Calcium in PDB 9dyj: BEST2 + Gaba Open State
Other elements in 9dyj:
The structure of BEST2 + Gaba Open State also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the BEST2 + Gaba Open State
(pdb code 9dyj). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
BEST2 + Gaba Open State, PDB code: 9dyj:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 9dyj
Go back to
Calcium Binding Sites List in 9dyj
Calcium binding site 1 out
of 5 in the BEST2 + Gaba Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of BEST2 + Gaba Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca601
b:35.8
occ:1.00
|
O
|
E:ASN296
|
2.2
|
37.2
|
1.0
|
|
O
|
E:GLN293
|
2.4
|
41.9
|
1.0
|
|
O
|
D:ALA10
|
2.6
|
38.1
|
1.0
|
|
OD2
|
E:ASP304
|
2.7
|
36.9
|
1.0
|
|
OD2
|
E:ASP301
|
2.8
|
37.1
|
1.0
|
|
OD1
|
E:ASP304
|
2.8
|
43.7
|
1.0
|
|
CG
|
E:ASP304
|
3.1
|
36.2
|
1.0
|
|
C
|
E:ASN296
|
3.3
|
32.1
|
1.0
|
|
C
|
E:GLN293
|
3.5
|
36.5
|
1.0
|
|
C
|
D:ALA10
|
3.7
|
35.4
|
1.0
|
|
CG
|
E:ASP301
|
3.8
|
39.7
|
1.0
|
|
CA
|
E:GLN293
|
4.0
|
38.8
|
1.0
|
|
N
|
E:PRO297
|
4.1
|
29.7
|
1.0
|
|
CA
|
E:PRO297
|
4.2
|
23.7
|
1.0
|
|
CA
|
E:ASN296
|
4.2
|
25.9
|
1.0
|
|
N
|
E:ASN296
|
4.2
|
30.6
|
1.0
|
|
CB
|
E:ASP301
|
4.3
|
40.9
|
1.0
|
|
N
|
E:GLY299
|
4.3
|
29.0
|
1.0
|
|
CB
|
E:ASN296
|
4.4
|
27.6
|
1.0
|
|
CA
|
D:ASN11
|
4.4
|
35.9
|
1.0
|
|
O
|
D:VAL9
|
4.4
|
42.4
|
1.0
|
|
N
|
D:ASN11
|
4.4
|
44.4
|
1.0
|
|
O
|
E:GLU292
|
4.5
|
50.2
|
1.0
|
|
CA
|
E:GLY299
|
4.5
|
30.4
|
1.0
|
|
CG
|
E:GLN293
|
4.5
|
39.1
|
1.0
|
|
NE2
|
E:GLN293
|
4.6
|
50.5
|
1.0
|
|
C
|
E:PRO297
|
4.6
|
25.9
|
1.0
|
|
CB
|
E:ASP304
|
4.6
|
30.7
|
1.0
|
|
N
|
E:LEU294
|
4.7
|
28.5
|
1.0
|
|
CA
|
D:ALA10
|
4.7
|
32.2
|
1.0
|
|
N
|
E:PHE298
|
4.9
|
30.2
|
1.0
|
|
CB
|
E:GLN293
|
4.9
|
37.6
|
1.0
|
|
OD1
|
E:ASP301
|
4.9
|
48.2
|
1.0
|
|
N
|
D:ALA12
|
4.9
|
47.8
|
1.0
|
|
C
|
D:ASN11
|
4.9
|
40.7
|
1.0
|
|
N
|
E:ASP301
|
5.0
|
35.0
|
1.0
|
|
CA
|
E:LEU294
|
5.0
|
26.9
|
1.0
|
|
Calcium binding site 2 out
of 5 in 9dyj
Go back to
Calcium Binding Sites List in 9dyj
Calcium binding site 2 out
of 5 in the BEST2 + Gaba Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of BEST2 + Gaba Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:36.6
