Magnesium in PDB 8olr: Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
Enzymatic activity of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
All present enzymatic activity of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A:
3.4.25.1;
Protein crystallography data
The structure of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A, PDB code: 8olr
was solved by
A.Illigmann,
M.-T.Vielberg,
M.Lakemeyer,
F.Wolf,
N.Staudt,
T.Dema,
P.Stange,
I.Malik,
S.Grond,
S.A.Sieber,
M.Groll,
L.Kaysser,
H.Broetz-Oesterhelt,
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 (°)
|
136.96,
302.05,
146.01,
90,
113.09,
90
|
R / Rfree (%)
|
18.2 /
20.8
|
Other elements in 8olr:
The structure of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
(pdb code 8olr). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A, PDB code: 8olr:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 8olr
Go back to
Magnesium Binding Sites List in 8olr
Magnesium binding site 1 out
of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg301
b:74.6
occ:1.00
|
O
|
G:MET125
|
2.0
|
88.6
|
1.0
|
O
|
G:TYR119
|
2.2
|
77.2
|
1.0
|
O
|
G:ARG122
|
2.6
|
73.5
|
1.0
|
OG1
|
G:THR8
|
2.6
|
75.8
|
1.0
|
C
|
G:MET125
|
3.3
|
84.6
|
1.0
|
CG2
|
G:THR8
|
3.3
|
69.8
|
1.0
|
C
|
G:TYR119
|
3.5
|
71.9
|
1.0
|
CB
|
G:THR8
|
3.5
|
72.4
|
1.0
|
C
|
G:ARG122
|
3.7
|
75.5
|
1.0
|
O
|
G:ALA123
|
3.8
|
85.4
|
1.0
|
CA
|
G:ARG126
|
4.0
|
75.5
|
1.0
|
N
|
G:ARG126
|
4.1
|
77.5
|
1.0
|
C
|
G:ALA123
|
4.1
|
82.9
|
1.0
|
CA
|
G:ALA123
|
4.1
|
78.3
|
1.0
|
CA
|
G:TYR119
|
4.2
|
69.7
|
1.0
|
N
|
G:ALA123
|
4.3
|
76.9
|
1.0
|
CA
|
G:MET125
|
4.3
|
93.4
|
1.0
|
CD
|
G:PRO127
|
4.4
|
75.2
|
1.0
|
N
|
G:MET125
|
4.4
|
89.7
|
1.0
|
N
|
G:THR120
|
4.5
|
70.8
|
1.0
|
N
|
G:THR8
|
4.5
|
75.2
|
1.0
|
C
|
G:ARG126
|
4.6
|
77.7
|
1.0
|
CA
|
G:THR8
|
4.6
|
72.6
|
1.0
|
CA
|
G:THR120
|
4.7
|
70.2
|
1.0
|
N
|
G:PRO127
|
4.7
|
75.5
|
1.0
|
CB
|
G:TYR119
|
4.8
|
68.3
|
1.0
|
CB
|
G:MET125
|
4.8
|
103.3
|
1.0
|
C
|
G:THR120
|
4.8
|
70.3
|
1.0
|
N
|
G:ARG122
|
4.8
|
72.6
|
1.0
|
CA
|
G:ARG122
|
4.9
|
76.6
|
1.0
|
N
|
G:TYR124
|
5.0
|
86.5
|
1.0
|
CG
|
G:PRO127
|
5.0
|
73.3
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 8olr
Go back to
Magnesium Binding Sites List in 8olr
Magnesium binding site 2 out
of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg301
b:77.6
occ:1.00
|
O
|
I:SER180
|
2.5
|
68.7
|
1.0
|
