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Magnesium in PDB 6hw6: Yeast 20S Proteasome in Complex with 20

Enzymatic activity of Yeast 20S Proteasome in Complex with 20

All present enzymatic activity of Yeast 20S Proteasome in Complex with 20:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with 20, PDB code: 6hw6 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.990, 299.930, 145.500, 90.00, 113.23, 90.00
R / Rfree (%) 17.5 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with 20 (pdb code 6hw6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Yeast 20S Proteasome in Complex with 20, PDB code: 6hw6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6hw6

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with 20


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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:61.0
occ:1.00
 O G:MET125 2.3 58.0 1.0
OG1 G:THR8 2.6 50.1 1.0
O G:ARG122 2.7 52.6 1.0
O G:TYR119 2.9 43.7 1.0
O G:ALA123 3.2 57.3 1.0
CG2 G:THR8 3.3 53.0 1.0
C G:MET125 3.4 54.8 1.0
CB G:THR8 3.5 52.5 1.0
C G:ALA123 3.7 53.8 1.0
CA G:ALA123 3.7 52.5 1.0
C G:ARG122 3.8 51.5 1.0
C G:TYR119 4.1 47.8 1.0
N G:THR8 4.1 54.4 1.0
CA G:ARG126 4.2 49.2 1.0
N G:ARG126 4.2 51.3 1.0
N G:ALA123 4.2 50.7 1.0
N G:MET125 4.3 54.3 1.0
CA G:MET125 4.5 57.8 1.0
CA G:THR8 4.5 54.0 1.0
CD G:PRO127 4.5 46.7 1.0
N G:TYR124 4.7 55.0 1.0
CA G:TYR119 4.8 46.5 1.0
C G:ARG126 4.8 47.8 1.0

Magnesium binding site 2 out of 8 in 6hw6

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with 20


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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg302

b:93.5
occ:1.00
 OE1 H:GLN91 2.5 71.7 1.0
OD1 N:ASP51 2.9 52.2 1.0
O N:ASN92 3.1 57.8 1.0
CD H:GLN91 3.4 62.0 1.0
NE2 H:GLN91 3.5 59.8 1.0
OD2 N:ASP51 3.5 56.6 1.0
CG N:ASP51 3.6 50.6 1.0
C N:ASN92 4.2 55.7 1.0
CG H:GLN91 4.8 57.8 1.0
CE1 H:PHE88 4.9 46.9 1.0
CZ H:PHE88 4.9 44.8 1.0

Magnesium binding site 3 out of 8 in 6hw6

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with 20


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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:69.7
occ:1.00
 O I:SER180 2.6 54.2 1.0
O I:ASP177 2.6 53.1 1.0
O I:ALA174 2.7 58.3 1.0
OXT I:ASP204 3.7 62.6 1.0
C I:ALA174 3.7 59.1 1.0
C I:ASP177 3.8 52.7 1.0
C I:SER180 3.8 52.6 1.0
CA I:ASP175 4.0 58.7 1.0
N I:ASP175 4.3 58.0 1.0
C I:ASP175 4.4 57.5 1.0
O I:ALA178 4.4 53.7 1.0
CA I:GLY181 4.5 52.9 1.0
O I:ASP175 4.5 60.8 1.0
CA I:ALA178 4.6 51.9 1.0
N I:ASP177 4.6 52.6 1.0
C I:ALA178 4.6 51.7 1.0
N I:ALA178 4.6 50.8 1.0
N I:GLY181 4.6 52.4 1.0
C I:ASP204 4.6 64.8 1.0
OD1 I:ASP175 4.6 63.0 1.0
O I:ASP204 4.7 67.2 1.0
N I:SER180 4.7 51.2 1.0
CA I:ASP177 4.8 52.8 1.0
CA I:SER180 4.8 52.9 1.0
NH2 Y:ARG19 4.8 57.6 1.0
CA I:ALA174 4.9 57.1 1.0
NH1 Y:ARG19 4.9 60.5 1.0

