Magnesium in PDB 6gop: Yeast 20S Proteasome in Complex with Homosalinosporamide A
Enzymatic activity of Yeast 20S Proteasome in Complex with Homosalinosporamide A
All present enzymatic activity of Yeast 20S Proteasome in Complex with Homosalinosporamide A:
3.4.25.1;
Protein crystallography data
The structure of Yeast 20S Proteasome in Complex with Homosalinosporamide A, PDB code: 6gop
was solved by
M.Groll,
D.Romo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.040,
299.810,
144.410,
90.00,
112.56,
90.00
|
R / Rfree (%)
|
19.7 /
23.3
|
Other elements in 6gop:
The structure of Yeast 20S Proteasome in Complex with Homosalinosporamide A also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Yeast 20S Proteasome in Complex with Homosalinosporamide A
(pdb code 6gop). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Yeast 20S Proteasome in Complex with Homosalinosporamide A, PDB code: 6gop:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 6gop
Go back to
Magnesium Binding Sites List in 6gop
Magnesium binding site 1 out
of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A
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 Homosalinosporamide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg301
b:46.4
occ:1.00
|
O
|
G:MET125
|
2.1
|
47.5
|
1.0
|
O
|
G:TYR119
|
2.6
|
36.7
|
1.0
|
OG1
|
G:THR8
|
2.6
|
39.2
|
1.0
|
O
|
G:ARG122
|
2.7
|
41.2
|
1.0
|
CG2
|
G:THR8
|
3.2
|
39.5
|
1.0
|
O
|
G:ALA123
|
3.3
|
54.8
|
1.0
|
C
|
G:MET125
|
3.3
|
45.6
|
1.0
|
CB
|
G:THR8
|
3.5
|
39.6
|
1.0
|
C
|
G:ALA123
|
3.7
|
47.5
|
1.0
|
CA
|
G:ALA123
|
3.8
|
45.0
|
1.0
|
C
|
G:TYR119
|
3.8
|
35.3
|
1.0
|
C
|
G:ARG122
|
3.8
|
42.9
|
1.0
|
CA
|
G:ARG126
|
4.0
|
40.0
|
1.0
|
N
|
G:ARG126
|
4.1
|
41.8
|
1.0
|
N
|
G:THR8
|
4.2
|
42.9
|
1.0
|
N
|
G:MET125
|
4.2
|
46.2
|
1.0
|
N
|
G:ALA123
|
4.3
|
43.3
|
1.0
|
CA
|
G:MET125
|
4.3
|
48.7
|
1.0
|
CD
|
G:PRO127
|
4.4
|
37.3
|
1.0
|
CA
|
G:THR8
|
4.5
|
41.3
|
1.0
|
CA
|
G:TYR119
|
4.6
|
33.3
|
1.0
|
C
|
G:ARG126
|
4.6
|
38.9
|
1.0
|
N
|
G:TYR124
|
4.7
|
48.9
|
1.0
|
N
|
G:PRO127
|
4.8
|
36.6
|
1.0
|
N
|
G:THR120
|
4.8
|
34.8
|
1.0
|
C
|
G:TYR124
|
4.9
|
44.7
|
1.0
|
CB
|
G:MET125
|
4.9
|
54.6
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 6gop
Go back to
Magnesium Binding Sites List in 6gop
Magnesium binding site 2 out
of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A
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 Homosalinosporamide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg301
b:39.4
occ:1.00
|
O
|
I:ASP204
|
2.2
|
52.7
|
1.0
|
O
|
Y:ASP168
|
2.4
|
38.0
|
1.0
|
O
|
Y:ALA165
|
2.5
|
36.3
|
1.0
|
C
|
I:ASP204
|
3.0
|
53.4
|
1.0
|
O
|
Y:SER171