O
|
I:ALA174
|
2.7
|
72.4
|
1.0
|
O
|
I:ASP177
|
2.7
|
70.2
|
1.0
|
C
|
I:ALA174
|
3.7
|
72.8
|
1.0
|
OXT
|
I:ASP204
|
3.7
|
84.5
|
1.0
|
C
|
I:SER180
|
3.7
|
68.6
|
1.0
|
C
|
I:ASP177
|
3.9
|
70.9
|
1.0
|
CA
|
I:ASP175
|
4.0
|
71.8
|
1.0
|
N
|
I:ASP175
|
4.3
|
71.0
|
1.0
|
C
|
I:ASP175
|
4.3
|
70.1
|
1.0
|
CA
|
I:GLY181
|
4.4
|
67.9
|
1.0
|
O
|
I:ASP175
|
4.4
|
73.0
|
1.0
|
N
|
I:GLY181
|
4.5
|
66.4
|
1.0
|
OD1
|
I:ASP175
|
4.5
|
77.1
|
1.0
|
N
|
I:ASP177
|
4.6
|
72.2
|
1.0
|
C
|
I:ASP204
|
4.7
|
79.6
|
1.0
|
O
|
I:ALA178
|
4.7
|
70.3
|
1.0
|
N
|
I:SER180
|
4.7
|
64.6
|
1.0
|
CA
|
I:SER180
|
4.8
|
65.9
|
1.0
|
N
|
I:ALA178
|
4.8
|
67.5
|
1.0
|
C
|
I:ALA178
|
4.8
|
68.0
|
1.0
|
CA
|
I:ASP177
|
4.8
|
73.4
|
1.0
|
O
|
I:ASP204
|
4.8
|
80.7
|
1.0
|
CA
|
I:ALA174
|
4.8
|
71.2
|
1.0
|
CA
|
I:ALA178
|
4.8
|
67.5
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 8olr
Go back to
Magnesium Binding Sites List in 8olr
Magnesium binding site 3 out
of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mg301
b:80.9
occ:1.00
|
O
|
K:ALA165
|
2.2
|
63.1
|
1.0
|
O
|
K:ASP168
|
2.2
|
59.7
|
1.0
|
O
|
W:ASP204
|
2.3
|
87.1
|
1.0
|
O
|
K:SER171
|
3.0
|
66.1
|
1.0
|
C
|
W:ASP204
|
3.1
|
90.2
|
1.0
|
C
|
K:ASP168
|
3.2
|
61.5
|
1.0
|
C
|
K:ALA165
|
3.4
|
65.4
|
1.0
|
CA
|
W:ASP204
|
3.5
|
82.8
|
1.0
|
O
|
K:HIS166
|
3.6
|
71.5
|
1.0
|
NH1
|
K:ARG19
|
3.8
|
77.8
|
1.0
|
CA
|
K:ALA169
|
3.8
|
63.0
|
1.0
|
N
|
K:ALA169
|
3.8
|
61.0
|
1.0
|
CB
|
W:ASP204
|
4.0
|
83.2
|
1.0
|
C
|
K:HIS166
|
4.0
|
68.8
|
1.0
|
OXT
|
W:ASP204
|
4.0
|
100.0
|
1.0
|
C
|
K:ALA169
|
4.1
|
65.8
|
1.0
|
N
|
K:ASP168
|
4.2
|
66.7
|
1.0
|
O
|
K:ALA169
|
4.2
|
69.1
|
1.0
|
C
|
K:SER171
|
4.3
|
65.7
|
1.0
|
CA
|
K:ASP168
|
4.3
|
63.2
|
1.0
|
N
|
K:HIS166
|
4.3
|
67.5
|
1.0
|
CA
|
K:ALA165
|
4.4
|
67.1
|
1.0
|
CA
|
K:HIS166
|
4.4
|
70.4
|
1.0
|
C
|
K:ARG167
|
4.6
|
69.9
|
1.0
|
N
|
K:ARG167
|
4.7
|
68.6
|
1.0
|
O
|
K:ALA164
|
4.7
|
68.8
|
1.0
|
N
|
K:SER171
|
4.8
|
65.7
|
1.0
|
CZ
|
K:ARG19
|
4.9
|
80.6
|
1.0
|
N
|
W:ASP204
|
4.9
|
79.4
|
1.0
|
O
|
K:ARG167
|
4.9
|
70.8
|
1.0
|
N
|
K:TYR170
|
4.9
|
67.6
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 8olr
Go back to
Magnesium Binding Sites List in 8olr
Magnesium binding site 4 out
of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg201
b:65.8
occ:1.00
|
O
|
N:ILE163
|
2.6
|
65.5
|
1.0
|
O
|
N:SER169
|
2.6
|
70.6
|
1.0
|
O
|
N:ASP166
|
