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Magnesium in PDB 6hvx: Yeast 20S Proteasome in Complex with 4

Enzymatic activity of Yeast 20S Proteasome in Complex with 4

All present enzymatic activity of Yeast 20S Proteasome in Complex with 4:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with 4, PDB code: 6hvx 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 (°) 136.780, 300.080, 145.730, 90.00, 113.11, 90.00
R / Rfree (%) 18.7 / 20.6

Other elements in 6hvx:

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

Magnesium binding site 1 out of 9 in 6hvx

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Magnesium binding site 1 out of 9 in the Yeast 20S Proteasome in Complex with 4


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

b:44.9
occ:1.00
 O G:MET125 2.3 48.3 1.0
OG1 G:THR8 2.6 40.1 1.0
O G:ARG122 2.8 39.6 1.0
O G:TYR119 3.0 34.9 1.0
O G:ALA123 3.1 47.0 1.0
CG2 G:THR8 3.2 42.6 1.0
CB G:THR8 3.5 41.8 1.0
C G:MET125 3.5 46.8 1.0
C G:ALA123 3.6 45.5 1.0
CA G:ALA123 3.7 43.7 1.0
C G:ARG122 3.8 42.0 1.0
N G:THR8 4.0 46.2 1.0
C G:TYR119 4.2 36.3 1.0
CA G:ARG126 4.2 41.5 1.0
N G:ARG126 4.2 44.0 1.0
N G:ALA123 4.3 42.0 1.0
N G:MET125 4.3 47.1 1.0
CA G:THR8 4.3 44.0 1.0
CA G:MET125 4.5 49.6 1.0
CD G:PRO127 4.6 39.1 1.0
N G:TYR124 4.6 47.8 1.0
C G:ARG126 4.9 41.0 1.0
CA G:TYR119 4.9 35.0 1.0
C G:TYR124 5.0 45.5 1.0

Magnesium binding site 2 out of 9 in 6hvx

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Magnesium binding site 2 out of 9 in the Yeast 20S Proteasome in Complex with 4


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

b:55.3
occ:1.00
 O I:ASP177 2.3 46.7 1.0
O I:SER180 2.7 45.8 1.0
O I:ALA174 2.7 52.0 1.0
C I:ASP177 3.5 45.2 1.0
OXT I:ASP204 3.6 64.5 1.0
C I:ALA174 3.8 50.6 1.0
C I:SER180 3.9 45.9 1.0
CA I:ASP175 4.1 51.2 1.0
CA I:ALA178 4.2 44.7 1.0
O I:ALA178 4.3 49.6 1.0
N I:ALA178 4.3 44.2 1.0
C I:ALA178 4.3 46.5 1.0
C I:ASP175 4.4 49.0 1.0
N I:ASP177 4.4 44.5 1.0
N I:ASP175 4.4 51.2 1.0
O I:ASP175 4.5 49.3 1.0
CA I:ASP177 4.6 45.4 1.0
C I:ASP204 4.6 65.3 1.0
N I:SER180 4.6 44.2 1.0
O I:ASP204 4.7 69.7 1.0
CA I:GLY181 4.7 48.0 1.0
N I:GLY181 4.7 47.0 1.0
NH1 Y:ARG19 4.7 61.0 1.0
NH2 Y:ARG19 4.8 62.8 1.0
CA I:SER180 4.8 45.1 1.0
OD1 I:ASP175 4.9 55.9 1.0
CA I:ALA174 5.0 48.7 1.0

Magnesium binding site 3 out of 9 in 6hvx

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Magnesium binding site 3 out of 9 in the Yeast 20S Proteasome in Complex with 4


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

b:50.9
occ:1.00
 O K:ASP168 2.1 53.3 1.0
O K:ALA165 2.2 51.0 1.0
O W:ASP204 2.5 65.7 1.0
C K:ASP168 3.1 51.1 1.0
O K:SER171 3.1 46.8 1.0
C W:ASP204 3.2 63.1 1.0
O K:HIS166 3.3 50.4 1.0
C K:ALA165 3.4 50.5 1.0
CA K:ALA169 3.6 52.2 1.0
CA W:ASP204 3.6 60.8 1.0
N K:ALA169 3.7 51.4 1.0
C K:HIS166 3.7 49.9 1.0
C K:ALA169 4.0 53.0 1.0
N K:ASP168 4.1 49.3 1.0
O K:ALA169 4.1 53.6 1.0
OXT W:ASP204 4.2 66.5 1.0
CA K:ASP168 4.2 48.8 1.0
CA K:HIS166 4.2 49.7 1.0
CB W:ASP204 4.2 60.0 1.0
N K:HIS166 4.2 48.7 1.0
C K:ARG167 4.2 49.8 1.0
C K:SER171 4.3 49.3 1.0
CA K:ALA165 4.4 51.6 1.0
N K:ARG167 4.4 48.7 1.0
NH1 K:ARG19 4.4 61.1 1.0
O K:ALA164 4.4 51.0 1.0
O K:ARG167 4.5 49.4 1.0
N K:SER171 4.7 49.9 1.0
CA K:ARG167 4.8 49.4 1.0
N K:TYR170 4.9 52.4 1.0
CB K:ALA169 4.9 52.3 1.0
N W:ASP204 4.9 59.2 1.0
CA K:SER171 5.0 48.7 1.0