|
3.2
|
37.5
|
1.0
|
C
|
Y:ASP168
|
3.2
|
38.4
|
1.0
|
CA
|
Y:ALA169
|
3.4
|
38.7
|
1.0
|
CA
|
I:ASP204
|
3.5
|
52.1
|
1.0
|
O
|
I:HOH414
|
3.6
|
47.0
|
1.0
|
O
|
Y:HIS166
|
3.6
|
35.1
|
1.0
|
NH1
|
Y:ARG19
|
3.6
|
55.0
|
1.0
|
N
|
Y:ALA169
|
3.7
|
39.3
|
1.0
|
C
|
Y:ALA165
|
3.7
|
36.8
|
1.0
|
O
|
Y:ALA169
|
3.8
|
36.0
|
1.0
|
C
|
Y:ALA169
|
3.8
|
37.7
|
1.0
|
CB
|
I:ASP204
|
3.9
|
53.2
|
1.0
|
OXT
|
I:ASP204
|
4.0
|
52.3
|
1.0
|
C
|
Y:HIS166
|
4.1
|
37.2
|
1.0
|
C
|
Y:SER171
|
4.4
|
38.0
|
1.0
|
N
|
Y:ASP168
|
4.4
|
37.4
|
1.0
|
CA
|
Y:ASP168
|
4.4
|
37.5
|
1.0
|
O
|
I:HOH410
|
4.5
|
59.3
|
1.0
|
N
|
Y:HIS166
|
4.5
|
37.5
|
1.0
|
CA
|
Y:HIS166
|
4.6
|
36.0
|
1.0
|
C
|
Y:ARG167
|
4.6
|
38.3
|
1.0
|
CA
|
Y:ALA165
|
4.6
|
37.1
|
1.0
|
N
|
Y:SER171
|
4.7
|
36.3
|
1.0
|
CB
|
Y:ALA169
|
4.7
|
38.0
|
1.0
|
N
|
Y:ARG167
|
4.7
|
37.6
|
1.0
|
N
|
Y:TYR170
|
4.8
|
38.7
|
1.0
|
CZ
|
Y:ARG19
|
4.8
|
53.7
|
1.0
|
O
|
Y:ALA164
|
4.8
|
38.8
|
1.0
|
O
|
Y:ARG167
|
4.8
|
36.7
|
1.0
|
N
|
I:ASP204
|
4.9
|
51.2
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 6gop
Go back to
Magnesium Binding Sites List in 6gop
Magnesium binding site 3 out
of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A
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 Homosalinosporamide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg201
b:34.7
occ:1.00
|
OE1
|
J:GLN118
|
3.3
|
34.8
|
1.0
|
O
|
J:THR124
|
3.6
|
34.5
|
1.0
|
CB
|
J:ASP120
|
3.7
|
33.0
|
1.0
|
OD2
|
J:ASP120
|
3.8
|
33.9
|
1.0
|
CG
|
J:ASP120
|
3.8
|
33.5
|
1.0
|
N
|
J:ASP120
|
4.0
|
31.5
|
1.0
|
CD
|
J:GLN118
|
4.2
|
32.5
|
1.0
|
CB
|
J:THR124
|
4.2
|
34.8
|
1.0
|
CE1
|
J:HIS133
|
4.2
|
33.1
|
1.0
|
CG2
|
J:THR124
|
4.3
|
34.3
|
1.0
|
CG
|
J:GLN118
|
4.4
|
32.6
|
1.0
|
CA
|
J:ASP120
|
4.5
|
31.6
|
1.0
|
OD1
|
J:ASP120
|
4.5
|
33.9
|
1.0
|
C
|
J:THR124
|
4.6
|
34.3
|
1.0
|
O
|
J:GLN118
|
4.6
|
30.1
|
1.0
|
CG1
|
I:VAL35
|
4.6
|
42.9
|
1.0
|
C
|
J:ILE119
|
4.8
|
30.8
|
1.0
|
ND1
|
J:HIS133
|
4.8
|
32.5
|
1.0
|
OG
|
I:SER30
|
5.0
|
46.8
|
1.0
|
C
|
J:GLN118
|
5.0
|
30.0
|
1.0
|
CA
|
J:ILE119
|
5.0
|
28.7
|
1.0
|
O
|
J:HOH307
|
5.0
|
36.3
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 6gop
Go back to
Magnesium Binding Sites List in 6gop
Magnesium binding site 4 out
of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A
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 Homosalinosporamide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mg302
b:37.6
occ:1.00
|
O
|
K:ALA165
|
2.4
|
40.5
|
1.0
|
O
|
K:ASP168
|
2.4
|
35.6
|
1.0
|
O
|
W:ASP204
|
2.5
|
53.5
|
1.0
|
C
|
K:ASP168
|
3.1
|
36.6
|
1.0
|
O
|
K:HIS166
|
3.2
|
42.9
|
1.0
|
C
|
W:ASP204
|
3.2
|
52.5
