soaked with MA9 Crude Extract within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:100.9
occ:1.00
 OXT L:ASP222 2.1 110.5 1.0
O V:ASP166 2.1 81.5 1.0
O V:ILE163 2.2 105.2 1.0
C V:ASP166 2.9 75.4 1.0
C L:ASP222 3.2 116.8 1.0
O V:TRP164 3.3 107.2 1.0
O V:SER169 3.3 92.7 1.0
C V:ILE163 3.3 98.3 1.0
C V:TRP164 3.5 92.7 1.0
N V:ASP166 3.5 74.5 1.0
N V:LEU167 3.7 84.0 1.0
CA V:LEU167 3.8 92.1 1.0
CA V:ASP166 3.8 74.5 1.0
CA L:ASP222 3.9 113.8 1.0
CA V:TRP164 3.9 92.2 1.0
NH2 V:ARG19 4.0 115.7 1.0
N V:TRP164 4.0 96.4 1.0
N V:ASN165 4.0 84.4 1.0
O L:ASP222 4.1 110.5 1.0
C V:ASN165 4.2 77.2 1.0
O L:ARG221 4.2 115.0 1.0
CA V:ILE163 4.4 85.6 1.0
O V:GLY162 4.4 96.7 1.0
C V:SER169 4.5 94.3 1.0
C V:LEU167 4.5 84.2 1.0
CA V:ASN165 4.6 74.1 1.0
CD2 V:LEU167 4.6 71.3 1.0
CB L:ASP222 4.8 111.2 1.0
CD1 L:ILE35 4.8 88.0 1.0
O V:LEU167 4.9 96.0 1.0
CB V:ASP166 4.9 94.4 1.0
N L:ASP222 5.0 121.3 1.0
O V:ASN165 5.0 82.9 1.0

Magnesium binding site 5 out of 7 in 9aw3

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Magnesium binding site 5 out of 7 in the Yeast 20S Proteasome Soaked with MA9 Crude Extract


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 Soaked with MA9 Crude Extract within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:72.8
occ:1.00
 O W:SER180 2.6 115.9 1.0
O W:ASP177 2.8 76.7 1.0
OXT W:ASP204 2.9 112.3 1.0
O W:ALA174 3.6 77.4 1.0
C W:SER180 3.8 102.2 1.0
NH2 K:ARG19 3.8 106.4 1.0
C W:ASP204 3.9 112.1 1.0
O W:ALA178 4.0 95.1 1.0
O W:ASP204 4.0 108.2 1.0
C W:ASP177 4.0 77.4 1.0
C W:ALA178 4.2 89.4 1.0
CA W:ALA178 4.3 69.4 1.0
NH1 K:ARG19 4.3 100.7 1.0
CZ K:ARG19 4.4 107.5 1.0
N W:SER180 4.5 99.1 1.0
CA W:GLY181 4.5 98.7 1.0
N W:GLY181 4.6 92.4 1.0
N W:ALA178 4.6 63.4 1.0
C W:ALA174 4.7 91.2 1.0
CA W:SER180 4.7 91.2 1.0
OD1 W:ASP204 4.9 90.5 1.0

Magnesium binding site 6 out of 7 in 9aw3

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Magnesium binding site 6 out of 7 in the Yeast 20S Proteasome Soaked with MA9 Crude Extract


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 Soaked with MA9 Crude Extract within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:114.2
occ:1.00
 O Y:ALA165 2.1 102.2 1.0
O Y:ASP168 2.1 100.6 1.0
O I:ASP204 2.5 144.1 1.0
O Y:SER171 2.7 104.2 1.0
CB I:ASP204 3.1 111.2 1.0
NH1 Y:ARG19 3.2 112.5 1.0
CA I:ASP204 3.2 114.8 1.0
C I:ASP204 3.2 137.7 1.0
C Y:ALA165 3.3 98.2 1.0
C Y:ASP168 3.3 99.2 1.0
CA Y:ALA169 3.7 96.2 1.0
C Y:SER171 3.9 95.1 1.0
N Y:ALA169 3.9 101.0 1.0
CA Y:ALA165 4.0 84.4 1.0
C Y:ALA169 4.0 92.4 1.0
O Y:HIS166 4.0 94.8 1.0
O Y:ALA169 4.1 97.0 1.0
CZ Y:ARG19 4.2 116.6 1.0
N Y:HIS166 4.3 101.7 1.0
C Y:HIS166 4.3 97.0 1.0
OXT I:ASP204 4.4 128.0 1.0
CG I:ASP204 4.4 118.7 1.0
CA Y:ASP168 4.5 100.3 1.0
CA Y:HIS166 4.5 96.5 1.0
N Y:ASP168 4.5 110.0 1.0
N Y:SER171 4.6 101.5 1.0
N I:ASP204 4.6 114.4 1.0
CB Y:ALA165 4.7 61.8 1.0
NH2 Y:ARG19 4.7 107.8 1.0
O Y:ALA164 4.7 98.7 1.0
N Y:TYR170 4.7 101.7 1.0
CA Y:GLY172 4.8 103.6 1.0
CA Y:SER171 4.8 92.9 1.0
N Y:GLY172 4.8 90.9 1.0
C Y:ARG167 4.9 110.1 1.0
OD2 I:ASP204 4.9 112.0 1.0
O I:GLN203 5.0 105.7 1.0

Magnesium binding site 7 out of 7 in 9aw3

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Magnesium binding site 7 out of 7 in the Yeast 20S Proteasome Soaked with MA9 Crude Extract


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 Soaked with MA9 Crude Extract within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:68.5
occ:1.00
 O Z:THR192 2.9 103.7 1.0
O Z:VAL198 2.9 110.0 1.0
O Z:HIS195 3.0 85.6 1.0
O Z:ASP222 3.3 116.8 1.0
NH1 Z:ARG28 3.4 110.8 1.0
OD1 Z:ASP222 3.5 125.2 1.0
O Z:ILE196 3.8 102.6 1.0
CG2 Z:THR192 3.9 98.3 1.0
C Z:THR192 3.9 103.3 1.0
CA Z:ILE196 3.9 86.7 1.0
NH2 H:ARG19 4.0 101.3 1.0
C Z:HIS195 4.1 84.0 1.0
C Z:ILE196 4.1 101.4 1.0
C Z:VAL198 4.1 96.0 1.0
CA Z:THR192 4.2 98.2 1.0
CG Z:ASP222 4.3 129.0 1.0
NH1 H:ARG19 4.3 93.8 1.0
C Z:ASP222 4.4 118.2 1.0
CZ Z:ARG28 4.5 106.3 1.0
N Z:ILE196 4.5 72.1 1.0
CZ H:ARG19 4.6 103.0 1.0
NH2 Z:ARG28 4.6 108.1 1.0
CB Z:THR192 4.7 103.1 1.0
OD2 Z:ASP222 4.7 137.6 1.0
CA Z:GLY199 4.7 98.6 1.0
N Z:VAL198 4.8 77.4 1.0
O Z:LYS220 4.9 99.4 1.0
N Z:GLY199 4.9 92.6 1.0

Reference:

R.Meneghello, J.K.Rustiguel, E.A.Araujo, R.Felicio, A.Z.N.Fernandes, E.L.F.Ferreira, J.R.Gubiani, A.A.S.Takeda, A.A.Souza, C.C.L.Silva, A.F.Bertonha, D.M.Trindade, T.M.Cunha, A.C.Cardoso, A.Dessen, R.G.S.Berlinck, Z.F.Z.Nascimento, D.B.B.Trivella. High-Throughput Protein Crystallography to Empower Natural Product-Based Drug Discovery To Be Published.
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