Sodium in PDB 7awe: Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Enzymatic activity of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
All present enzymatic activity of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid:
3.4.25.1;
Protein crystallography data
The structure of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid, PDB code: 7awe
was solved by
D.Musil,
M.Klein,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
155.95 /
2.29
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
119.471,
206.048,
162.808,
90,
106.69,
90
|
R / Rfree (%)
|
17.8 /
21.4
|
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Sodium atom in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
(pdb code 7awe). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the
Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid, PDB code: 7awe:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 13 in 7awe
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Sodium Binding Sites List in 7awe
Sodium binding site 1 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na301
b:48.2
occ:1.00
|
O
|
A:MET131
|
2.2
|
49.8
|
1.0
|
O
|
A:ASN128
|
2.3
|
47.5
|
1.0
|
O
|
A:HOH423
|
2.4
|
42.3
|
1.0
|
O
|
A:TYR125
|
2.5
|
47.9
|
1.0
|
OG1
|
A:THR14
|
2.5
|
55.1
|
1.0
|
CG2
|
A:THR14
|
3.4
|
54.0
|
1.0
|
C
|
A:ASN128
|
3.4
|
47.0
|
1.0
|
C
|
A:MET131
|
3.5
|
49.5
|
1.0
|
CB
|
A:THR14
|
3.5
|
54.2
|
1.0
|
CA
|
A:ALA129
|
3.7
|
47.6
|
1.0
|
O
|
A:ALA129
|
3.7
|
48.5
|
1.0
|
C
|
A:TYR125
|
3.7
|
48.0
|
1.0
|
C
|
A:ALA129
|
3.8
|
48.2
|
1.0
|
N
|
A:ALA129
|
4.0
|
47.0
|
1.0
|
O
|
G:HOH308
|
4.1
|
43.3
|
1.0
|
N
|
A:MET131
|
4.1
|
48.8
|
1.0
|
N
|
A:THR14
|
4.3
|
53.5
|
1.0
|
CA
|
A:MET131
|
4.4
|
49.4
|
1.0
|
N
|
A:ARG132
|
4.4
|
49.0
|
1.0
|
CA
|
A:ARG132
|
4.5
|
49.4
|
1.0
|
CA
|
A:TYR125
|
4.5
|
48.2
|
1.0
|
SD
|
A:MET131
|
4.5
|
57.1
|
1.0
|
CA
|
A:THR14
|
4.5
|
53.5
|
1.0
|
N
|
A:GLU130
|
4.6
|
48.2
|
1.0
|
CA
|
A:ASN128
|
4.6
|
46.9
|
1.0
|
N
|
A:ASN128
|
4.7
|
46.9
|
1.0
|
N
|
A:THR126
|
4.7
|
47.5
|
1.0
|
CD
|
A:PRO133
|
4.9
|
50.5
|
1.0
|
CG
|
A:MET131
|
4.9
|
51.8
|
1.0
|
C
|
A:ARG132
|
4.9
|
50.4
|
1.0
|
|
Sodium binding site 2 out
of 13 in 7awe
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Sodium Binding Sites List in 7awe