2.9
|
63.1
|
1.0
|
NH1
|
N:ARG19
|
3.6
|
71.8
|
1.0
|
C
|
N:ILE163
|
3.8
|
67.3
|
1.0
|
C
|
N:SER169
|
3.8
|
67.0
|
1.0
|
CD1
|
a:LEU34
|
3.9
|
72.2
|
1.0
|
C
|
N:ASP166
|
4.0
|
63.6
|
1.0
|
CG2
|
N:ILE163
|
4.0
|
64.9
|
1.0
|
CZ
|
N:ARG19
|
4.2
|
70.8
|
1.0
|
CA
|
N:GLY170
|
4.3
|
67.2
|
1.0
|
CA
|
N:GLY167
|
4.3
|
63.2
|
1.0
|
CA
|
N:ILE163
|
4.4
|
67.0
|
1.0
|
NH2
|
N:ARG19
|
4.4
|
68.0
|
1.0
|
N
|
N:GLY170
|
4.5
|
66.0
|
1.0
|
O
|
N:GLY167
|
4.5
|
60.9
|
1.0
|
N
|
N:GLY167
|
4.5
|
62.8
|
1.0
|
C
|
N:GLY167
|
4.6
|
62.7
|
1.0
|
N
|
N:LYS164
|
4.8
|
71.7
|
1.0
|
CA
|
N:SER169
|
4.8
|
63.8
|
1.0
|
CB
|
N:ILE163
|
4.8
|
66.5
|
1.0
|
O
|
N:LYS164
|
4.9
|
79.3
|
1.0
|
N
|
N:SER169
|
4.9
|
65.7
|
1.0
|
C
|
N:LYS164
|
5.0
|
73.7
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 8olr
Go back to
Magnesium Binding Sites List in 8olr
Magnesium binding site 5 out
of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Mg301
b:81.1
occ:1.00
|
O
|
W:ASP177
|
2.4
|
68.0
|
1.0
|
O
|
W:ALA174
|
2.5
|
70.6
|
1.0
|
O
|
W:SER180
|
2.5
|
75.2
|
1.0
|
C
|
W:ASP177
|
3.6
|
68.1
|
1.0
|
C
|
W:ALA174
|
3.6
|
70.8
|
1.0
|
C
|
W:SER180
|
3.7
|
72.5
|
1.0
|
OXT
|
W:ASP204
|
4.0
|
100.0
|
1.0
|
CA
|
W:ASP175
|
4.0
|
76.2
|
1.0
|
N
|
W:ASP175
|
4.2
|
73.5
|
1.0
|
C
|
W:ASP175
|
4.3
|
73.6
|
1.0
|
N
|
W:ASP177
|
4.3
|
71.7
|
1.0
|
O
|
W:ASP175
|
4.4
|
71.2
|
1.0
|
N
|
W:ALA178
|
4.5
|
64.8
|
1.0
|
O
|
W:ALA178
|
4.5
|
68.3
|
1.0
|
CA
|
W:ASP177
|
4.5
|
70.1
|
1.0
|
N
|
W:GLY181
|
4.5
|
65.3
|
1.0
|
CA
|
W:GLY181
|
4.5
|
66.0
|
1.0
|
N
|
W:SER180
|
4.5
|
73.3
|
1.0
|
C
|
W:ALA178
|
4.6
|
66.8
|
1.0
|
CA
|
W:ALA178
|
4.6
|
64.2
|
1.0
|
OD1
|
W:ASP175
|
4.6
|
82.5
|
1.0
|
CA
|
W:SER180
|
4.6
|
70.7
|
1.0
|
CA
|
W:ALA174
|
4.7
|
68.5
|
1.0
|
C
|
W:ASP204
|
4.9
|
90.2
|
1.0
|
N
|
W:ARG176
|
4.9
|
74.3
|
1.0
|
O
|
W:ASP204
|
5.0
|
87.1
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 8olr
Go back to
Magnesium Binding Sites List in 8olr
Magnesium binding site 6 out
of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Mg301
b:86.8
occ:1.00
|
O
|
Y:ASP168
|
2.2
|
65.5
|
1.0
|
O
|
I:ASP204
|
2.2
|
80.7
|
1.0
|
O
|
Y:ALA165
|
2.5
|
69.5
|
1.0
|
O
|
Y:SER171
|
2.9
|
68.3
|
1.0
|
C
|
I:ASP204
|
3.1
|
79.6
|
1.0
|
C
|
Y:ASP168
|
3.1
|
63.8
|
1.0
|
NH1
|
Y:ARG19
|
3.5
|
72.6
|
1.0
|
CA
|
Y:ALA169
|
3.6
|
65.0
|
1.0
|
N
|
Y:ALA169
|
3.7
|
64.2
|
1.0
|
C
|
Y:ALA165
|
3.7
|
65.1
|
1.0
