Sodium in PDB 6e5b: Human Immunoproteasome 20S Particle in Complex with Compound 1
Enzymatic activity of Human Immunoproteasome 20S Particle in Complex with Compound 1
All present enzymatic activity of Human Immunoproteasome 20S Particle in Complex with Compound 1:
3.4.25.1;
Protein crystallography data
The structure of Human Immunoproteasome 20S Particle in Complex with Compound 1, PDB code: 6e5b
was solved by
S.Steinbacher,
M.Augustin,
M.Blaesse,
S.F.Harris,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
154.58 /
2.77
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.573,
203.142,
161.487,
90.00,
106.82,
90.00
|
|
R / Rfree (%)
|
24.8 /
29.2
|
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the Human Immunoproteasome 20S Particle in Complex with Compound 1
(pdb code 6e5b). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
Human Immunoproteasome 20S Particle in Complex with Compound 1, PDB code: 6e5b:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 1 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Na301
b:58.8
occ:1.00
|
O
|
G:MET131
|
2.2
|
48.0
|
1.0
|
|
O
|
G:ASN128
|
2.2
|
57.2
|
1.0
|
|
O
|
G:TYR125
|
2.2
|
72.9
|
1.0
|
|
OG1
|
G:THR14
|
2.2
|
60.9
|
1.0
|
|
C
|
G:ASN128
|
3.4
|
66.4
|
1.0
|
|
C
|
G:TYR125
|
3.4
|
63.1
|
1.0
|
|
CB
|
G:THR14
|
3.4
|
57.1
|
1.0
|
|
C
|
G:MET131
|
3.5
|
50.6
|
1.0
|
|
CG2
|
G:THR14
|
3.6
|
59.2
|
1.0
|
|
CA
|
G:ALA129
|
4.0
|
65.9
|
1.0
|
|
O
|
G:ALA129
|
4.0
|
64.8
|
1.0
|
|
C
|
G:ALA129
|
4.1
|
60.3
|
1.0
|
|
N
|
G:ALA129
|
4.1
|
65.8
|
1.0
|
|
CA
|
G:TYR125
|
4.1
|
66.2
|
1.0
|
|
N
|
G:MET131
|
4.3
|
63.4
|
1.0
|
|
N
|
G:ARG132
|
4.3
|
48.5
|
1.0
|
|
CA
|
G:ARG132
|
4.4
|
52.8
|
1.0
|
|
SD
|
G:MET131
|
4.5
|
72.0
|
1.0
|
|
CA
|
G:MET131
|
4.5
|
61.0
|
1.0
|
|
N
|
G:ASN128
|
4.5
|
68.4
|
1.0
|
|
N
|
G:THR14
|
4.5
|
73.2
|
1.0
|
|
N
|
G:THR126
|
4.5
|
58.5
|
1.0
|
|
CD
|
G:PRO133
|
4.5
|
56.5
|
1.0
|
|
CA
|
G:ASN128
|
4.5
|
68.2
|
1.0
|
|
C
|
G:ARG132
|
4.6
|
55.8
|
1.0
|
|
CA
|
G:THR14
|
4.6
|
63.4
|
1.0
|
|
CB
|
G:TYR125
|
4.7
|
66.2
|
1.0
|
|
N
|
G:GLU130
|
4.8
|
64.7
|
1.0
|
|
N
|
G:PRO133
|
4.8
|
54.4
|
1.0