Sodium binding site 2 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na902
b:51.4
occ:1.00
|
O
|
H:MET163
|
2.3
|
41.5
|
1.0
|
O
|
H:SER169
|
2.5
|
38.9
|
1.0
|
O
|
H:ASP166
|
2.6
|
41.0
|
1.0
|
C
|
H:MET163
|
3.5
|
41.3
|
1.0
|
C
|
H:ASP166
|
3.6
|
40.8
|
1.0
|
NH1
|
H:ARG19
|
3.7
|
54.0
|
1.0
|
C
|
H:SER169
|
3.7
|
38.7
|
1.0
|
CA
|
H:GLY167
|
4.2
|
40.3
|
1.0
|
N
|
H:GLY167
|
4.3
|
40.5
|
1.0
|
CA
|
H:GLY170
|
4.4
|
39.9
|
1.0
|
O
|
b:HOH354
|
4.4
|
41.5
|
1.0
|
CA
|
H:MET163
|
4.4
|
40.9
|
1.0
|
O
|
H:GLY167
|
4.4
|
40.3
|
1.0
|
C
|
H:GLY167
|
4.5
|
40.1
|
1.0
|
N
|
H:SER164
|
4.5
|
41.1
|
1.0
|
N
|
H:GLY170
|
4.5
|
39.0
|
1.0
|
CZ
|
H:ARG19
|
4.5
|
55.7
|
1.0
|
N
|
H:ASP166
|
4.6
|
39.5
|
1.0
|
CA
|
H:SER164
|
4.6
|
40.9
|
1.0
|
C
|
H:SER164
|
4.6
|
40.4
|
1.0
|
CA
|
H:ASP166
|
4.7
|
40.1
|
1.0
|
N
|
H:SER169
|
4.7
|
38.4
|
1.0
|
CA
|
H:SER169
|
4.8
|
38.2
|
1.0
|
O
|
H:SER164
|
4.8
|
41.0
|
1.0
|
NH2
|
H:ARG19
|
4.9
|
56.3
|
1.0
|
|
Sodium binding site 3 out
of 13 in 7awe
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Sodium Binding Sites List in 7awe
Sodium binding site 3 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na301
b:39.1
occ:1.00
|
O
|
I:ILE163
|
2.2
|
43.1
|
1.0
|
O
|
I:ASP166
|
2.3
|
36.9
|
1.0
|
O
|
I:SER169
|
2.3
|
40.9
|
1.0
|
OXT
|
a:ASP213
|
2.4
|
54.8
|
1.0
|
O
|
I:HOH427
|
2.4
|
37.7
|
1.0
|
C
|
a:ASP213
|
3.4
|
54.6
|
1.0
|
C
|
I:ASP166
|
3.4
|
37.0
|
1.0
|
C
|
I:ILE163
|
3.4
|
42.5
|
1.0
|
C
|
I:SER169
|
3.4
|
40.5
|
1.0
|
CA
|
a:ASP213
|
3.6
|
53.4
|
1.0
|
NH1
|
I:ARG19
|
3.7
|
52.1
|
1.0
|
CB
|
a:ASP213
|
3.7
|
54.3
|
1.0
|
CA
|
I:LEU167
|
4.0
|
37.1
|
1.0
|
N
|
I:LEU167
|
4.1
|
37.4
|
1.0
|
N
|
I:SER169
|
4.3
|
40.1
|
1.0
|
C
|
I:LEU167
|
4.3
|
37.8
|
1.0
|
CA
|
I:SER169
|
4.3
|
40.0
|
1.0
|
O
|
I:LEU164
|
4.3
|
41.0
|
1.0
|
N
|
I:GLY170
|
4.3
|
40.8
|
1.0
|
N
|
I:ASP166
|
4.3
|
37.7
|
1.0
|
CA
|
I:ILE163
|
4.3
|
41.2
|
1.0
|
O
|
I:LEU167
|
4.4
|
38.1
|
1.0
|
CA
|
I:GLY170
|
4.4
|
42.2
|
1.0
|
N
|
I:LEU164
|
4.4
|
42.0
|
1.0
|
C
|
I:LEU164
|
4.4
|
40.8
|
1.0
|
CA
|
I:ASP166
|
4.4
|
36.9
|
1.0
|
CZ
|
I:ARG19
|
4.4
|
54.1
|
1.0
|
CA
|
I:LEU164
|
4.5
|
41.6
|
1.0
|
O
|
I:GLY162
|
4.5
|
41.9
|
1.0
|
O
|
a:ASP213
|
4.5
|
55.1
|
1.0
|
CB
|
I:SER169
|
4.6
|
40.9
|
1.0
|
NH2
|
I:ARG19
|
4.7
|
56.0
|
1.0
|
CG
|
a:ASP213
|
4.7
|
58.1
|
1.0
|
N
|
I:GLY165
|
5.0