|
1.0
|
O
|
K:SER171
|
3.4
|
40.0
|
1.0
|
C
|
K:ALA165
|
3.5
|
39.0
|
1.0
|
CA
|
W:ASP204
|
3.5
|
51.4
|
1.0
|
CA
|
K:ALA169
|
3.6
|
38.3
|
1.0
|
N
|
K:ALA169
|
3.6
|
37.5
|
1.0
|
C
|
K:HIS166
|
3.7
|
40.0
|
1.0
|
CB
|
W:ASP204
|
4.0
|
49.8
|
1.0
|
NH1
|
K:ARG19
|
4.0
|
51.6
|
1.0
|
C
|
K:ALA169
|
4.1
|
38.9
|
1.0
|
OXT
|
W:ASP204
|
4.1
|
58.6
|
1.0
|
N
|
K:ASP168
|
4.1
|
36.7
|
1.0
|
O
|
K:ALA169
|
4.2
|
38.9
|
1.0
|
CA
|
K:HIS166
|
4.2
|
39.6
|
1.0
|
C
|
K:ARG167
|
4.2
|
39.0
|
1.0
|
CA
|
K:ASP168
|
4.2
|
36.5
|
1.0
|
N
|
K:HIS166
|
4.3
|
38.8
|
1.0
|
N
|
K:ARG167
|
4.3
|
39.2
|
1.0
|
O
|
K:ARG167
|
4.5
|
41.0
|
1.0
|
CA
|
K:ALA165
|
4.5
|
38.4
|
1.0
|
O
|
K:ALA164
|
4.6
|
39.8
|
1.0
|
C
|
K:SER171
|
4.6
|
38.4
|
1.0
|
CA
|
K:ARG167
|
4.8
|
38.8
|
1.0
|
CB
|
K:ALA169
|
4.8
|
37.6
|
1.0
|
N
|
W:ASP204
|
4.9
|
49.6
|
1.0
|
N
|
K:SER171
|
4.9
|
35.0
|
1.0
|
NE1
|
W:TRP182
|
4.9
|
44.2
|
1.0
|
N
|
K:TYR170
|
5.0
|
38.9
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 6gop
Go back to
Magnesium Binding Sites List in 6gop
Magnesium binding site 5 out
of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A
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 Homosalinosporamide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg301
b:56.7
occ:1.00
|
O
|
V:ASP166
|
2.0
|
36.1
|
1.0
|
OXT
|
L:ASP222
|
2.1
|
66.0
|
1.0
|
O
|
V:ILE163
|
2.3
|
40.3
|
1.0
|
O
|
V:SER169
|
2.7
|
35.7
|
1.0
|
C
|
V:ASP166
|
3.0
|
36.9
|
1.0
|
C
|
L:ASP222
|
3.1
|
59.6
|
1.0
|
C
|
V:ILE163
|
3.4
|
42.6
|
1.0
|
O
|
V:TRP164
|
3.6
|
50.4
|
1.0
|
N
|
V:LEU167
|
3.6
|
36.5
|
1.0
|
CA
|
V:LEU167
|
3.7
|
36.4
|
1.0
|
CA
|
L:ASP222
|
3.7
|
57.5
|
1.0
|
N
|
V:ASP166
|
3.9
|
36.8
|
1.0
|
C
|
V:TRP164
|
3.9
|
44.6
|
1.0
|
C
|
V:SER169
|
3.9
|
36.2
|
1.0
|
O
|
V:GLY162
|
3.9
|
41.3
|
1.0
|
O
|
L:ASP222
|
4.0
|
61.2
|
1.0
|
CA
|
V:ASP166
|
4.0
|
36.8
|
1.0
|
N
|
V:TRP164
|
4.2
|
43.0
|
1.0
|
C
|
V:LEU167
|
4.2
|
36.2
|
1.0
|
CA
|
V:TRP164
|
4.2
|
42.9
|
1.0
|
NH1
|
V:ARG19
|
4.3
|
51.2
|
1.0
|
CB
|
L:ASP222
|
4.3
|
56.7
|
1.0
|
CA
|
V:ILE163
|
4.3
|
42.5
|
1.0
|
N
|
V:ASN165
|
4.4
|
42.4
|
1.0
|
C
|
V:ASN165
|
4.4
|
39.6
|
1.0
|
O
|
V:LEU167
|
4.5
|
38.0
|
1.0
|
N
|
V:SER169
|
4.5
|
34.9
|
1.0
|
CA
|
V:SER169
|
4.7
|
34.9
|
1.0
|
CD2
|
V:LEU167
|
4.7
|
31.2
|
1.0
|
O
|
L:ARG221
|
4.7
|
54.4
|
1.0
|
CB
|
V:ASP166
|
4.9
|
35.7
|
1.0
|
N
|
V:GLY170
|
4.9
|
37.1
|
1.0
|
CB
|
V:SER169
|
4.9
|
35.2
|
1.0
|
C
|
V:GLY162
|
4.9
|
41.5
|
1.0
|
N
|
L:ASP222
|
4.9
|
54.7
|
1.0
|
CB
|
V:LEU167
|
4.9
|
34.6
|
1.0
|
CA
|
V:GLY170
|
4.9
|
39.4
|
1.0
|
CA
|
V:ASN165
|
5.0
|
40.9
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 6gop
Go back to
