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Magnesium in PDB 6hw9: Yeast 20S Proteasome in Complex with 41B

Enzymatic activity of Yeast 20S Proteasome in Complex with 41B

All present enzymatic activity of Yeast 20S Proteasome in Complex with 41B:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with 41B, PDB code: 6hw9 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 136.860, 299.890, 145.390, 90.00, 113.12, 90.00
R / Rfree (%) 17.4 / 20.5

Other elements in 6hw9:

The structure of Yeast 20S Proteasome in Complex with 41B 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 41B (pdb code 6hw9). 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 41B, PDB code: 6hw9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6hw9

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Magnesium binding site 1 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:58.9
occ:1.00
 O G:MET125 2.4 52.4 1.0
OG1 G:THR8 2.6 44.1 1.0
O G:ARG122 2.8 46.7 1.0
O G:TYR119 3.1 42.4 1.0
O G:ALA123 3.1 54.6 1.0
CG2 G:THR8 3.3 46.8 1.0
CB G:THR8 3.4 46.5 1.0
C G:MET125 3.5 52.6 1.0
C G:ALA123 3.6 51.9 1.0
CA G:ALA123 3.7 50.4 1.0
C G:ARG122 3.8 48.6 1.0
N G:THR8 3.9 51.2 1.0
CA G:ARG126 4.2 47.2 1.0
N G:ARG126 4.2 48.9 1.0
N G:ALA123 4.2 48.7 1.0
C G:TYR119 4.3 42.8 1.0
N G:MET125 4.3 53.2 1.0
CA G:THR8 4.3 49.0 1.0
CA G:MET125 4.5 56.1 1.0
N G:TYR124 4.6 54.0 1.0
CD G:PRO127 4.7 45.7 1.0
C G:ARG126 4.9 47.2 1.0
CB G:ALA123 5.0 49.1 1.0
C G:ILE7 5.0 54.0 1.0
C G:TYR124 5.0 52.4 1.0

Magnesium binding site 2 out of 10 in 6hw9

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Magnesium binding site 2 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:65.5
occ:1.00
 O I:ASP177 2.6 50.0 1.0
O I:SER180 2.8 54.7 1.0
O I:ALA174 3.0 49.5 1.0
OXT I:ASP204 3.3 86.4 1.0
C I:ASP177 3.7 49.2 1.0
C I:SER180 4.0 51.8 1.0
C I:ALA174 4.1 54.1 1.0
O I:ASP204 4.2 79.4 1.0
C I:ASP204 4.2 77.6 1.0
O I:ALA178 4.2 55.0 1.0
CA I:ASP175 4.3 55.6 1.0
CA I:ALA178 4.3 48.2 1.0
C I:ALA178 4.4 49.5 1.0
N I:ALA178 4.5 47.0 1.0
NH1 Y:ARG19 4.5 66.9 1.0
C I:ASP175 4.6 54.8 1.0
O I:ASP175 4.6 57.1 1.0
N I:ASP175 4.6 54.7 1.0
N I:ASP177 4.6 48.1 1.0
NH2 Y:ARG19 4.8 66.7 1.0
N I:SER180 4.8 48.8 1.0
CA I:ASP177 4.8 49.6 1.0
CA I:GLY181 4.8 53.6 1.0
N I:GLY181 4.9 52.0 1.0
CA I:SER180 5.0 50.6 1.0

Magnesium binding site 3 out of 10 in 6hw9

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Magnesium binding site 3 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg302

b:64.7
occ:1.00
 O Y:ASP168 2.3 48.1 1.0
O I:ASP204 2.3 79.4 1.0
O Y:ALA165 2.6 47.7 1.0
O Y:SER171 2.9 50.4 1.0
C I:ASP204 3.1 77.6 1.0
C Y:ASP168 3.3 45.3 1.0
CA Y:ALA169 3.5 45.8 1.0
CA I:ASP204 3.6 70.5 1.0
O Y:HIS166 3.7 48.7 1.0
C Y:ALA165 3.8 47.9 1.0
N Y:ALA169 3.8 45.5 1.0
C Y:ALA169 3.9 45.6 1.0
O Y:ALA169 3.9 50.4 1.0
NH1 Y:ARG19 3.9 66.9 1.0
CB I:ASP204 4.0 69.4 1.0
OXT I:ASP204 4.0 86.4 1.0
C Y:SER171 4.1 46.2 1.0
C Y:HIS166 4.3 47.6 1.0
N Y:SER171 4.5 42.8 1.0
CA Y:ASP168 4.5 45.3 1.0
N Y:ASP168 4.5 46.7 1.0
CZ Y:ARG19 4.6 62.5 1.0
N Y:HIS166 4.7 46.9 1.0
CA Y:HIS166 4.7 45.2 1.0
CA Y:ALA165 4.7 48.0 1.0
N Y:TYR170 4.7 44.6 1.0
C Y:ARG167 4.8 48.6 1.0
NH2 Y:ARG19 4.8 66.7 1.0
CB Y:ALA169 4.8 45.2 1.0
CA Y:SER171 4.9 42.3 1.0
O Y:ALA164 4.9 46.0 1.0
N I:ASP204 4.9 67.1 1.0
N Y:ARG167 5.0 46.8 1.0