|
|
C
|
G:THR126
|
4.8
|
55.6
|
1.0
|
|
CG
|
G:MET131
|
4.8
|
65.7
|
1.0
|
|
CA
|
G:THR126
|
4.9
|
54.4
|
1.0
|
|
C
|
G:GLN127
|
5.0
|
71.5
|
1.0
|
|
N
|
G:GLN127
|
5.0
|
62.5
|
1.0
|
|
Sodium binding site 2 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 2 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na301
b:62.1
occ:1.00
|
O
|
H:ASP166
|
2.2
|
58.6
|
1.0
|
|
O
|
H:ILE163
|
2.2
|
63.8
|
1.0
|
|
OXT
|
Z:ASP213
|
2.2
|
85.7
|
1.0
|
|
O
|
H:SER169
|
2.2
|
61.0
|
1.0
|
|
C
|
H:ASP166
|
3.2
|
57.0
|
1.0
|
|
C
|
Z:ASP213
|
3.3
|
82.7
|
1.0
|
|
C
|
H:SER169
|
3.4
|
56.4
|
1.0
|
|
C
|
H:ILE163
|
3.4
|
59.7
|
1.0
|
|
CA
|
Z:ASP213
|
3.7
|
79.7
|
1.0
|
|
O
|
H:LEU164
|
3.9
|
52.1
|
1.0
|
|
NH1
|
H:ARG19
|
3.9
|
93.9
|
1.0
|
|
CA
|
H:LEU167
|
3.9
|
55.5
|
1.0
|
|
N
|
H:LEU167
|
3.9
|
56.6
|
1.0
|
|
CB
|
Z:ASP213
|
4.0
|
79.3
|
1.0
|
|
C
|
H:LEU164
|
4.1
|
62.3
|
1.0
|
|
C
|
H:LEU167
|
4.2
|
64.4
|
1.0
|
|
O
|
H:GLY162
|
4.2
|
63.6
|
1.0
|
|
O
|
H:LEU167
|
4.2
|
62.1
|
1.0
|
|
N
|
H:ASP166
|
4.2
|
58.0
|
1.0
|
|
CA
|
H:SER169
|
4.2
|
54.1
|
1.0
|
|
N
|
H:GLY170
|
4.2
|
57.7
|
1.0
|
|
N
|
H:LEU164
|
4.3
|
60.3
|
1.0
|
|
CA
|
H:ILE163
|
4.3
|
57.4
|
1.0
|
|
O
|
Z:ASP213
|
4.3
|
70.2
|
1.0
|
|
N
|
H:SER169
|
4.3
|
60.2
|
1.0
|
|
CA
|
H:ASP166
|
4.3
|
60.1
|
1.0
|
|
CA
|
H:GLY170
|
4.4
|
56.2
|
1.0
|
|
CA
|
H:LEU164
|
4.4
|
66.7
|
1.0
|
|
CB
|
H:SER169
|
4.5
|
48.5
|
1.0
|
|
CZ
|
H:ARG19
|
4.7
|
92.0
|
1.0
|
|
N
|
H:GLY165
|
4.8
|
65.4
|
1.0
|
|
C
|
H:GLY165
|
4.9
|
63.5
|
1.0
|
|
N
|
H:GLY168
|
5.0
|
82.6
|
1.0
|
|
CG
|
Z:ASP213
|
5.0
|
81.0
|
1.0
|
|
Sodium binding site 3 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 3 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na301
b:66.4
occ:1.00
|
O
|
I:SER181
|
2.2
|
52.5
|
1.0
|
|
O
|
I:ASP178
|
2.2
|
59.8
|
1.0
|
|
O
|
I:VAL175
|
2.3
|
57.0
|
1.0
|
|
C
|
I:VAL175
|
3.4
|
56.6
|
1.0
|
|
C
|
I:ASP178
|
3.5
|
57.6
|
1.0
|
|
C
|
I:SER181
|
3.5
|
52.5
|
1.0
|
|
OXT
|
I:ASP205
|
3.8
|
71.2
|
1.0
|
|
O
|
Y:HOH1003
|
3.8
|
37.4
|
1.0
|
|
CA
|
I:ASP176
|
4.1
|
57.7
|
1.0
|
|
N
|
I:ASP176
|
4.2
|
53.6
|
1.0
|
|
N
|
I:ASP178
|
