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Magnesium in PDB 6hw0: Yeast 20S Proteasome in Complex with 7

Enzymatic activity of Yeast 20S Proteasome in Complex with 7

All present enzymatic activity of Yeast 20S Proteasome in Complex with 7:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome in Complex with 7, PDB code: 6hw0 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 (°) 137.300, 299.660, 145.350, 90.00, 113.43, 90.00
R / Rfree (%) 17.4 / 20.6

Other elements in 6hw0:

The structure of Yeast 20S Proteasome in Complex with 7 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 7 (pdb code 6hw0). 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 7, PDB code: 6hw0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6hw0

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Magnesium binding site 1 out of 8 in the Yeast 20S Proteasome in Complex with 7


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

b:55.3
occ:1.00
 O G:MET125 2.3 55.5 1.0
OG1 G:THR8 2.6 45.7 1.0
O G:ARG122 2.8 49.6 1.0
O G:TYR119 3.0 45.6 1.0
O G:ALA123 3.1 54.5 1.0
CG2 G:THR8 3.2 48.7 1.0
C G:MET125 3.4 52.7 1.0
CB G:THR8 3.5 47.6 1.0
C G:ALA123 3.6 52.5 1.0
CA G:ALA123 3.7 50.8 1.0
C G:ARG122 3.9 48.7 1.0
N G:THR8 4.0 53.5 1.0
CA G:ARG126 4.1 46.7 1.0
N G:ARG126 4.2 48.4 1.0
C G:TYR119 4.2 44.5 1.0
N G:ALA123 4.3 47.8 1.0
N G:MET125 4.3 53.2 1.0
CA G:THR8 4.4 50.2 1.0
CA G:MET125 4.5 56.0 1.0
CD G:PRO127 4.6 45.0 1.0
N G:TYR124 4.7 55.2 1.0
C G:ARG126 4.8 46.3 1.0
CA G:TYR119 5.0 41.9 1.0
C G:TYR124 5.0 52.0 1.0

Magnesium binding site 2 out of 8 in 6hw0

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Magnesium binding site 2 out of 8 in the Yeast 20S Proteasome in Complex with 7


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

b:69.2
occ:1.00
 O I:ASP177 2.6 54.0 1.0
O I:SER180 2.8 59.6 1.0
O I:ALA174 3.2 59.4 1.0
OXT I:ASP204 3.3 84.4 1.0
C I:ASP177 3.7 54.9 1.0
O I:ASP204 4.0 91.6 1.0
O I:ALA178 4.0 61.2 1.0
C I:SER180 4.0 54.8 1.0
C I:ASP204 4.1 83.3 1.0
CA I:ALA178 4.2 53.8 1.0
C I:ALA174 4.3 59.1 1.0
C I:ALA178 4.3 56.4 1.0
N I:ALA178 4.4 53.5 1.0
NH1 Y:ARG19 4.4 72.6 1.0
NH2 Y:ARG19 4.4 73.9 1.0
CA I:ASP175 4.4 59.0 1.0
O I:ASP175 4.6 60.5 1.0
C I:ASP175 4.6 57.4 1.0
N I:ASP177 4.7 52.8 1.0
N I:SER180 4.8 52.1 1.0
N I:ASP175 4.8 58.6 1.0
CA I:ASP177 4.8 55.0 1.0
CZ Y:ARG19 4.8 70.8 1.0
CA I:GLY181 4.8 56.6 1.0
N I:GLY181 4.9 54.8 1.0

Magnesium binding site 3 out of 8 in 6hw0

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Magnesium binding site 3 out of 8 in the Yeast 20S Proteasome in Complex with 7


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

b:65.7
occ:1.00
 O I:ASP204 2.4 91.6 1.0
O Y:ASP168 2.4 52.8 1.0
O Y:ALA165 2.5 48.3 1.0
O Y:SER171 3.0 56.2 1.0
C I:ASP204 3.1 83.3 1.0
C Y:ASP168 3.3 54.1 1.0
CA I:ASP204 3.5 74.6 1.0
CA Y:ALA169 3.6 53.2 1.0
O Y:HIS166 3.6 58.6 1.0
C Y:ALA165 3.7 52.7 1.0
O Y:ALA169 3.8 56.6 1.0
N Y:ALA169 3.8 55.5 1.0
C Y:ALA169 3.9 52.6 1.0
NH1 Y:ARG19 3.9 72.6 1.0
CB I:ASP204 3.9 73.3 1.0
OXT I:ASP204 4.0 84.4 1.0
C Y:HIS166 4.1 54.0 1.0
C Y:SER171 4.2 53.3 1.0
N Y:ASP168 4.5 54.5 1.0
N Y:HIS166 4.5 52.5 1.0
CA Y:HIS166 4.5 52.1 1.0
CA Y:ASP168 4.5 52.0 1.0
C Y:ARG167 4.6 55.6 1.0
CA Y:ALA165 4.6 53.2 1.0
N Y:SER171 4.7 52.1 1.0
O Y:ARG167 4.8 55.8 1.0
O Y:ALA164 4.8 49.2 1.0
N Y:ARG167 4.8 51.7 1.0
N Y:TYR170 4.8 50.3 1.0
N I:ASP204 4.9 73.0 1.0
CB Y:ALA169 4.9 51.9 1.0
CZ Y:ARG19 4.9 70.8 1.0
CA Y:SER171 5.0 50.1 1.0