Magnesium binding site 4 out of 10 in 6hw9

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Magnesium binding site 4 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg302

b:64.5
occ:1.00
 O K:ASP168 2.2 48.1 1.0
O K:ALA165 2.3 47.3 1.0
O W:ASP204 2.5 70.0 1.0
O K:SER171 3.1 49.9 1.0
C K:ASP168 3.2 48.1 1.0
C W:ASP204 3.2 68.2 1.0
O K:HIS166 3.4 45.1 1.0
C K:ALA165 3.5 50.1 1.0
CA W:ASP204 3.5 65.2 1.0
CA K:ALA169 3.7 49.8 1.0
N K:ALA169 3.8 49.3 1.0
C K:HIS166 3.9 46.5 1.0
CB W:ASP204 4.0 63.7 1.0
C K:ALA169 4.1 52.0 1.0
OXT W:ASP204 4.2 67.5 1.0
O K:ALA169 4.2 57.1 1.0
N K:ASP168 4.2 48.1 1.0
C K:SER171 4.3 48.7 1.0
CA K:HIS166 4.3 46.8 1.0
N K:HIS166 4.3 48.0 1.0
CA K:ASP168 4.3 46.9 1.0
NH1 K:ARG19 4.3 65.0 1.0
C K:ARG167 4.4 47.9 1.0
CA K:ALA165 4.5 50.3 1.0
N K:ARG167 4.6 45.9 1.0
O K:ALA164 4.6 52.4 1.0
N K:SER171 4.6 47.2 1.0
O K:ARG167 4.7 47.6 1.0
N W:ASP204 4.9 62.1 1.0
N K:TYR170 4.9 49.8 1.0
CB K:ALA169 5.0 47.6 1.0
CZ K:ARG19 5.0 62.8 1.0

Magnesium binding site 5 out of 10 in 6hw9

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Magnesium binding site 5 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg303

b:38.6
occ:1.00
 O13 K:GWK301 3.4 50.2 1.0
OG1 K:THR21 3.5 56.5 1.0
CG K:TYR170 4.0 45.0 1.0
CB K:TYR170 4.1 45.0 1.0
CD2 K:TYR170 4.2 44.9 1.0
O2S K:MES304 4.3 54.4 0.8
CD1 K:TYR170 4.4 44.9 1.0
C11 K:GWK301 4.4 49.2 1.0
C40 K:GWK301 4.5 44.9 1.0
C10 K:GWK301 4.5 48.3 1.0
CB K:THR21 4.6 53.2 1.0
CE2 K:TYR170 4.8 44.0 1.0
O3S K:MES304 4.8 45.1 0.8
CG2 K:THR21 4.9 54.5 1.0
CE1 K:TYR170 4.9 43.8 1.0
CB K:SER131 5.0 38.3 1.0

Magnesium binding site 6 out of 10 in 6hw9

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Magnesium binding site 6 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:79.6
occ:1.00
 OXT L:ASP222 2.2 78.0 1.0
O V:ASP166 2.3 52.3 1.0
O V:ILE163 2.3 54.0 1.0
C L:ASP222 3.1 77.5 1.0
C V:ASP166 3.1 54.2 1.0
O V:TRP164 3.2 60.5 1.0
O V:SER169 3.3 51.5 1.0
C V:ILE163 3.4 57.5 1.0
C V:TRP164 3.5 58.3 1.0
CA L:ASP222 3.7 74.4 1.0
N V:ASP166 3.7 48.5 1.0
N V:LEU167 3.8 53.6 1.0
CA V:LEU167 3.9 54.9 1.0
O L:ASP222 4.0 81.7 1.0
CA V:TRP164 4.0 57.0 1.0
O V:GLY162 4.0 60.2 1.0
CA V:ASP166 4.0 52.1 1.0
N V:ASN165 4.0 57.1 1.0
N V:TRP164 4.1 54.7 1.0
C V:ASN165 4.2 54.4 1.0
CA V:ILE163 4.5 58.8 1.0
C V:SER169 4.5 52.2 1.0
O L:ARG221 4.5 67.2 1.0
CB L:ASP222 4.5 72.4 1.0
CD2 V:LEU167 4.5 54.1 1.0
CA V:ASN165 4.6 55.6 1.0
NH1 V:ARG19 4.6 71.7 1.0
C V:LEU167 4.7 54.6 1.0
CD1 L:ILE35 4.8 61.7 1.0
N L:ASP222 4.8 73.2 1.0
O V:ASN165 4.9 52.3 1.0
C V:GLY162 5.0 59.4 1.0