4.3
|
52.7
|
1.0
|
|
O
|
I:ALA179
|
4.3
|
49.2
|
1.0
|
|
N
|
I:SER181
|
4.3
|
61.0
|
1.0
|
|
N
|
I:GLY182
|
4.3
|
53.0
|
1.0
|
|
N
|
I:ALA179
|
4.4
|
58.3
|
1.0
|
|
CA
|
I:GLY182
|
4.4
|
52.6
|
1.0
|
|
CA
|
I:ASP178
|
4.4
|
52.0
|
1.0
|
|
C
|
I:ALA179
|
4.4
|
49.6
|
1.0
|
|
CA
|
I:ALA179
|
4.5
|
53.0
|
1.0
|
|
CA
|
I:SER181
|
4.5
|
52.5
|
1.0
|
|
CD1
|
Y:ILE26
|
4.5
|
61.9
|
1.0
|
|
C
|
I:ASP176
|
4.5
|
50.2
|
1.0
|
|
CA
|
I:VAL175
|
4.5
|
59.9
|
1.0
|
|
NH1
|
Y:ARG19
|
4.7
|
76.3
|
1.0
|
|
CB
|
I:VAL175
|
4.7
|
63.1
|
1.0
|
|
NH2
|
Y:ARG19
|
4.7
|
75.5
|
1.0
|
|
O
|
I:ASP176
|
4.8
|
43.6
|
1.0
|
|
CB
|
I:ASP178
|
4.8
|
52.5
|
1.0
|
|
C
|
I:ASP205
|
4.9
|
66.3
|
1.0
|
|
OD1
|
I:ASP176
|
4.9
|
59.9
|
1.0
|
|
CB
|
I:SER181
|
5.0
|
54.7
|
1.0
|
|
Sodium binding site 4 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 4 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na302
b:58.7
occ:1.00
|
O
|
Y:THR164
|
2.2
|
59.0
|
1.0
|
|
O
|
I:ASP205
|
2.2
|
77.3
|
1.0
|
|
O
|
Y:SER170
|
2.2
|
45.8
|
1.0
|
|
O
|
Y:ASP167
|
2.2
|
48.4
|
1.0
|
|
C
|
I:ASP205
|
3.2
|
66.3
|
1.0
|
|
C
|
Y:THR164
|
3.3
|
50.9
|
1.0
|
|
C
|
Y:ASP167
|
3.4
|
45.9
|
1.0
|
|
C
|
Y:SER170
|
3.5
|
50.9
|
1.0
|
|
O
|
Y:SER168
|
3.6
|
54.0
|
1.0
|
|
NH1
|
Y:ARG19
|
3.7
|
76.3
|
1.0
|
|
CA
|
I:ASP205
|
3.7
|
58.2
|
1.0
|
|
CA
|
Y:THR164
|
3.8
|
55.1
|
1.0
|
|
C
|
Y:SER168
|
3.9
|
56.7
|
1.0
|
|
CA
|
Y:SER168
|
3.9
|
55.9
|
1.0
|
|
N
|
Y:SER168
|
4.0
|
47.8
|
1.0
|
|
CB
|
I:ASP205
|
4.1
|
52.8
|
1.0
|
|
N
|
Y:SER170
|
4.1
|
59.2
|
1.0
|
|
OXT
|
I:ASP205
|
4.1
|
71.2
|
1.0
|
|
CA
|
Y:SER170
|
4.3
|
53.9
|
1.0
|
|
CB
|
Y:THR164
|
4.3
|
58.6
|
1.0
|
|
CZ
|
Y:ARG19
|
4.4
|
64.2
|
1.0
|
|
N
|
Y:GLY171
|
4.4
|
44.1
|
1.0
|
|
N
|
Y:HIS165
|
4.5
|
51.6
|
1.0
|
|
CA
|
Y:ASP167
|
4.5
|
41.3
|
1.0
|
|
CA
|
Y:GLY171
|
4.6
|
51.6
|
1.0
|
|
N
|
Y:ASP167
|
4.6
|
42.5
|
1.0
|
|
CE
|
I:MET183
|
4.7
|
76.9
|
1.0
|
|
N
|
Y:TYR169
|
4.7
|
65.1
|
1.0
|
|
CB
|
Y:SER170
|
4.8
|
48.1
|
1.0
|
|
C
|
Y:HIS165
|
4.8
|
53.0
|
1.0
|
|
O
|
Y:HIS165
|
4.8
|
48.7
|
1.0
|
|
NH2
|
Y:ARG19
|
4.9
|
75.5
|
1.0
|
|
CA
|
Y:HIS165
|
4.9
|
50.8
|
1.0
|
|