Magnesium binding site 4 out of 8 in 6hw0

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Magnesium binding site 4 out of 8 in the Yeast 20S Proteasome in Complex with 7


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

b:77.9
occ:1.00
 O K:ASP168 2.2 52.9 1.0
O K:ALA165 2.4 56.6 1.0
O W:ASP204 2.5 83.8 1.0
O K:SER171 3.0 56.2 1.0
C K:ASP168 3.2 55.5 1.0
C W:ASP204 3.2 80.3 1.0
O K:HIS166 3.5 58.1 1.0
CA K:ALA169 3.5 58.4 1.0
C K:ALA165 3.5 56.6 1.0
CA W:ASP204 3.6 72.3 1.0
N K:ALA169 3.7 57.4 1.0
O K:ALA169 3.8 58.6 1.0
C K:ALA169 3.9 59.7 1.0
C K:HIS166 4.0 56.5 1.0
CB W:ASP204 4.0 70.7 1.0
NH1 K:ARG19 4.1 67.5 1.0
OXT W:ASP204 4.1 89.9 1.0
C K:SER171 4.2 57.6 1.0
N K:ASP168 4.3 55.6 1.0
CA K:ASP168 4.4 54.0 1.0
N K:HIS166 4.4 54.8 1.0
CA K:HIS166 4.4 54.8 1.0
C K:ARG167 4.5 56.6 1.0
CA K:ALA165 4.5 56.5 1.0
O K:ALA164 4.6 55.5 1.0
N K:SER171 4.6 56.6 1.0
O K:ARG167 4.6 60.5 1.0
N K:ARG167 4.7 54.0 1.0
N K:TYR170 4.8 58.0 1.0
CA K:SER171 4.9 55.9 1.0
CB K:ALA169 4.9 57.9 1.0
N W:ASP204 5.0 69.7 1.0

Magnesium binding site 5 out of 8 in 6hw0

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Magnesium binding site 5 out of 8 in the Yeast 20S Proteasome in Complex with 7


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

b:82.6
occ:1.00
 OXT L:ASP222 2.0 88.3 1.0
O V:ASP166 2.0 56.5 1.0
O V:ILE163 2.2 58.6 1.0
O V:SER169 2.6 59.5 1.0
C V:ASP166 3.1 59.1 1.0
C L:ASP222 3.1 83.9 1.0
C V:ILE163 3.3 62.5 1.0
CA L:ASP222 3.7 77.7 1.0
C V:SER169 3.7 56.8 1.0
CA V:LEU167 3.8 61.1 1.0
N V:LEU167 3.8 60.4 1.0
O V:GLY162 3.8 59.0 1.0
O V:TRP164 3.9 65.6 1.0
N V:ASP166 4.0 55.9 1.0
C V:TRP164 4.0 63.5 1.0
O L:ASP222 4.0 89.2 1.0
CA V:ASP166 4.1 57.7 1.0
N V:TRP164 4.2 61.5 1.0
CA V:ILE163 4.2 62.6 1.0
NH1 V:ARG19 4.2 77.2 1.0
C V:LEU167 4.2 60.0 1.0
CB L:ASP222 4.3 77.1 1.0
CA V:TRP164 4.3 63.0 1.0
O V:LEU167 4.4 63.5 1.0
N V:SER169 4.5 57.2 1.0
N V:ASN165 4.5 60.7 1.0
CA V:SER169 4.6 56.6 1.0
N V:GLY170 4.6 57.1 1.0
CA V:GLY170 4.6 59.0 1.0
C V:ASN165 4.7 57.8 1.0
CZ V:ARG19 4.7 71.2 1.0
C V:GLY162 4.8 60.2 1.0
NH2 V:ARG19 4.8 72.7 1.0
CB V:ASP166 4.9 56.3 1.0
CB V:SER169 4.9 57.5 1.0
O L:ARG221 5.0 69.4 1.0
N V:GLY168 5.0 57.9 1.0
N V:ILE163 5.0 58.9 1.0
CD2 V:LEU167 5.0 61.6 1.0