Magnesium binding site 4 out of 9 in 6hvx

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Magnesium binding site 4 out of 9 in the Yeast 20S Proteasome in Complex with 4


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

b:47.6
occ:1.00
 O N:SER169 2.7 43.6 1.0
O N:ILE163 2.9 45.4 1.0
O N:ASP166 3.1 45.9 1.0
CD1 a:LEU34 3.6 49.2 1.0
NH1 N:ARG19 3.6 47.3 1.0
C N:SER169 4.0 42.7 1.0
C N:ILE163 4.0 45.5 1.0
C N:ASP166 4.1 44.2 1.0
CA N:GLY167 4.1 42.9 1.0
CZ N:ARG19 4.2 46.4 1.0
CG2 N:ILE163 4.2 45.8 1.0
NH2 N:ARG19 4.3 45.9 1.0
O N:GLY167 4.3 45.5 1.0
CA N:GLY170 4.5 45.5 1.0
C N:GLY167 4.5 43.1 1.0
N N:GLY167 4.5 43.1 1.0
N N:GLY170 4.7 44.0 1.0
CA N:ILE163 4.7 45.1 1.0
CG a:LEU34 4.8 51.4 1.0
N N:SER169 4.9 40.9 1.0

Magnesium binding site 5 out of 9 in 6hvx

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Magnesium binding site 5 out of 9 in the Yeast 20S Proteasome in Complex with 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg302

b:66.7
occ:1.00
 O V:ASP166 2.0 49.7 1.0
OXT L:ASP222 2.1 71.7 1.0
O V:ILE163 2.3 52.9 1.0
O V:SER169 2.9 50.1 1.0
C V:ASP166 2.9 50.6 1.0
C L:ASP222 3.0 70.7 1.0
C V:ILE163 3.3 54.1 1.0
O V:TRP164 3.6 56.6 1.0
N V:LEU167 3.6 52.2 1.0
CA L:ASP222 3.7 68.7 1.0
CA V:LEU167 3.7 53.2 1.0
N V:ASP166 3.7 48.3 1.0
C V:TRP164 3.8 53.8 1.0
O V:GLY162 3.8 52.3 1.0
CA V:ASP166 3.9 48.7 1.0
O L:ASP222 3.9 71.5 1.0
C V:SER169 4.1 48.2 1.0
N V:TRP164 4.1 53.8 1.0
CA V:TRP164 4.2 54.1 1.0
CA V:ILE163 4.3 55.2 1.0
C V:LEU167 4.3 52.5 1.0
NH1 V:ARG19 4.3 66.7 1.0
N V:ASN165 4.3 52.0 1.0
CB L:ASP222 4.4 67.6 1.0
C V:ASN165 4.4 50.2 1.0
O V:LEU167 4.6 54.8 1.0
N V:SER169 4.7 47.9 1.0
CD2 V:LEU167 4.7 54.4 1.0
O L:ARG221 4.8 64.7 1.0
C V:GLY162 4.8 52.5 1.0
CB V:ASP166 4.9 47.5 1.0
CA V:ASN165 4.9 51.6 1.0
CA V:SER169 4.9 48.0 1.0
CZ V:ARG19 4.9 62.9 1.0
NH2 V:ARG19 4.9 64.5 1.0
N L:ASP222 4.9 65.7 1.0
CB V:LEU167 5.0 54.5 1.0
N V:GLY170 5.0 48.5 1.0
N V:GLY168 5.0 51.3 1.0

Magnesium binding site 6 out of 9 in 6hvx

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Magnesium binding site 6 out of 9 in the Yeast 20S Proteasome in Complex with 4


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

b:39.8
occ:1.00
 OE1 X:GLN118 3.4 47.0 1.0
O X:THR124 3.7 45.5 1.0
CB X:ASP120 3.8 40.1 1.0
N X:ASP120 4.0 36.4 1.0
CG X:ASP120 4.0 43.7 1.0
OD2 X:ASP120 4.1 46.2 1.0
CD X:GLN118 4.2 42.4 1.0
CG X:GLN118 4.3 40.5 1.0
CE1 X:HIS133 4.3 44.0 1.0
CB X:THR124 4.4 42.7 1.0
O X:GLN118 4.5 40.5 1.0
CA X:ASP120 4.5 38.0 1.0
CG2 X:THR124 4.5 42.1 1.0
OD1 X:ASP120 4.7 49.5 1.0
C X:THR124 4.7 44.4 1.0
C X:ILE119 4.7 36.9 1.0
CG1 W:VAL35 4.8 52.0 1.0
C X:GLN118 4.9 40.0 1.0
CA X:ILE119 5.0 37.7 1.0
CD2 W:LEU28 5.0 50.1 1.0