Sodium binding site 5 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 5 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Na902
b:48.0
occ:1.00
|
O
|
W:ASP205
|
2.2
|
64.0
|
1.0
|
|
O
|
K:THR164
|
2.2
|
42.5
|
1.0
|
|
O
|
K:SER170
|
2.2
|
52.1
|
1.0
|
|
O
|
K:ASP167
|
2.2
|
54.4
|
1.0
|
|
O
|
K:HOH1003
|
2.7
|
43.8
|
1.0
|
|
C
|
W:ASP205
|
3.2
|
68.6
|
1.0
|
|
C
|
K:THR164
|
3.3
|
39.7
|
1.0
|
|
C
|
K:ASP167
|
3.4
|
53.3
|
1.0
|
|
C
|
K:SER170
|
3.5
|
50.1
|
1.0
|
|
O
|
K:SER168
|
3.6
|
53.4
|
1.0
|
|
NH1
|
K:ARG19
|
3.7
|
79.4
|
1.0
|
|
CA
|
W:ASP205
|
3.8
|
56.6
|
1.0
|
|
CA
|
K:THR164
|
3.8
|
47.4
|
1.0
|
|
C
|
K:SER168
|
3.9
|
53.0
|
1.0
|
|
CA
|
K:SER168
|
3.9
|
56.6
|
1.0
|
|
N
|
K:SER168
|
4.0
|
57.0
|
1.0
|
|
CB
|
W:ASP205
|
4.1
|
51.7
|
1.0
|
|
N
|
K:SER170
|
4.1
|
50.5
|
1.0
|
|
OXT
|
W:ASP205
|
4.1
|
75.6
|
1.0
|
|
CB
|
K:THR164
|
4.3
|
48.8
|
1.0
|
|
CA
|
K:SER170
|
4.3
|
49.4
|
1.0
|
|
CZ
|
K:ARG19
|
4.3
|
70.6
|
1.0
|
|
N
|
K:GLY171
|
4.4
|
41.1
|
1.0
|
|
N
|
K:HIS165
|
4.5
|
41.3
|
1.0
|
|
CA
|
K:ASP167
|
4.5
|
46.9
|
1.0
|
|
N
|
K:ASP167
|
4.6
|
43.5
|
1.0
|
|
CA
|
K:GLY171
|
4.6
|
46.7
|
1.0
|
|
CE
|
W:MET183
|
4.8
|
88.4
|
1.0
|
|
N
|
K:TYR169
|
4.8
|
60.6
|
1.0
|
|
CB
|
K:SER170
|
4.8
|
50.2
|
1.0
|
|
C
|
K:HIS165
|
4.8
|
47.1
|
1.0
|
|
O
|
K:HIS165
|
4.8
|
40.1
|
1.0
|
|
NH2
|
K:ARG19
|
4.8
|
75.5
|
1.0
|
|
CA
|
K:HIS165
|
4.9
|
44.5
|
1.0
|
|
Sodium binding site 6 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 6 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na302
b:68.9
occ:1.00
|
O
|
L:ASP186
|
2.2
|
67.9
|
1.0
|
|
O
|
L:ALA183
|
2.2
|
57.5
|
1.0
|
|
O
|
L:THR189
|
2.2
|
65.7
|
1.0
|
|
C
|
L:ALA183
|
3.3
|
49.5
|
1.0
|
|
C
|
L:ASP186
|
3.4
|
62.9
|
1.0
|
|
C
|
L:THR189
|
3.5
|
61.1
|
1.0
|
|
CA
|
L:ALA183
|
3.7
|
50.3
|
1.0
|
|
O
|
L:ASP213
|
3.8
|
95.7
|
1.0
|
|
NH1
|
L:ARG28
|
3.8
|
84.2
|
1.0
|
|
O
|
L:VAL187
|
3.9
|
68.8
|
1.0
|
|
CA
|
L:VAL187
|
4.0
|
66.7
|
1.0
|
|
C
|
L:VAL187
|
4.0
|
65.5
|
1.0
|
|
N
|
L:VAL187
|
4.1
|
65.5
|
1.0
|
|
N
|
L:GLY190
|
4.4
|
62.5
|
1.0
|
|
CA
|
L:GLY190
|
4.4
|
65.0
|
1.0
|
|
N
|
L:THR189
|
4.4
|