|
39.5
|
1.0
|
|
Sodium binding site 4 out
of 13 in 7awe
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Sodium Binding Sites List in 7awe
Sodium binding site 4 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Na301
b:45.0
occ:1.00
|
O
|
J:ASP178
|
2.2
|
37.9
|
1.0
|
O
|
J:SER181
|
2.3
|
42.2
|
1.0
|
O
|
J:HOH428
|
2.4
|
39.3
|
1.0
|
O
|
J:VAL175
|
2.6
|
39.4
|
1.0
|
C
|
J:ASP178
|
3.5
|
36.9
|
1.0
|
C
|
J:SER181
|
3.5
|
41.8
|
1.0
|
O
|
J:HOH425
|
3.6
|
50.5
|
1.0
|
O
|
J:HOH417
|
3.8
|
39.0
|
1.0
|
C
|
J:VAL175
|
3.8
|
38.5
|
1.0
|
OXT
|
J:ASP205
|
4.1
|
39.8
|
1.0
|
O
|
J:HOH406
|
4.1
|
38.2
|
1.0
|
O
|
J:ALA179
|
4.1
|
36.4
|
1.0
|
N
|
J:SER181
|
4.2
|
40.8
|
1.0
|
C
|
J:ALA179
|
4.2
|
36.8
|
1.0
|
N
|
J:ALA179
|
4.3
|
36.4
|
1.0
|
CA
|
J:ALA179
|
4.3
|
36.1
|
1.0
|
N
|
J:ASP178
|
4.4
|
34.5
|
1.0
|
CA
|
J:ASP176
|
4.4
|
36.3
|
1.0
|
CA
|
J:SER181
|
4.4
|
41.4
|
1.0
|
N
|
J:GLY182
|
4.4
|
41.8
|
1.0
|
CA
|
J:ASP178
|
4.4
|
35.7
|
1.0
|
CA
|
J:GLY182
|
4.5
|
42.2
|
1.0
|
CD1
|
Z:ILE26
|
4.5
|
40.3
|
1.0
|
N
|
J:ASP176
|
4.6
|
37.0
|
1.0
|
C
|
J:ASP176
|
4.7
|
35.4
|
1.0
|
CB
|
J:ASP178
|
4.8
|
38.0
|
1.0
|
N
|
J:VAL180
|
4.8
|
37.5
|
1.0
|
CA
|
J:VAL175
|
4.8
|
38.2
|
1.0
|
OD1
|
J:ASP176
|
4.8
|
42.7
|
1.0
|
CB
|
J:SER181
|
4.9
|
42.8
|
1.0
|
NH2
|
Z:ARG19
|
4.9
|
52.6
|
1.0
|
CB
|
J:VAL175
|
4.9
|
38.6
|
1.0
|
C
|
J:ASP205
|
5.0
|
40.8
|
1.0
|
|
Sodium binding site 5 out
of 13 in 7awe
Go back to
Sodium Binding Sites List in 7awe
Sodium binding site 5 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Na302
b:55.3
occ:1.00
|
O
|
J:HOH424
|
2.2
|
47.0
|
1.0
|
OG
|
J:SER139
|
2.5
|
44.3
|
1.0
|
O
|
J:VAL138
|
2.5
|
39.8
|
1.0
|
O
|
J:HOH450
|
2.8
|
46.5
|
1.0
|
O
|
J:HOH442
|
3.3
|
25.8
|
1.0
|
CB
|
J:SER139
|
3.5
|
41.2
|
1.0
|
O
|
J:HOH405
|
3.5
|
60.0
|
1.0
|
CA
|
J:SER139
|
3.5
|
39.7
|
1.0
|
C
|
J:VAL138
|
3.6
|
40.0
|
1.0
|
O
|
I:HOH435
|
3.7
|
52.7
|
1.0
|
N
|
J:SER139
|
4.0
|
39.8
|
1.0
|
O
|
J:HOH433
|
4.5
|
36.9
|
1.0
|
OE1
|
J:GLU106
|
4.5
|
49.5
|
1.0
|
CB
|
J:GLU106
|
4.6
|
42.3
|
1.0
|
CD
|
J:GLU106
|
4.6
|
48.9
|
1.0
|
OG
|
J:SER123
|
4.8
|
48.9
|
1.0
|
C
|
J:SER139
|
4.8
|
39.1
|
1.0
|
CA
|
J:VAL138
|
4.9
|
40.2
|
1.0
|
OH
|
J:TYR147
|
4.9
|
42.6
|
1.0
|
OE2
|
J:GLU106
|
4.9
|
49.5
|
1.0
|
CB
|
J:SER123
|
5.0
|
45.7
|
1.0
|
|