Magnesium binding site 6 out of 8 in 6hw0

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Magnesium binding site 6 out of 8 in the Yeast 20S Proteasome in Complex with 7


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

b:51.5
occ:1.00
 O N:SER169 2.5 51.0 1.0
O N:HOH306 2.7 55.6 1.0
O N:ILE163 2.8 48.5 1.0
O N:ASP166 2.8 48.6 1.0
NH1 N:ARG19 3.5 53.2 1.0
CD1 a:LEU34 3.6 51.1 1.0
C N:SER169 3.7 47.2 1.0
C N:ASP166 3.8 48.1 1.0
C N:ILE163 3.9 50.8 1.0
CA N:GLY167 4.0 47.8 1.0
O N:GLY167 4.1 48.9 1.0
CZ N:ARG19 4.2 52.2 1.0
CG2 N:ILE163 4.2 50.2 1.0
C N:GLY167 4.3 47.3 1.0
N N:GLY167 4.3 47.3 1.0
CA N:GLY170 4.4 49.3 1.0
NH2 N:ARG19 4.4 53.5 1.0
N N:GLY170 4.5 47.1 1.0
CA N:ILE163 4.6 50.1 1.0
N N:SER169 4.7 46.6 1.0
CA N:SER169 4.8 45.0 1.0
CG a:LEU34 4.8 53.2 1.0
N N:LYS164 4.9 51.8 1.0
O N:LYS164 5.0 50.2 1.0

Magnesium binding site 7 out of 8 in 6hw0

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


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

b:46.8
occ:1.00
 OE1 X:GLN118 3.6 55.2 1.0
O X:THR124 3.7 52.6 1.0
CB X:ASP120 3.9 49.9 1.0
N X:ASP120 4.1 44.1 1.0
CG X:ASP120 4.1 54.6 1.0
CG X:GLN118 4.3 48.9 1.0
OD2 X:ASP120 4.3 57.4 1.0
CB X:THR124 4.3 50.8 1.0
CD X:GLN118 4.3 49.6 1.0
O X:GLN118 4.4 53.8 1.0
CG2 X:THR124 4.4 52.1 1.0
CE1 X:HIS133 4.4 52.9 1.0
CA X:ASP120 4.6 46.3 1.0
CG1 W:VAL35 4.6 58.9 1.0
C X:THR124 4.7 51.6 1.0
OD1 X:ASP120 4.7 63.5 1.0
C X:ILE119 4.8 45.4 1.0
C X:GLN118 4.8 49.8 1.0
CD2 W:LEU28 4.9 58.3 1.0

Magnesium binding site 8 out of 8 in 6hw0

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


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

b:65.2
occ:1.00
 O Z:HOH404 2.3 62.4 1.0
O Z:VAL198 2.6 60.0 1.0
O Z:THR192 2.7 62.5 1.0
O Z:HIS195 3.0 47.7 1.0
O Z:ASP222 3.4 74.7 1.0
NH2 Z:ARG28 3.5 72.2 1.0
O Z:ILE196 3.7 57.4 1.0
C Z:THR192 3.8 64.1 1.0
C Z:VAL198 3.8 58.0 1.0
CG2 Z:THR192 3.9 63.9 1.0
C Z:HIS195 4.0 51.9 1.0
CA Z:ILE196 4.0 52.7 1.0
C Z:ILE196 4.1 52.8 1.0
CA Z:THR192 4.1 64.2 1.0
NH2 H:ARG19 4.3 71.7 1.0
OD1 Z:ASP222 4.4 80.4 1.0
N Z:ILE196 4.4 51.7 1.0
N Z:VAL198 4.5 52.5 1.0
C Z:ASP222 4.5 78.2 1.0
CZ Z:ARG28 4.6 66.6 1.0
N Z:GLY199 4.6 58.1 1.0
CB Z:THR192 4.6 63.6 1.0
CA Z:GLY199 4.6 60.2 1.0
CA Z:VAL198 4.7 55.3 1.0
NH1 Z:ARG28 4.9 67.6 1.0
NH1 H:ARG19 4.9 71.8 1.0
N Z:GLU193 5.0 63.0 1.0
CZ H:ARG19 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 02:35:33 2024

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