58.5
|
1.0
|
|
CB
|
L:ALA183
|
4.4
|
55.0
|
1.0
|
|
CA
|
L:THR189
|
4.5
|
60.0
|
1.0
|
|
N
|
L:GLU184
|
4.5
|
56.8
|
1.0
|
|
NH2
|
V:ARG19
|
4.5
|
95.4
|
1.0
|
|
CZ
|
L:ARG28
|
4.5
|
71.0
|
1.0
|
|
CA
|
L:ASP186
|
4.6
|
53.5
|
1.0
|
|
O
|
L:ALA182
|
4.6
|
62.2
|
1.0
|
|
N
|
L:ASP186
|
4.7
|
46.7
|
1.0
|
|
NH2
|
L:ARG28
|
4.8
|
70.1
|
1.0
|
|
CB
|
L:THR189
|
4.9
|
55.1
|
1.0
|
|
N
|
L:TYR188
|
4.9
|
62.7
|
1.0
|
|
C
|
L:GLU184
|
4.9
|
59.2
|
1.0
|
|
O
|
L:GLU184
|
4.9
|
64.1
|
1.0
|
|
N
|
L:ALA183
|
5.0
|
48.5
|
1.0
|
|
C
|
L:ASP213
|
5.0
|
91.8
|
1.0
|
|
Sodium binding site 7 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 7 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na303
b:68.3
occ:1.00
|
O
|
V:ILE163
|
2.2
|
58.8
|
1.0
|
|
O
|
V:ASP166
|
2.2
|
54.1
|
1.0
|
|
O
|
V:SER169
|
2.2
|
65.5
|
1.0
|
|
OXT
|
L:ASP213
|
2.2
|
87.0
|
1.0
|
|
C
|
V:ASP166
|
3.3
|
50.2
|
1.0
|
|
C
|
L:ASP213
|
3.3
|
91.8
|
1.0
|
|
C
|
V:SER169
|
3.4
|
55.8
|
1.0
|
|
C
|
V:ILE163
|
3.4
|
51.4
|
1.0
|
|
CA
|
L:ASP213
|
3.7
|
79.2
|
1.0
|
|
O
|
V:LEU164
|
3.9
|
62.5
|
1.0
|
|
NH1
|
V:ARG19
|
3.9
|
74.6
|
1.0
|
|
CA
|
V:LEU167
|
3.9
|
52.0
|
1.0
|
|
N
|
V:LEU167
|
4.0
|
51.9
|
1.0
|
|
CB
|
L:ASP213
|
4.0
|
77.5
|
1.0
|
|
C
|
V:LEU164
|
4.1
|
55.2
|
1.0
|
|
O
|
V:GLY162
|
4.2
|
51.9
|
1.0
|
|
C
|
V:LEU167
|
4.2
|
51.5
|
1.0
|
|
O
|
V:LEU167
|
4.2
|
59.2
|
1.0
|
|
N
|
V:ASP166
|
4.2
|
55.2
|
1.0
|
|
N
|
V:GLY170
|
4.2
|
48.4
|
1.0
|
|
CA
|
V:SER169
|
4.3
|
56.0
|
1.0
|
|
N
|
V:LEU164
|
4.3
|
51.9
|
1.0
|
|
CA
|
V:ILE163
|
4.3
|
53.6
|
1.0
|
|
O
|
L:ASP213
|
4.3
|
95.7
|
1.0
|
|
N
|
V:SER169
|
4.3
|
58.0
|
1.0
|
|
CA
|
V:ASP166
|
4.3
|
56.4
|
1.0
|
|
CA
|
V:GLY170
|
4.4
|
46.8
|
1.0
|
|
CA
|
V:LEU164
|
4.4
|
54.5
|
1.0
|
|
CB
|
V:SER169
|
4.5
|
56.4
|
1.0
|
|
CZ
|
V:ARG19
|
4.7
|
82.6
|
1.0
|
|
N
|
V:GLY165
|
4.8
|
54.7
|
1.0
|
|
C
|
V:GLY165
|
4.9
|
56.6
|
1.0
|
|
CG
|
L:ASP213
|
5.0
|
71.9
|
1.0
|
|
N
|
V:GLY168
|
5.0
|
58.3
|
1.0
|
|
Sodium binding site 8 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 8 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Na902
b:49.7
occ:1.00
|
O
|