Magnesium binding site 7 out of 9 in 6hvx

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Magnesium binding site 7 out of 9 in the Yeast 20S Proteasome in Complex with 4


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

b:49.1
occ:1.00
 O I:ASP204 2.2 69.7 1.0
O Y:ASP168 2.3 48.1 1.0
O Y:ALA165 2.4 45.3 1.0
O Y:SER171 2.8 47.4 1.0
C I:ASP204 3.1 65.3 1.0
C Y:ASP168 3.3 45.7 1.0
CA Y:ALA169 3.5 45.4 1.0
C Y:ALA165 3.6 46.1 1.0
CA I:ASP204 3.6 64.1 1.0
O Y:HIS166 3.7 48.0 1.0
O Y:ALA169 3.8 47.2 1.0
N Y:ALA169 3.8 46.2 1.0
C Y:ALA169 3.8 45.6 1.0
NH1 Y:ARG19 3.9 61.0 1.0
C Y:SER171 4.0 45.0 1.0
OXT I:ASP204 4.0 64.5 1.0
CB I:ASP204 4.0 64.7 1.0
C Y:HIS166 4.2 46.1 1.0
N Y:SER171 4.4 42.2 1.0
N Y:ASP168 4.5 45.0 1.0
CA Y:ASP168 4.5 44.3 1.0
N Y:HIS166 4.5 45.9 1.0
CA Y:ALA165 4.5 46.8 1.0
CA Y:HIS166 4.5 46.0 1.0
CZ Y:ARG19 4.6 60.2 1.0
C Y:ARG167 4.7 45.8 1.0
N Y:TYR170 4.7 46.0 1.0
O Y:ALA164 4.8 45.1 1.0
CA Y:SER171 4.8 41.9 1.0
NH2 Y:ARG19 4.8 62.8 1.0
CB Y:ALA169 4.9 45.9 1.0
N Y:ARG167 4.9 45.5 1.0
N I:ASP204 4.9 63.1 1.0
O Y:ARG167 4.9 46.1 1.0
N Y:GLY172 5.0 47.6 1.0

Magnesium binding site 8 out of 9 in 6hvx

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Magnesium binding site 8 out of 9 in the Yeast 20S Proteasome in Complex with 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg303

b:78.5
occ:1.00
 OG1 Y:THR21 3.1 53.7 1.0
O Y:GLY23 3.4 54.4 1.0
CD1 Y:TYR170 3.9 48.0 1.0
CE1 Y:TYR170 4.0 46.1 1.0
C28 Y:GQH301 4.0 54.1 1.0
CG Y:TYR170 4.0 48.1 1.0
CB Y:THR21 4.1 49.9 1.0
N Y:GLY23 4.1 50.2 1.0
C Y:GLY23 4.2 53.6 1.0
CA Y:GLY23 4.2 52.1 1.0
CZ Y:TYR170 4.2 44.2 1.0
CD2 Y:TYR170 4.3 48.2 1.0
CE2 Y:TYR170 4.4 47.2 1.0
C32 Y:GQH301 4.5 51.2 1.0
CB Y:TYR170 4.7 46.6 1.0
OH Y:TYR170 4.9 49.8 1.0
CG2 Y:THR21 4.9 49.9 1.0

Magnesium binding site 9 out of 9 in 6hvx

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Magnesium binding site 9 out of 9 in the Yeast 20S Proteasome in Complex with 4


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

b:61.2
occ:1.00
 O Z:VAL198 2.6 48.2 1.0
O Z:THR192 2.6 56.2 1.0
O Z:HIS195 3.0 45.0 1.0
O Z:ASP222 3.4 65.7 1.0
C Z:THR192 3.7 57.5 1.0
NH2 Z:ARG28 3.7 63.3 1.0
C Z:VAL198 3.8 50.5 1.0
CG2 Z:THR192 3.9 55.5 1.0
O Z:ILE196 3.9 48.1 1.0
C Z:HIS195 4.0 45.3 1.0
CA Z:ILE196 4.0 45.7 1.0
NH2 H:ARG19 4.0 64.0 1.0
CA Z:THR192 4.2 56.4 1.0
C Z:ILE196 4.2 45.5 1.0
OD1 Z:ASP222 4.3 67.3 1.0
N Z:ILE196 4.4 45.0 1.0
C Z:ASP222 4.5 68.2 1.0
N Z:VAL198 4.6 47.5 1.0
CB Z:THR192 4.7 55.0 1.0
N Z:GLY199 4.7 52.2 1.0
CA Z:GLY199 4.7 52.9 1.0
CA Z:VAL198 4.7 48.5 1.0
CZ Z:ARG28 4.8 58.9 1.0
CZ H:ARG19 4.8 61.6 1.0
NH1 H:ARG19 4.9 63.9 1.0
N Z:GLU193 4.9 57.1 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 07:33:47 2025

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