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Magnesium in PDB 9c97: Yeast 20S Proteasome Soaked with Bra-346 Fraction

Enzymatic activity of Yeast 20S Proteasome Soaked with Bra-346 Fraction

All present enzymatic activity of Yeast 20S Proteasome Soaked with Bra-346 Fraction:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome Soaked with Bra-346 Fraction, PDB code: 9c97 was solved by R.Meneghello, J.K.Rustiguel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.11 / 3.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 117.511, 299.917, 143.913, 90, 108.46, 90
R / Rfree (%) 20 / 25.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome Soaked with Bra-346 Fraction (pdb code 9c97). 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 Soaked with Bra-346 Fraction, PDB code: 9c97:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 9c97

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:47.4
occ:1.00
 O H:ASP166 1.9 39.0 1.0
O H:SER169 2.0 31.0 1.0
OXT Z:ASP222 2.1 48.6 1.0
O H:ILE163 2.7 44.0 1.0
NH1 H:ARG19 3.1 38.8 1.0
C H:ASP166 3.1 36.5 1.0
C H:SER169 3.2 29.7 1.0
C Z:ASP222 3.2 47.0 1.0
CA H:LEU167 3.7 27.9 1.0
C H:ILE163 3.7 33.9 1.0
N H:LEU167 3.9 26.5 1.0
C H:LEU167 3.9 27.2 1.0
CZ H:ARG19 3.9 42.2 1.0
N H:SER169 3.9 28.1 1.0
CA Z:ASP222 4.0 45.0 1.0
O Z:ASP222 4.1 45.0 1.0
O H:LEU167 4.1 26.6 1.0
N H:GLY170 4.2 36.9 1.0
CA H:SER169 4.2 26.0 1.0
O H:GLY162 4.2 31.5 1.0
CB Z:ASP222 4.2 33.6 1.0
CA H:GLY170 4.2 35.2 1.0
NH2 H:ARG19 4.2 51.9 1.0
CA H:ASP166 4.3 45.0 1.0
CA H:ILE163 4.3 30.4 1.0
N H:ASP166 4.3 49.9 1.0
N H:GLY168 4.5 25.0 1.0
N H:TRP164 4.7 32.7 1.0
CB H:SER169 4.8 29.4 1.0
NE H:ARG19 4.8 40.6 1.0
C H:TRP164 4.9 33.5 1.0
CB H:ASP166 4.9 31.5 1.0
C H:GLY168 4.9 25.2 1.0
CA H:TRP164 4.9 33.4 1.0
O H:TRP164 4.9 30.2 1.0

Magnesium binding site 2 out of 9 in 9c97

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:27.9
occ:1.00
 O I:ASP177 2.1 37.6 1.0
O I:ALA174 2.4 35.9 1.0
O I:SER180 2.7 39.3 1.0
C I:ASP177 3.3 33.6 1.0
C I:ALA174 3.6 31.3 1.0
OXT I:ASP204 3.7 34.1 1.0
C I:SER180 3.9 29.4 1.0
N I:ASP177 4.0 28.4 1.0
CA I:ASP175 4.1 36.5 1.0
N I:ALA178 4.2 27.6 1.0
C I:ASP175 4.2 40.2 1.0
CA I:ALA178 4.2 26.2 1.0
CA I:ASP177 4.2 26.0 1.0
O I:ALA178 4.2 25.1 1.0
N I:ASP175 4.3 27.6 1.0
C I:ALA178 4.3 30.2 1.0
O I:ASP175 4.4 42.1 1.0
N I:SER180 4.5 28.6 1.0
NH1 Y:ARG19 4.5 51.8 1.0
NH2 Y:ARG19 4.6 51.6 1.0
C I:ASP204 4.7 33.9 1.0
CA I:ALA174 4.7 30.0 1.0
CA I:SER180 4.7 28.3 1.0
N I:ARG176 4.7 30.3 1.0
O I:ASP204 4.8 37.9 1.0
CB I:ASP177 4.8 36.2 1.0
N I:GLY181 4.8 16.4 1.0
CA I:GLY181 4.9 25.6 1.0
CZ Y:ARG19 4.9 55.1 1.0