N:SER169
|
2.2
|
49.5
|
1.0
|
|
O
|
N:ASP166
|
2.2
|
58.6
|
1.0
|
|
O
|
N:MET163
|
2.2
|
57.0
|
1.0
|
|
C
|
N:MET163
|
3.4
|
48.4
|
1.0
|
|
C
|
N:ASP166
|
3.4
|
56.6
|
1.0
|
|
C
|
N:SER169
|
3.4
|
49.7
|
1.0
|
|
NH1
|
N:ARG19
|
3.8
|
70.5
|
1.0
|
|
CA
|
N:MET163
|
4.0
|
49.5
|
1.0
|
|
O
|
N:GLY167
|
4.0
|
57.7
|
1.0
|
|
CA
|
N:GLY167
|
4.0
|
56.2
|
1.0
|
|
N
|
N:GLY167
|
4.1
|
59.7
|
1.0
|
|
CA
|
N:GLY170
|
4.2
|
53.0
|
1.0
|
|
N
|
N:GLY170
|
4.2
|
49.4
|
1.0
|
|
C
|
N:GLY167
|
4.2
|
59.2
|
1.0
|
|
CA
|
N:SER169
|
4.5
|
52.2
|
1.0
|
|
N
|
N:SER164
|
4.5
|
56.7
|
1.0
|
|
CA
|
N:ASP166
|
4.5
|
48.9
|
1.0
|
|
N
|
N:ASP166
|
4.5
|
47.5
|
1.0
|
|
N
|
N:SER169
|
4.5
|
54.5
|
1.0
|
|
O
|
N:SER164
|
4.6
|
81.2
|
1.0
|
|
C
|
N:SER164
|
4.7
|
63.6
|
1.0
|
|
CZ
|
N:ARG19
|
4.7
|
71.8
|
1.0
|
|
CB
|
N:MET163
|
4.7
|
57.0
|
1.0
|
|
CB
|
N:SER169
|
4.8
|
58.3
|
1.0
|
|
CA
|
N:SER164
|
4.8
|
60.7
|
1.0
|
|
O
|
N:ALA162
|
4.9
|
46.4
|
1.0
|
|
Sodium binding site 9 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 9 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Na301
b:60.8
occ:1.00
|
O
|
U:ASN128
|
2.2
|
62.4
|
1.0
|
|
O
|
U:MET131
|
2.2
|
52.1
|
1.0
|
|
O
|
U:TYR125
|
2.2
|
50.8
|
1.0
|
|
OG1
|
U:THR14
|
2.2
|
62.5
|
1.0
|
|
C
|
U:ASN128
|
3.4
|
59.4
|
1.0
|
|
C
|
U:TYR125
|
3.4
|
49.3
|
1.0
|
|
CB
|
U:THR14
|
3.4
|
59.1
|
1.0
|
|
C
|
U:MET131
|
3.5
|
61.0
|
1.0
|
|
CG2
|
U:THR14
|
3.6
|
63.8
|
1.0
|
|
CA
|
U:ALA129
|
4.0
|
66.7
|
1.0
|
|
O
|
U:ALA129
|
4.0
|
57.8
|
1.0
|
|
C
|
U:ALA129
|
4.1
|
60.1
|
1.0
|
|
N
|
U:ALA129
|
4.1
|
61.3
|
1.0
|
|
CA
|
U:TYR125
|
4.1
|
58.1
|
1.0
|
|
N
|
U:MET131
|
4.3
|
70.4
|
1.0
|
|
N
|
U:ARG132
|
4.3
|
58.8
|
1.0
|
|
CA
|
U:ARG132
|
4.3
|
57.5
|
1.0
|
|
N
|
U:ASN128
|
4.5
|
61.3
|
1.0
|
|
SD
|
U:MET131
|
4.5
|
66.9
|
1.0
|
|
CA
|
U:MET131
|
4.5
|
69.2
|
1.0
|
|
N
|
U:THR14
|
4.5
|
61.8
|
1.0
|
|
N
|
U:THR126
|
4.5
|
55.2
|
1.0
|
|
CA
|
U:ASN128
|
4.5
|
57.1
|
1.0
|
|
CD
|
U:PRO133
|
4.5
|
62.0
|
1.0
|
|
C
|
U:ARG132
|
4.5
|
51.9
|
1.0
|
|
CA
|
U:THR14
|
4.6
|
61.5
|
1.0
|
|
CB
|
U:TYR125
|
4.7
|
57.9
|
1.0
|
|
N
|
U:PRO133
|
4.8
|
52.3
|
1.0
|
|
C
|