Sodium binding site 6 out
of 13 in 7awe
Go back to
Sodium Binding Sites List in 7awe
Sodium binding site 6 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na902
b:34.5
occ:1.00
|
O
|
L:ASP167
|
2.2
|
39.8
|
1.0
|
O
|
X:ASP205
|
2.2
|
44.1
|
1.0
|
O
|
L:THR164
|
2.3
|
39.7
|
1.0
|
O
|
X:HOH460
|
2.3
|
32.5
|
1.0
|
O
|
L:SER170
|
2.5
|
40.6
|
1.0
|
C
|
X:ASP205
|
3.1
|
43.4
|
1.0
|
C
|
L:ASP167
|
3.2
|
39.4
|
1.0
|
C
|
L:THR164
|
3.4
|
39.6
|
1.0
|
CA
|
L:SER168
|
3.5
|
41.1
|
1.0
|
NH1
|
L:ARG19
|
3.6
|
46.9
|
1.0
|
N
|
L:SER168
|
3.7
|
40.2
|
1.0
|
C
|
L:SER170
|
3.7
|
39.9
|
1.0
|
CA
|
X:ASP205
|
3.8
|
42.6
|
1.0
|
C
|
L:SER168
|
3.8
|
41.2
|
1.0
|
OXT
|
X:ASP205
|
4.0
|
43.3
|
1.0
|
O
|
L:SER168
|
4.0
|
41.7
|
1.0
|
CA
|
L:THR164
|
4.1
|
40.1
|
1.0
|
CB
|
X:ASP205
|
4.1
|
43.9
|
1.0
|
N
|
L:SER170
|
4.2
|
39.8
|
1.0
|
O
|
X:HOH419
|
4.2
|
42.0
|
1.0
|
CA
|
L:ASP167
|
4.4
|
37.9
|
1.0
|
CZ
|
L:ARG19
|
4.4
|
47.8
|
1.0
|
N
|
L:ASP167
|
4.5
|
37.0
|
1.0
|
N
|
L:HIS165
|
4.5
|
39.1
|
1.0
|
CA
|
L:SER170
|
4.5
|
39.3
|
1.0
|
N
|
L:TYR169
|
4.6
|
41.0
|
1.0
|
O
|
L:HIS165
|
4.6
|
37.0
|
1.0
|
C
|
L:HIS165
|
4.6
|
37.0
|
1.0
|
CB
|
L:THR164
|
4.6
|
41.6
|
1.0
|
N
|
L:GLY171
|
4.7
|
39.4
|
1.0
|
CA
|
L:HIS165
|
4.8
|
38.3
|
1.0
|
CB
|
L:SER168
|
4.8
|
43.6
|
1.0
|
NH2
|
L:ARG19
|
4.8
|
47.4
|
1.0
|
CB
|
L:SER170
|
4.8
|
39.4
|
1.0
|
CA
|
L:GLY171
|
4.9
|
40.1
|
1.0
|
O
|
X:HOH424
|
4.9
|
48.4
|
1.0
|
|
Sodium binding site 7 out
of 13 in 7awe
Go back to
Sodium Binding Sites List in 7awe
Sodium binding site 7 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Na301
b:51.2
occ:1.00
|
O
|
M:THR189
|
2.4
|
42.7
|
1.0
|
O
|
M:ALA183
|
2.5
|
45.0
|
1.0
|
O
|
M:ASP186
|
2.8
|
41.8
|
1.0
|
C
|
M:ALA183
|
3.5
|
44.0
|
1.0
|
C
|
M:THR189
|
3.6
|
42.0
|
1.0
|
O
|
M:ASP213
|
3.7
|
53.2
|
1.0
|
CA
|
M:ALA183
|
3.8
|
44.1
|
1.0
|
NH1
|
M:ARG28
|
3.8
|
35.0
|
1.0
|
C
|
M:ASP186
|
3.9
|
40.8
|
1.0
|
CA
|
M:VAL187
|
4.1
|
39.5
|
1.0
|
O
|
M:VAL187
|
4.1
|
40.5
|
1.0
|
C
|
M:VAL187
|
4.2
|
39.7
|
1.0
|
CB
|
M:ALA183
|
4.3
|
43.6
|
1.0
|
CA
|
M:GLY190
|
4.3
|
42.2
|
1.0
|
N
|
M:GLY190
|
4.4
|
41.6
|
1.0
|
N
|
M:VAL187
|
4.4
|
40.1
|
1.0
|
N
|
M:THR189
|
4.5
|
42.0
|
1.0
|
CZ
|
M:ARG28
|
4.5
|
36.5
|
1.0
|
C
|
M:ASP213
|
4.6
|
52.4
|
1.0
|
CA
|
M:THR189
|
4.7
|
41.9
|
1.0
|
NH2
|
M:ARG28