Magnesium Binding Sites List in 6gop
Magnesium binding site 6 out
of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A
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 Homosalinosporamide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg202
b:30.8
occ:1.00
|
O
|
N:SER169
|
2.5
|
32.3
|
1.0
|
O
|
N:ILE163
|
2.7
|
34.4
|
1.0
|
O
|
N:ASP166
|
3.1
|
34.8
|
1.0
|
NH1
|
N:ARG19
|
3.6
|
37.1
|
1.0
|
C
|
N:SER169
|
3.7
|
33.0
|
1.0
|
CD1
|
a:LEU34
|
3.7
|
42.6
|
1.0
|
C
|
N:ILE163
|
3.8
|
35.6
|
1.0
|
CG2
|
N:ILE163
|
3.9
|
35.6
|
1.0
|
CA
|
N:GLY170
|
4.2
|
35.7
|
1.0
|
C
|
N:ASP166
|
4.2
|
35.4
|
1.0
|
CZ
|
N:ARG19
|
4.3
|
36.8
|
1.0
|
NH2
|
N:ARG19
|
4.4
|
36.5
|
1.0
|
N
|
N:GLY170
|
4.4
|
33.5
|
1.0
|
CA
|
N:ILE163
|
4.4
|
35.8
|
1.0
|
O
|
N:GLY167
|
4.5
|
34.4
|
1.0
|
CA
|
N:GLY167
|
4.5
|
35.8
|
1.0
|
C
|
N:GLY167
|
4.7
|
34.4
|
1.0
|
O
|
a:HOH322
|
4.8
|
22.8
|
1.0
|
N
|
N:GLY167
|
4.8
|
34.8
|
1.0
|
CB
|
N:ILE163
|
4.8
|
35.3
|
1.0
|
N
|
N:LYS164
|
4.8
|
37.6
|
1.0
|
CA
|
N:SER169
|
4.9
|
31.9
|
1.0
|
N
|
N:SER169
|
4.9
|
33.5
|
1.0
|
O
|
N:LYS164
|
5.0
|
38.5
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 6gop
Go back to
Magnesium Binding Sites List in 6gop
Magnesium binding site 7 out
of 7 in the Yeast 20S Proteasome in Complex with Homosalinosporamide A
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 Homosalinosporamide A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mg301
b:35.9
occ:1.00
|
O
|
Z:VAL198
|
2.2
|
46.6
|
1.0
|
O
|
Z:HOH406
|
2.5
|
27.8
|
1.0
|
O
|
Z:THR192
|
2.9
|
51.1
|
1.0
|
O
|
Z:HIS195
|
3.2
|
38.3
|
1.0
|
O
|
Z:ASP222
|
3.3
|
60.0
|
1.0
|
NH2
|
Z:ARG28
|
3.4
|
50.4
|
1.0
|
C
|
Z:VAL198
|
3.5
|
45.5
|
1.0
|
CG2
|
Z:THR192
|
3.5
|
50.3
|
1.0
|
C
|
Z:THR192
|
3.8
|
52.0
|
1.0
|
O
|
Z:ILE196
|
3.9
|
36.8
|
1.0
|
CA
|
Z:THR192
|
4.1
|
51.3
|
1.0
|
OD1
|
Z:ASP222
|
4.2
|
59.9
|
1.0
|
CA
|
Z:GLY199
|
4.3
|
46.4
|
1.0
|
C
|
Z:HIS195
|
4.3
|
39.6
|
1.0
|
C
|
Z:ILE196
|
4.3
|
37.2
|
1.0
|
N
|
Z:GLY199
|
4.3
|
45.7
|
1.0
|
CA
|
Z:ILE196
|
4.3
|
39.5
|
1.0
|
CZ
|
Z:ARG28
|
4.3
|
47.9
|
1.0
|
C
|
Z:ASP222
|
4.4
|
62.0
|
1.0
|
CB
|
Z:THR192
|
4.4
|
50.5
|
1.0
|
N
|
Z:VAL198
|
4.4
|
40.0
|
1.0
|
CA
|
Z:VAL198
|
4.5
|
41.7
|
1.0
|
NH1
|
Z:ARG28
|
4.5
|
48.2
|
1.0
|
O
|
Z:LYS220
|
4.6
|
53.1
|
1.0
|
NH2
|
H:ARG19
|
4.6
|
60.5
|
1.0
|
N
|
Z:ILE196
|
4.8
|
39.0
|
1.0
|
OXT
|
Z:ASP222
|
5.0
|
57.3
|
1.0
|
|
Reference:
M.Groll,
H.Nguyen,
S.Vellalath,
D.Romo.
(-)-Homosalinosporamide A and Its Mode of Proteasome Inhibition: An X-Ray Crystallographic Study. Mar Drugs V. 16 2018.
ISSN: ISSN 1660-3397
PubMed: 30029468
DOI: 10.3390/MD16070240
Page generated: Tue Oct 1 01:19:03 2024
|