U:THR126
|
4.8
|
56.4
|
1.0
|
|
N
|
U:GLU130
|
4.8
|
63.5
|
1.0
|
|
CG
|
U:MET131
|
4.8
|
62.3
|
1.0
|
|
CA
|
U:THR126
|
4.8
|
62.6
|
1.0
|
|
C
|
U:GLN127
|
5.0
|
58.8
|
1.0
|
|
N
|
U:GLN127
|
5.0
|
55.1
|
1.0
|
|
Sodium binding site 10 out
of 12 in 6e5b
Go back to
Sodium Binding Sites List in 6e5b
Sodium binding site 10 out
of 12 in the Human Immunoproteasome 20S Particle in Complex with Compound 1
 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 Compound 1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Na301
b:66.6
occ:1.00
|
O
|
W:SER181
|
2.2
|
63.6
|
1.0
|
|
O
|
W:ASP178
|
2.2
|
58.1
|
1.0
|
|
O
|
W:VAL175
|
2.2
|
66.7
|
1.0
|
|
C
|
W:VAL175
|
3.4
|
62.6
|
1.0
|
|
C
|
W:ASP178
|
3.5
|
58.6
|
1.0
|
|
C
|
W:SER181
|
3.5
|
65.0
|
1.0
|
|
OXT
|
W:ASP205
|
3.9
|
75.6
|
1.0
|
|
CA
|
W:ASP176
|
4.1
|
58.4
|
1.0
|
|
N
|
W:ASP176
|
4.2
|
60.7
|
1.0
|
|
N
|
W:ASP178
|
4.3
|
58.6
|
1.0
|
|
O
|
W:ALA179
|
4.3
|
41.1
|
1.0
|
|
N
|
W:SER181
|
4.3
|
64.2
|
1.0
|
|
N
|
W:GLY182
|
4.4
|
61.4
|
1.0
|
|
N
|
W:ALA179
|
4.4
|
52.5
|
1.0
|
|
CA
|
W:ASP178
|
4.4
|
57.9
|
1.0
|
|
CA
|
W:GLY182
|
4.4
|
56.4
|
1.0
|
|
C
|
W:ALA179
|
4.4
|
44.0
|
1.0
|
|
CA
|
W:SER181
|
4.5
|
61.1
|
1.0
|
|
CA
|
W:ALA179
|
4.5
|
50.2
|
1.0
|
|
C
|
W:ASP176
|
4.5
|
50.5
|
1.0
|
|
CA
|
W:VAL175
|
4.5
|
60.4
|
1.0
|
|
CD1
|
K:ILE26
|
4.5
|
48.7
|
1.0
|
|
NH1
|
K:ARG19
|
4.7
|
79.4
|
1.0
|
|
NH2
|
K:ARG19
|
4.7
|
75.5
|
1.0
|
|
CB
|
W:VAL175
|
4.7
|
61.1
|
1.0
|
|
O
|
W:ASP176
|
4.7
|
49.5
|
1.0
|
|
CB
|
W:ASP178
|
4.8
|
67.0
|
1.0
|
|
C
|
W:ASP205
|
4.9
|
68.6
|
1.0
|
|
OD1
|
W:ASP176
|
4.9
|
62.4
|
1.0
|
|
CB
|
W:SER181
|
5.0
|
65.4
|
1.0
|
|
Reference:
E.Ladi,
C.Everett,
C.E.Stivala,
B.E.Daniels,
M.R.Durk,
S.F.Harris,
M.P.Huestis,
H.E.Purkey,
S.T.Staben,
M.Augustin,
M.Blaesse,
S.Steinbacher,
C.Eidenschenk,
R.Pappu,
M.Siu.
Design and Evaluation of Highly Selective Human Immunoproteasome Inhibitors Reveal A Compensatory Process That Preserves Immune Cell Viability. J.Med.Chem. V. 62 7032 2019.
ISSN: ISSN 0022-2623
PubMed: 31283222
DOI: 10.1021/ACS.JMEDCHEM.9B00509
Page generated: Tue Dec 15 12:09:28 2020
|