|
4.7
|
34.1
|
1.0
|
N
|
M:GLU184
|
4.7
|
43.0
|
1.0
|
OXT
|
M:ASP213
|
4.9
|
50.5
|
1.0
|
O
|
M:ARG211
|
4.9
|
48.3
|
1.0
|
N
|
M:TYR188
|
4.9
|
39.3
|
1.0
|
|
Sodium binding site 8 out
of 13 in 7awe
Go back to
Sodium Binding Sites List in 7awe
Sodium binding site 8 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Na301
b:42.7
occ:1.00
|
O
|
O:ASN128
|
2.2
|
46.8
|
1.0
|
O
|
O:TYR125
|
2.2
|
46.4
|
1.0
|
O
|
O:MET131
|
2.4
|
44.5
|
1.0
|
OG1
|
O:THR14
|
2.4
|
53.0
|
1.0
|
O
|
O:HOH411
|
2.6
|
41.6
|
1.0
|
CG2
|
O:THR14
|
3.3
|
52.3
|
1.0
|
C
|
O:ASN128
|
3.4
|
46.3
|
1.0
|
CB
|
O:THR14
|
3.4
|
52.2
|
1.0
|
C
|
O:TYR125
|
3.4
|
46.6
|
1.0
|
C
|
O:MET131
|
3.6
|
44.9
|
1.0
|
CA
|
O:ALA129
|
3.8
|
46.2
|
1.0
|
O
|
O:ALA129
|
3.9
|
46.4
|
1.0
|
C
|
O:ALA129
|
4.0
|
46.5
|
1.0
|
N
|
O:ALA129
|
4.1
|
45.8
|
1.0
|
CA
|
O:TYR125
|
4.2
|
46.9
|
1.0
|
N
|
O:MET131
|
4.3
|
46.4
|
1.0
|
O
|
U:HOH405
|
4.4
|
37.5
|
1.0
|
N
|
O:THR14
|
4.4
|
52.0
|
1.0
|
N
|
O:THR126
|
4.4
|
46.3
|
1.0
|
N
|
O:ASN128
|
4.5
|
45.2
|
1.0
|
SD
|
O:MET131
|
4.5
|
54.5
|
1.0
|
CA
|
O:ASN128
|
4.5
|
45.8
|
1.0
|
CA
|
O:THR14
|
4.5
|
51.8
|
1.0
|
CA
|
O:MET131
|
4.5
|
45.7
|
1.0
|
N
|
O:ARG132
|
4.5
|
44.5
|
1.0
|
CA
|
O:ARG132
|
4.5
|
44.6
|
1.0
|
C
|
O:THR126
|
4.8
|
46.3
|
1.0
|
N
|
O:GLU130
|
4.8
|
46.5
|
1.0
|
CA
|
O:THR126
|
4.8
|
46.2
|
1.0
|
CD
|
O:PRO133
|
4.8
|
43.7
|
1.0
|
CB
|
O:TYR125
|
4.9
|
46.9
|
1.0
|
CG
|
O:MET131
|
4.9
|
47.6
|
1.0
|
C
|
O:ARG132
|
4.9
|
45.1
|
1.0
|
N
|
O:GLN127
|
5.0
|
45.9
|
1.0
|
|
Sodium binding site 9 out
of 13 in 7awe
Go back to
Sodium Binding Sites List in 7awe
Sodium binding site 9 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Na902
b:52.7
occ:1.00
|
O
|
V:MET163
|
2.3
|
41.8
|
1.0
|
O
|
V:ASP166
|
2.4
|
40.4
|
1.0
|
O
|
V:SER169
|
2.5
|
38.8
|
1.0
|
C
|
V:ASP166
|
3.4
|
40.5
|
1.0
|
C
|
V:MET163
|
3.5
|
41.4
|
1.0
|
C
|
V:SER169
|
3.7
|
38.2
|
1.0
|
NH1
|
V:ARG19
|
3.8
|
56.1
|
1.0
|
CA
|
V:GLY167
|
4.1
|
39.6
|
1.0
|
N
|
V:GLY167
|
4.1
|
39.8
|
1.0
|
N
|
V:ASP166
|
4.3
|
40.6
|
1.0
|
CA
|
V:MET163
|
4.4
|
40.6
|
1.0
|
O
|
V:GLY167
|
4.4
|
40.2
|
1.0
|
C
|
V:GLY167
|
4.4
|
39.9
|
1.0
|
CA
|
V:ASP166
|
4.4
|
40.7
|
1.0
|
N
|
V:SER164
|
4.4
|
41.9
|
1.0
|
CA
|
V:GLY170
|
4.5
|
38.3
|
1.0
|
O
|
N:HOH352
|
4.5
|
50.5
|
1.0
|
CA
|
V:SER164
|
4.5
|