Magnesium binding site 7 out of 10 in 6hw9

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Magnesium binding site 7 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg201

b:59.9
occ:1.00
 O N:ILE163 3.0 46.2 1.0
O N:SER169 3.0 55.1 1.0
O N:ASP166 3.4 52.2 1.0
NH1 N:ARG19 3.4 53.7 1.0
CD1 a:LEU34 3.5 52.2 1.0
CZ N:ARG19 4.1 51.6 1.0
C N:ILE163 4.1 51.3 1.0
NH2 N:ARG19 4.2 50.5 1.0
C N:SER169 4.2 50.0 1.0
CG2 N:ILE163 4.3 52.7 1.0
CA N:GLY167 4.4 49.5 1.0
C N:ASP166 4.4 49.0 1.0
O N:GLY167 4.5 49.5 1.0
CA N:GLY170 4.6 51.6 1.0
C N:GLY167 4.7 49.0 1.0
N N:GLY167 4.8 47.5 1.0
N N:GLY170 4.9 50.5 1.0
CG a:LEU34 4.9 53.5 1.0
CA N:ILE163 4.9 52.2 1.0

Magnesium binding site 8 out of 10 in 6hw9

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Magnesium binding site 8 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg201

b:38.4
occ:1.00
 OE1 X:GLN118 3.6 48.8 1.0
O X:THR124 3.7 52.8 1.0
CB X:ASP120 3.8 43.6 1.0
CG X:ASP120 4.0 47.2 1.0
N X:ASP120 4.1 40.2 1.0
OD2 X:ASP120 4.1 49.1 1.0
CB X:THR124 4.3 46.2 1.0
CD X:GLN118 4.3 44.2 1.0
CG X:GLN118 4.4 43.8 1.0
CG2 X:THR124 4.4 45.9 1.0
CE1 X:HIS133 4.4 46.3 1.0
O X:GLN118 4.5 46.7 1.0
CA X:ASP120 4.5 41.2 1.0
OD1 X:ASP120 4.6 54.4 1.0
C X:THR124 4.7 48.8 1.0
CG1 W:VAL35 4.7 48.3 1.0
C X:ILE119 4.8 41.0 1.0
CD2 W:LEU28 4.9 50.7 1.0
C X:GLN118 4.9 43.8 1.0

Magnesium binding site 9 out of 10 in 6hw9

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Magnesium binding site 9 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg302

b:34.4
occ:1.00
 OG1 Y:THR21 3.4 48.8 1.0
O13 Y:GWK301 3.5 51.7 1.0
CG Y:TYR170 3.9 44.9 1.0
CB Y:TYR170 4.1 44.0 1.0
CD2 Y:TYR170 4.2 44.3 1.0
CD1 Y:TYR170 4.2 44.8 1.0
CB Y:THR21 4.5 48.3 1.0
C40 Y:GWK301 4.5 44.8 1.0
O2S Y:MES303 4.5 60.0 1.0
C11 Y:GWK301 4.6 48.3 1.0
C10 Y:GWK301 4.7 48.4 1.0
CE2 Y:TYR170 4.7 44.9 1.0
CE1 Y:TYR170 4.7 44.0 1.0
CG2 Y:THR21 4.8 49.1 1.0
O3S Y:MES303 4.9 51.5 1.0
CZ Y:TYR170 5.0 45.7 1.0

Magnesium binding site 10 out of 10 in 6hw9

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Magnesium binding site 10 out of 10 in the Yeast 20S Proteasome in Complex with 41B


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 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg301

b:71.0
occ:1.00
 O Z:VAL198 2.6 54.0 1.0
O Z:THR192 2.8 56.1 1.0
O Z:ASP222 3.1 76.8 1.0
O Z:HIS195 3.3 50.2 1.0
NH2 Z:ARG28 3.5 67.0 1.0
CG2 Z:THR192 3.6 62.4 1.0
C Z:THR192 3.8 61.6 1.0
C Z:VAL198 3.8 54.8 1.0
O Z:ILE196 4.0 56.1 1.0
OD1 Z:ASP222 4.1 69.2 1.0
CA Z:THR192 4.2 61.5 1.0
NH2 H:ARG19 4.2 71.5 1.0
C Z:ASP222 4.2 75.1 1.0
CA Z:ILE196 4.3 51.1 1.0
C Z:HIS195 4.3 51.6 1.0
C Z:ILE196 4.4 50.5 1.0
CZ Z:ARG28 4.5 65.6 1.0
CA Z:GLY199 4.5 57.0 1.0
CB Z:THR192 4.5 61.6 1.0
O Z:LYS220 4.6 63.0 1.0
N Z:GLY199 4.6 55.5 1.0
NH1 Z:ARG28 4.6 69.2 1.0
N Z:VAL198 4.7 51.3 1.0
N Z:ILE196 4.8 49.9 1.0
OXT Z:ASP222 4.8 76.7 1.0
CA Z:VAL198 4.9 52.9 1.0
CG Z:ASP222 5.0 69.0 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: Tue Oct 1 02:41:00 2024

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