Magnesium binding site 4 out of 8 in 6hw6

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with 20


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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:64.3
occ:1.00
 O I:ASP204 2.2 67.2 1.0
O Y:ASP168 2.3 55.3 1.0
O Y:ALA165 2.5 47.4 1.0
O Y:SER171 2.8 59.2 1.0
C I:ASP204 3.0 64.8 1.0
C Y:ASP168 3.3 51.3 1.0
CA Y:ALA169 3.5 49.8 1.0
O Y:ALA169 3.6 53.9 1.0
CA I:ASP204 3.6 62.4 1.0
C Y:ALA165 3.7 51.7 1.0
C Y:ALA169 3.7 49.5 1.0
N Y:ALA169 3.8 51.4 1.0
OXT I:ASP204 3.9 62.6 1.0
O Y:HIS166 3.9 52.0 1.0
NH1 Y:ARG19 3.9 60.5 1.0
C Y:SER171 4.0 55.0 1.0
CB I:ASP204 4.1 63.8 1.0
C Y:HIS166 4.3 51.7 1.0
N Y:SER171 4.5 51.5 1.0
CA Y:ASP168 4.5 49.2 1.0
N Y:ASP168 4.5 50.5 1.0
CA Y:ALA165 4.6 52.0 1.0
N Y:HIS166 4.6 51.5 1.0
CZ Y:ARG19 4.6 57.2 1.0
N Y:TYR170 4.6 49.5 1.0
CA Y:HIS166 4.7 50.6 1.0
CA Y:SER171 4.7 52.3 1.0
O Y:ALA164 4.8 49.4 1.0
C Y:ARG167 4.8 51.7 1.0
CB Y:ALA169 4.8 49.5 1.0
NH2 Y:ARG19 4.9 57.6 1.0
N Y:GLY172 4.9 56.8 1.0
N I:ASP204 5.0 60.8 1.0
N Y:ARG167 5.0 51.1 1.0

Magnesium binding site 5 out of 8 in 6hw6

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with 20


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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:69.3
occ:1.00
 O K:ASP168 2.1 51.1 1.0
O K:ALA165 2.3 53.5 1.0
O W:ASP204 2.4 62.4 1.0
O K:SER171 2.7 57.2 1.0
C W:ASP204 3.2 60.0 1.0
C K:ASP168 3.2 48.9 1.0
C K:ALA165 3.4 52.6 1.0
CA K:ALA169 3.6 48.8 1.0
CA W:ASP204 3.7 56.5 1.0
O K:ALA169 3.7 51.6 1.0
N K:ALA169 3.8 48.4 1.0
C K:ALA169 3.8 50.0 1.0
O K:HIS166 3.8 52.2 1.0
C K:SER171 3.8 52.3 1.0
CB W:ASP204 4.0 56.0 1.0
NH1 K:ARG19 4.1 54.7 1.0
OXT W:ASP204 4.1 61.9 1.0
C K:HIS166 4.2 51.5 1.0
CA K:ALA165 4.3 51.8 1.0
N K:SER171 4.3 49.9 1.0
N K:ASP168 4.4 49.2 1.0
N K:HIS166 4.4 49.5 1.0
CA K:ASP168 4.4 48.1 1.0
O K:ALA164 4.5 52.5 1.0
CA K:HIS166 4.5 50.6 1.0
CA K:SER171 4.6 50.5 1.0
N K:TYR170 4.6 49.5 1.0
C K:ARG167 4.7 51.4 1.0
CZ K:ARG19 4.7 54.1 1.0
N K:ARG167 4.8 51.1 1.0
N K:GLY172 4.8 53.0 1.0
CB K:SER171 4.9 49.6 1.0
CA K:GLY172 4.9 53.3 1.0
NH2 K:ARG19 5.0 58.3 1.0
CB K:ALA169 5.0 48.4 1.0

Magnesium binding site 6 out of 8 in 6hw6

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with 20


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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:0.6
occ:1.00
 O V:ASP166 2.3 57.0 1.0
O V:ILE163 2.3 58.1 1.0
OXT L:ASP222 2.5 72.1 1.0
C V:ASP166 3.1 59.4 1.0
C L:ASP222 3.1 70.7 1.0
O V:TRP164 3.2 64.5 1.0
O V:SER169 3.3 61.4 1.0
C V:ILE163 3.4 61.9 1.0
C V:TRP164 3.5 64.2 1.0
N V:ASP166 3.6 56.7 1.0
CA L:ASP222 3.7 67.1 1.0
O L:ASP222 3.8 79.5 1.0
N V:LEU167 3.8 60.7 1.0
CA V:LEU167 3.9 59.5 1.0
O V:GLY162 3.9 60.6 1.0
N V:ASN165 3.9 62.5 1.0
CA V:TRP164 4.0 63.7 1.0
CA V:ASP166 4.0 58.4 1.0
N V:TRP164 4.1 60.6 1.0
C V:ASN165 4.1 59.1 1.0
CA V:ILE163 4.5 62.4 1.0
CA V:ASN165 4.5 60.8 1.0
C V:SER169 4.5 59.9 1.0
O L:ARG221 4.5 62.9 1.0
CB L:ASP222 4.6 67.9 1.0
C V:LEU167 4.6 58.8 1.0
CD2 V:LEU167 4.6 56.0 1.0
NH1 V:ARG19 4.7 64.7 1.0
CD1 L:ILE35 4.8 62.6 1.0
O V:ASN165 4.8 61.0 1.0
N L:ASP222 4.9 66.6 1.0
O V:LEU167 4.9 61.6 1.0
C V:GLY162 4.9 60.7 1.0
CB V:ASP166 5.0 57.9 1.0