Magnesium binding site 3 out of 9 in 9c97

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:27.1
occ:1.00
 O K:ALA165 2.0 22.6 1.0
O W:ASP204 2.2 41.7 1.0
O K:ASP168 2.3 15.3 1.0
O K:SER171 2.5 24.4 1.0
C W:ASP204 3.0 44.4 1.0
C K:ALA165 3.2 18.7 1.0
CA W:ASP204 3.2 35.0 1.0
C K:ASP168 3.4 13.0 1.0
CB W:ASP204 3.6 24.8 1.0
NH1 K:ARG19 3.7 27.1 1.0
C K:SER171 3.7 21.1 1.0
O K:HIS166 3.8 17.9 1.0
CA K:ALA169 4.0 17.8 1.0
CA K:ALA165 4.0 19.2 1.0
C K:ALA169 4.1 18.7 1.0
OXT W:ASP204 4.1 45.9 1.0
O K:ALA169 4.1 12.4 1.0
N K:ALA169 4.1 11.7 1.0
C K:HIS166 4.2 16.2 1.0
N K:HIS166 4.2 15.6 1.0
N K:SER171 4.3 22.1 1.0
CA K:HIS166 4.4 14.8 1.0
CZ K:ARG19 4.4 34.4 1.0
N K:ASP168 4.5 22.2 1.0
CA K:ASP168 4.5 20.6 1.0
CA K:SER171 4.6 14.9 1.0
N W:ASP204 4.6 31.5 1.0
O K:ALA164 4.7 16.7 1.0
CB K:ALA165 4.7 11.6 1.0
N K:GLY172 4.7 22.5 1.0
CA K:GLY172 4.7 24.2 1.0
NH2 K:ARG19 4.8 42.5 1.0
CG W:ASP204 4.8 26.5 1.0
N K:TYR170 4.8 21.5 1.0
C K:ARG167 4.9 18.0 1.0
N K:ARG167 4.9 24.8 1.0
O W:GLN203 4.9 17.2 1.0
CB K:SER171 5.0 14.3 1.0

Magnesium binding site 4 out of 9 in 9c97

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:17.7
occ:1.00
 O L:VAL198 2.3 24.5 1.0
O L:THR192 2.9 33.0 1.0
O L:HIS195 3.0 21.3 1.0
CG2 L:THR192 3.3 26.0 1.0
O L:ASP222 3.3 39.8 1.0
OD1 L:ASP222 3.4 64.7 1.0
C L:VAL198 3.5 18.6 1.0
NH1 L:ARG28 3.5 39.9 1.0
C L:THR192 3.7 29.1 1.0
CA L:THR192 3.8 21.0 1.0
NH2 V:ARG19 4.1 36.7 1.0
CB L:THR192 4.1 18.0 1.0
C L:HIS195 4.2 23.0 1.0
CZ L:ARG28 4.3 24.0 1.0
N L:VAL198 4.3 22.6 1.0
CA L:GLY199 4.3 14.9 1.0
CA L:ILE196 4.4 21.3 1.0
N L:GLY199 4.4 12.7 1.0
CG L:ASP222 4.4 46.2 1.0
C L:ASP222 4.4 44.4 1.0
C L:ILE196 4.4 25.8 1.0
O L:ILE196 4.5 30.7 1.0
NH2 L:ARG28 4.5 22.0 1.0
CA L:VAL198 4.5 24.1 1.0
O L:LYS220 4.6 18.3 1.0
N L:ILE196 4.8 21.8 1.0
OG1 L:THR192 4.9 16.4 1.0
OD2 L:ASP222 5.0 46.8 1.0

Magnesium binding site 5 out of 9 in 9c97

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:10.3
occ:1.00
 O N:ILE163 2.2 24.7 1.0
O N:SER169 2.5 27.3 1.0
O N:ASP166 2.7 20.0 1.0
O N:HOH303 2.9 20.7 1.0
C N:ILE163 3.3 22.1 1.0
NH1 N:ARG19 3.6 27.4 1.0
CG2 N:ILE163 3.6 27.4 1.0
C N:SER169 3.7 31.1 1.0
CD1 a:LEU34 3.7 22.8 1.0
C N:ASP166 3.8 17.2 1.0
CA N:ILE163 3.9 22.2 1.0
CA N:GLY167 4.1 19.8 1.0
CZ N:ARG19 4.2 36.4 1.0
O N:GLY167 4.4 24.5 1.0
N N:LYS164 4.4 17.3 1.0
CB N:ILE163 4.4 18.9 1.0
N N:GLY167 4.4 16.1 1.0
C N:GLY167 4.4 16.9 1.0
NH2 N:ARG19 4.5 43.5 1.0
CA N:GLY170 4.5 20.1 1.0
N N:GLY170 4.6 24.6 1.0
N N:SER169 4.6 22.5 1.0
CA N:LYS164 4.7 20.6 1.0
CA N:SER169 4.7 23.2 1.0
C N:LYS164 4.7 24.2 1.0
O N:LYS164 4.7 20.4 1.0
CG a:LEU34 4.8 24.0 1.0
N N:ASP166 4.9 20.4 1.0
CA N:ASP166 4.9 17.4 1.0