|
CA
|
I:ASP204
|
3.7
|
78.7
|
1.0
|
O
|
Y:ALA169
|
3.8
|
65.2
|
1.0
|
C
|
Y:ALA169
|
3.8
|
66.7
|
1.0
|
O
|
Y:HIS166
|
3.9
|
64.8
|
1.0
|
OXT
|
I:ASP204
|
4.0
|
84.5
|
1.0
|
C
|
Y:SER171
|
4.2
|
66.2
|
1.0
|
CB
|
I:ASP204
|
4.2
|
79.2
|
1.0
|
N
|
Y:ASP168
|
4.3
|
65.4
|
1.0
|
CA
|
Y:ASP168
|
4.3
|
63.4
|
1.0
|
C
|
Y:HIS166
|
4.4
|
62.4
|
1.0
|
CA
|
Y:ALA165
|
4.6
|
63.3
|
1.0
|
N
|
Y:SER171
|
4.6
|
61.9
|
1.0
|
CZ
|
Y:ARG19
|
4.6
|
74.0
|
1.0
|
N
|
Y:HIS166
|
4.7
|
65.1
|
1.0
|
N
|
Y:TYR170
|
4.7
|
65.8
|
1.0
|
C
|
Y:ARG167
|
4.7
|
66.9
|
1.0
|
CA
|
Y:HIS166
|
4.8
|
65.4
|
1.0
|
O
|
Y:ALA164
|
4.9
|
65.7
|
1.0
|
CB
|
Y:ALA169
|
4.9
|
65.8
|
1.0
|
CA
|
Y:SER171
|
4.9
|
62.2
|
1.0
|
N
|
Y:ARG167
|
5.0
|
62.4
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 8olr
Go back to
Magnesium Binding Sites List in 8olr
Magnesium binding site 7 out
of 7 in the Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Yeast 20S Proteasome in Complex with the Natural Product Beta-Lactone Inhibitor Cystargolide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mg301
b:80.4
occ:1.00
|
O
|
Z:VAL198
|
2.6
|
75.9
|
1.0
|
O
|
Z:THR192
|
2.7
|
74.7
|
1.0
|
O
|
Z:HIS195
|
3.0
|
64.0
|
1.0
|
O
|
Z:ASP222
|
3.4
|
90.4
|
1.0
|
NH2
|
Z:ARG28
|
3.7
|
82.4
|
1.0
|
C
|
Z:THR192
|
3.8
|
76.8
|
1.0
|
C
|
Z:VAL198
|
3.8
|
76.0
|
1.0
|
O
|
Z:ILE196
|
3.8
|
76.8
|
1.0
|
CG2
|
Z:THR192
|
3.9
|
75.9
|
1.0
|
C
|
Z:HIS195
|
4.0
|
66.1
|
1.0
|
CA
|
Z:ILE196
|
4.0
|
70.3
|
1.0
|
C
|
Z:ILE196
|
4.0
|
71.3
|
1.0
|
NH2
|
H:ARG19
|
4.1
|
84.9
|
1.0
|
OD1
|
Z:ASP222
|
4.1
|
95.5
|
1.0
|
CA
|
Z:THR192
|
4.1
|
76.6
|
1.0
|
N
|
Z:VAL198
|
4.4
|
71.7
|
1.0
|
N
|
Z:ILE196
|
4.4
|
66.7
|
1.0
|
C
|
Z:ASP222
|
4.6
|
95.6
|
1.0
|
CB
|
Z:THR192
|
4.6
|
76.2
|
1.0
|
CA
|
Z:VAL198
|
4.6
|
71.2
|
1.0
|
N
|
Z:GLY199
|
4.7
|
75.0
|
1.0
|
CA
|
Z:GLY199
|
4.8
|
76.5
|
1.0
|
CZ
|
Z:ARG28
|
4.8
|
80.1
|
1.0
|
N
|
Z:GLN197
|
4.9
|
70.1
|
1.0
|
N
|
Z:GLU193
|
5.0
|
79.2
|
1.0
|
|
Reference:
A.Illigmann,
M.T.Vielberg,
M.Lakemeyer,
F.Wolf,
T.Dema,
P.Stange,
W.Kuttenlochner,
E.Liebhart,
A.Kulik,
N.Staudt,
I.Malik,
S.Grond,
S.A.Sieber,
L.Kaysser,
M.Groll,
H.Brotz-Oesterhelt.
Structure of Staphylococcus Aureus Clpp Bound to the Covalent Active Site Inhibitor Cystargolide A. Angew.Chem.Int.Ed.Engl. 14028 2023.
ISSN: ESSN 1521-3773
PubMed: 38029352
DOI: 10.1002/ANIE.202314028
Page generated: Fri Oct 4 14:52:41 2024
|