Magnesium binding site 7 out of 8 in 6hw6

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Magnesium binding site 7 out of 8 in the Yeast 20S Proteasome in Complex with 20


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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:50.7
occ:1.00
 O N:SER169 2.5 53.2 1.0
O N:ILE163 2.7 50.6 1.0
O N:ASP166 2.8 52.4 1.0
NH1 N:ARG19 3.5 50.9 1.0
CD1 a:LEU34 3.6 47.9 1.0
C N:SER169 3.7 49.6 1.0
C N:ILE163 3.8 51.7 1.0
C N:ASP166 3.9 50.5 1.0
CG2 N:ILE163 4.1 50.2 1.0
CA N:GLY167 4.1 49.0 1.0
CZ N:ARG19 4.2 49.8 1.0
O N:GLY167 4.3 53.2 1.0
CA N:GLY170 4.4 51.0 1.0
C N:GLY167 4.4 49.2 1.0
N N:GLY167 4.4 49.2 1.0
NH2 N:ARG19 4.5 47.0 1.0
N N:GLY170 4.5 50.1 1.0
CA N:ILE163 4.5 51.0 1.0
N N:SER169 4.7 48.4 1.0
CA N:SER169 4.7 47.7 1.0
N N:LYS164 4.9 50.5 1.0
CG a:LEU34 4.9 49.6 1.0
CB N:ILE163 4.9 49.5 1.0
O N:LYS164 5.0 52.3 1.0

Magnesium binding site 8 out of 8 in 6hw6

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Magnesium binding site 8 out of 8 in the Yeast 20S Proteasome in Complex with 20


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 20 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:69.2
occ:1.00
 O Z:VAL198 2.5 61.0 1.0
O Z:THR192 2.9 62.9 1.0
O Z:HIS195 3.4 50.6 1.0
NH2 Z:ARG28 3.4 66.0 1.0
O Z:ASP222 3.5 81.8 1.0
CG2 Z:THR192 3.5 63.6 1.0
C Z:VAL198 3.7 58.8 1.0
C Z:THR192 3.8 63.8 1.0
O Z:ILE196 3.9 57.8 1.0
CA Z:THR192 4.1 62.6 1.0
OD1 Z:ASP222 4.2 73.2 1.0
CA Z:GLY199 4.4 60.6 1.0
CZ Z:ARG28 4.4 62.0 1.0
C Z:ILE196 4.4 52.8 1.0
C Z:ASP222 4.4 76.3 1.0
CB Z:THR192 4.4 63.1 1.0
N Z:GLY199 4.4 58.4 1.0
C Z:HIS195 4.5 53.2 1.0
CA Z:ILE196 4.5 53.1 1.0
NH2 H:ARG19 4.5 68.1 1.0
O Z:LYS220 4.6 61.7 1.0
N Z:VAL198 4.6 55.0 1.0
NH1 Z:ARG28 4.6 64.7 1.0
CA Z:VAL198 4.7 56.7 1.0
N Z:ILE196 4.9 52.2 1.0
OXT Z:ASP222 5.0 82.0 1.0

Reference:

B.T.Xin, E.M.Huber, G.De Bruin, W.Heinemeyer, E.Maurits, C.Espinal, Y.Du, M.Janssens, E.S.Weyburne, A.F.Kisselev, B.I.Florea, C.Driessen, G.A.Van Der Marel, M.Groll, H.S.Overkleeft. Structure-Based Design of Inhibitors Selective For Human Proteasome Beta 2C or Beta 2I Subunits. J.Med.Chem. V. 62 1626 2019.
ISSN: ISSN 0022-2623
PubMed: 30657666
DOI: 10.1021/ACS.JMEDCHEM.8B01884
Page generated: Wed Aug 13 07:36:52 2025

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