Magnesium binding site 6 out of 9 in 9c97

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg301

b:40.3
occ:1.00
 OXT L:ASP222 2.0 36.4 1.0
O V:ASP166 2.1 31.1 1.0
O V:SER169 2.1 29.2 1.0
O V:ILE163 2.1 48.2 1.0
C L:ASP222 3.1 44.4 1.0
C V:ILE163 3.2 37.2 1.0
C V:ASP166 3.3 20.2 1.0
C V:SER169 3.3 29.6 1.0
CA L:ASP222 3.7 38.9 1.0
CA V:ILE163 3.9 26.5 1.0
O V:GLY162 3.9 28.6 1.0
CA V:LEU167 4.0 24.9 1.0
O L:ASP222 4.1 39.8 1.0
N V:LEU167 4.1 24.4 1.0
N V:TRP164 4.1 29.1 1.0
CA V:GLY170 4.1 30.6 1.0
CB L:ASP222 4.2 21.2 1.0
N V:GLY170 4.2 27.1 1.0
N V:ASP166 4.2 18.1 1.0
N V:SER169 4.2 21.2 1.0
CA V:SER169 4.3 28.4 1.0
C V:LEU167 4.3 27.1 1.0
CA V:ASP166 4.3 14.7 1.0
NH1 V:ARG19 4.4 39.4 1.0
CA V:TRP164 4.4 26.9 1.0
C V:TRP164 4.4 31.7 1.0
O V:TRP164 4.6 35.5 1.0
O V:LEU167 4.6 28.6 1.0
CZ V:ARG19 4.7 33.8 1.0
CG2 V:ILE163 4.8 22.2 1.0
C V:GLY162 4.8 26.2 1.0
N V:ILE163 4.8 22.1 1.0
N V:ASN165 4.8 19.3 1.0
N V:GLY168 4.8 21.5 1.0
CB V:SER169 4.9 23.5 1.0
CB V:ILE163 4.9 20.4 1.0
CB V:ASP166 5.0 20.7 1.0

Magnesium binding site 7 out of 9 in 9c97

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Mg301

b:23.2
occ:1.00
 O W:ASP177 2.0 23.1 1.0
O W:SER180 2.2 27.1 1.0
O W:ALA174 2.9 27.3 1.0
C W:ASP177 3.2 23.5 1.0
C W:SER180 3.4 21.7 1.0
OXT W:ASP204 3.6 45.9 1.0
O W:ALA178 3.7 28.6 1.0
C W:ALA178 3.9 18.6 1.0
CA W:ALA178 3.9 16.4 1.0
N W:SER180 4.0 30.6 1.0
N W:ALA178 4.0 16.2 1.0
C W:ALA174 4.1 30.4 1.0
CA W:SER180 4.2 22.7 1.0
CA W:ASP177 4.3 22.1 1.0
N W:ASP177 4.3 21.2 1.0
N W:GLY181 4.4 25.2 1.0
O W:ASP204 4.5 41.7 1.0
C W:ASP204 4.5 44.4 1.0
CA W:GLY181 4.6 35.5 1.0
N W:LEU179 4.6 15.6 1.0
NH1 K:ARG19 4.7 27.1 1.0
CB W:ASP177 4.7 27.8 1.0
CB W:SER180 4.8 22.6 1.0
CA W:ASP175 4.8 43.5 1.0
NH2 K:ARG19 4.8 42.5 1.0
C W:ASP175 4.9 36.0 1.0
N W:ASP175 4.9 30.6 1.0