43.0
|
1.0
|
C
|
V:SER164
|
4.5
|
43.2
|
1.0
|
N
|
V:GLY170
|
4.5
|
37.6
|
1.0
|
N
|
V:SER169
|
4.6
|
38.4
|
1.0
|
CZ
|
V:ARG19
|
4.7
|
57.1
|
1.0
|
CA
|
V:SER169
|
4.7
|
37.9
|
1.0
|
O
|
V:SER164
|
4.7
|
44.2
|
1.0
|
N
|
V:ARG165
|
5.0
|
42.5
|
1.0
|
|
Sodium binding site 10 out
of 13 in 7awe
Go back to
Sodium Binding Sites List in 7awe
Sodium binding site 10 out
of 13 in the Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Human Immunoproteasome 20S Particle in Complex with [(1R)-2-(1- Benzofuran-3-Yl)-1-{[(1S,2R,4R)-7-Oxabicyclo[2.2.1]Heptan-2- Yl]Formamido}Ethyl]Boronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Na301
b:40.9
occ:1.00
|
O
|
W:ILE163
|
2.2
|
40.6
|
1.0
|
O
|
W:ASP166
|
2.3
|
41.1
|
1.0
|
O
|
W:HOH416
|
2.4
|
37.7
|
1.0
|
OXT
|
M:ASP213
|
2.4
|
50.5
|
1.0
|
O
|
W:SER169
|
2.5
|
39.4
|
1.0
|
C
|
M:ASP213
|
3.3
|
52.4
|
1.0
|
C
|
W:ASP166
|
3.3
|
40.1
|
1.0
|
C
|
W:ILE163
|
3.4
|
39.5
|
1.0
|
CA
|
M:ASP213
|
3.6
|
51.2
|
1.0
|
C
|
W:SER169
|
3.6
|
39.1
|
1.0
|
CB
|
M:ASP213
|
3.8
|
51.5
|
1.0
|
NH1
|
W:ARG19
|
3.8
|
55.7
|
1.0
|
CA
|
W:LEU167
|
4.0
|
39.4
|
1.0
|
N
|
W:LEU167
|
4.0
|
39.4
|
1.0
|
O
|
W:LEU164
|
4.2
|
40.2
|
1.0
|
N
|
W:ASP166
|
4.2
|
40.6
|
1.0
|
C
|
W:LEU164
|
4.3
|
39.6
|
1.0
|
C
|
W:LEU167
|
4.3
|
39.2
|
1.0
|
N
|
W:LEU164
|
4.3
|
38.9
|
1.0
|
CA
|
W:ASP166
|
4.3
|
40.0
|
1.0
|
CA
|
W:LEU164
|
4.4
|
38.6
|
1.0
|
N
|
W:SER169
|
4.4
|
37.7
|
1.0
|
CA
|
W:ILE163
|
4.4
|
37.8
|
1.0
|
O
|
W:LEU167
|
4.4
|
39.7
|
1.0
|
O
|
M:ASP213
|
4.4
|
53.2
|
1.0
|
CA
|
W:SER169
|
4.4
|
37.8
|
1.0
|
O
|
W:GLY162
|
4.5
|
39.5
|
1.0
|
N
|
W:GLY170
|
4.5
|
39.6
|
1.0
|
CA
|
W:GLY170
|
4.5
|
40.5
|
1.0
|
CZ
|
W:ARG19
|
4.6
|
57.3
|
1.0
|
CB
|
W:SER169
|
4.7
|
38.0
|
1.0
|
CG
|
M:ASP213
|
4.7
|
53.4
|
1.0
|
NH2
|
W:ARG19
|
4.8
|
59.4
|
1.0
|
N
|
W:GLY165
|
4.9
|
39.6
|
1.0
|
N
|
M:ASP213
|
5.0
|
50.6
|
1.0
|
|
Reference:
M.P.Sanderson,
M.Friese-Hamim,
G.Walter-Bausch,
M.Busch,
S.Gaus,
D.Musil,
F.Rohdich,
U.Zanelli,
S.L.Downey-Kopyscinski,
C.S.Mitsiades,
O.Schadt,
M.Klein,
C.Esdar.
M3258 Is A Selective Inhibitor of the Immunoproteasome Subunit LMP7 ( Beta 5I) Delivering Efficacy in Multiple Myeloma Models. Mol.Cancer Ther. 2021.
ISSN: ESSN 1538-8514
PubMed: 34045234
DOI: 10.1158/1535-7163.MCT-21-0005
Page generated: Tue Oct 8 16:03:59 2024
|