Magnesium binding site 8 out of 9 in 9c97

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Soaked with Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg301

b:29.6
occ:0.77
 O I:ASP204 2.0 37.9 1.0
O Y:ALA165 2.1 22.2 1.0
O Y:ASP168 2.2 23.9 1.0
O Y:SER171 2.4 28.3 1.0
C I:ASP204 2.9 33.9 1.0
CA I:ASP204 3.2 31.7 1.0
C Y:ALA165 3.3 20.2 1.0
C Y:ASP168 3.4 19.9 1.0
CB I:ASP204 3.5 29.1 1.0
C Y:SER171 3.6 26.7 1.0
NH1 Y:ARG19 3.7 51.8 1.0
CA Y:ALA169 3.9 22.0 1.0
O Y:HIS166 3.9 19.9 1.0
O Y:ALA169 3.9 50.8 1.0
C Y:ALA169 3.9 30.8 1.0
OXT I:ASP204 4.0 34.1 1.0
CA Y:ALA165 4.0 20.9 1.0
N Y:ALA169 4.1 18.1 1.0
N Y:SER171 4.1 26.6 1.0
C Y:HIS166 4.3 21.7 1.0
N Y:HIS166 4.3 23.1 1.0
CA Y:SER171 4.4 23.3 1.0
CA Y:HIS166 4.5 18.8 1.0
CA Y:ASP168 4.5 23.3 1.0
CZ Y:ARG19 4.5 55.1 1.0
N Y:ASP168 4.5 18.9 1.0
N Y:GLY172 4.6 26.3 1.0
N I:ASP204 4.6 27.8 1.0
N Y:TYR170 4.6 33.2 1.0
CA Y:GLY172 4.7 26.6 1.0
O Y:ALA164 4.7 21.8 1.0
CG I:ASP204 4.7 28.5 1.0
CB Y:ALA165 4.8 19.6 1.0
CB Y:SER171 4.9 21.9 1.0
C Y:ARG167 4.9 22.8 1.0
O I:GLN203 5.0 38.1 1.0

Magnesium binding site 9 out of 9 in 9c97

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome Soaked with Bra-346 Fraction


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 Soaked with Bra-346 Fraction within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:67.8
occ:1.00
 O Z:HIS195 2.1 39.5 1.0
N Z:VAL198 2.1 34.4 1.0
C Z:HIS195 2.2 38.6 1.0
N Z:GLN197 2.2 41.0 1.0
N Z:ILE196 2.6 31.1 1.0
C Z:ILE196 2.7 40.7 1.0
CB Z:HIS195 2.9 22.1 1.0
C Z:GLN197 3.0 33.8 1.0
CA Z:ILE196 3.0 39.8 1.0
ND1 Z:HIS195 3.0 38.0 1.0
CA Z:VAL198 3.1 33.7 1.0
CA Z:GLN197 3.1 43.3 1.0
CA Z:HIS195 3.1 30.9 1.0
O Z:VAL198 3.2 47.3 1.0
CB Z:VAL198 3.3 28.6 1.0
CG Z:HIS195 3.4 33.9 1.0
CG2 Z:VAL198 3.4 24.9 1.0
C Z:VAL198 3.6 40.0 1.0
O Z:ILE196 3.6 38.8 1.0
O Z:ALA191 4.0 41.7 1.0
N Z:HIS195 4.0 40.8 1.0
CB Z:GLN197 4.1 38.8 1.0
O Z:GLN197 4.1 30.2 1.0
CE1 Z:HIS195 4.3 30.1 1.0
NH1 Z:ARG28 4.5 54.3 1.0
CB Z:ILE196 4.5 36.1 1.0
CD2 Z:HIS195 4.7 27.2 1.0
CG1 Z:VAL198 4.7 42.2 1.0
C Z:ALA191 4.8 39.5 1.0
CA Z:THR192 4.9 32.3 1.0
CG1 Z:ILE196 4.9 37.8 1.0
N Z:GLY199 4.9 37.8 1.0
O Z:THR192 4.9 44.9 1.0
CG Z:GLN197 5.0 25.9 1.0

Reference:

R.Meneghello, J.K.Rustiguel, E.A.De Araujo, R.De Felicio, A.Z.N.Fernandes, E.L.F.Ferreira, J.R.Gubiani, A.A.S.Takeda, A.Araujo, C.C.De Lima Silva, A.F.Bertonha, R.P.M.Urano, D.M.Trindade, T.M.Cunha, A.C.Cardoso, R.G.S.Berlinck, A.F.Z.Nascimento, D.B.B.Trivella. High-Throughput Protein Crystallography to Empower Natural Product-Based Drug Discovery. Acta Crystallogr.,Sect.F 2025.
ISSN: ESSN 2053-230X
PubMed: 40237633
DOI: 10.1107/S2053230X25001542
Page generated: Fri Aug 15 23:58:10 2025

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