occ:1.00
|
O
|
B:ASN296
|
2.2
|
39.4
|
1.0
|
|
O
|
B:GLN293
|
2.5
|
44.0
|
1.0
|
|
O
|
A:ALA10
|
2.6
|
39.1
|
1.0
|
|
OD2
|
B:ASP304
|
2.7
|
38.9
|
1.0
|
|
OD2
|
B:ASP301
|
2.8
|
40.0
|
1.0
|
|
OD1
|
B:ASP304
|
2.8
|
43.3
|
1.0
|
|
CG
|
B:ASP304
|
3.1
|
35.9
|
1.0
|
|
C
|
B:ASN296
|
3.3
|
34.3
|
1.0
|
|
C
|
B:GLN293
|
3.5
|
40.0
|
1.0
|
|
C
|
A:ALA10
|
3.7
|
36.3
|
1.0
|
|
CG
|
B:ASP301
|
3.8
|
39.7
|
1.0
|
|
CA
|
B:GLN293
|
4.0
|
38.7
|
1.0
|
|
N
|
B:PRO297
|
4.1
|
31.1
|
1.0
|
|
CA
|
B:PRO297
|
4.2
|
23.1
|
1.0
|
|
CA
|
B:ASN296
|
4.2
|
27.7
|
1.0
|
|
N
|
B:ASN296
|
4.2
|
31.4
|
1.0
|
|
CB
|
B:ASP301
|
4.3
|
41.9
|
1.0
|
|
N
|
B:GLY299
|
4.3
|
26.8
|
1.0
|
|
CB
|
B:ASN296
|
4.4
|
27.4
|
1.0
|
|
CA
|
A:ASN11
|
4.4
|
33.1
|
1.0
|
|
O
|
A:VAL9
|
4.4
|
41.4
|
1.0
|
|
N
|
A:ASN11
|
4.4
|
41.1
|
1.0
|
|
O
|
B:GLU292
|
4.5
|
51.5
|
1.0
|
|
CA
|
B:GLY299
|
4.5
|
29.2
|
1.0
|
|
CG
|
B:GLN293
|
4.5
|
42.0
|
1.0
|
|
NE2
|
B:GLN293
|
4.6
|
50.1
|
1.0
|
|
C
|
B:PRO297
|
4.6
|
25.5
|
1.0
|
|
CB
|
B:ASP304
|
4.6
|
28.7
|
1.0
|
|
N
|
B:LEU294
|
4.7
|
28.1
|
1.0
|
|
CA
|
A:ALA10
|
4.7
|
33.4
|
1.0
|
|
N
|
B:PHE298
|
4.9
|
31.8
|
1.0
|
|
CB
|
B:GLN293
|
4.9
|
38.8
|
1.0
|
|
OD1
|
B:ASP301
|
4.9
|
48.4
|
1.0
|
|
N
|
A:ALA12
|
4.9
|
46.7
|
1.0
|
|
C
|
A:ASN11
|
5.0
|
38.5
|
1.0
|
|
N
|
B:ASP301
|
5.0
|
36.0
|
1.0
|
|
CA
|
B:LEU294
|
5.0
|
28.0
|
1.0
|
|
Calcium binding site 3 out
of 5 in 9dyj
Go back to
Calcium Binding Sites List in 9dyj
Calcium binding site 3 out
of 5 in the BEST2 + Gaba Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of BEST2 + Gaba Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca601
b:35.2
occ:1.00
|
O
|
C:ASN296
|
2.2
|
36.9
|
1.0
|
|
O
|
C:GLN293
|
2.4
|
40.8
|
1.0
|
|
O
|
B:ALA10
|
2.6
|
37.4
|
1.0
|
|
OD2
|
C:ASP304
|
2.7
|
36.0
|
1.0
|
|
OD2
|
C:ASP301
|
2.8
|
39.0
|
1.0
|
|
OD1
|
C:ASP304
|
2.8
|
41.7
|
1.0
|
|
CG
|
C:ASP304
|
3.1
|
34.3
|
1.0
|
|
C
|
C:ASN296
|
3.3
|
31.9
|
1.0
|
|
C
|
C:GLN293
|
3.5
|
35.9
|
1.0
|
|
C
|
B:ALA10
|
3.7
|
32.1
|
1.0
|
|
CG
|
C:ASP301
|
3.8
|
40.6
|
1.0
|
|
CA
|
C:GLN293
|
4.0
|
37.3
|
1.0
|
|
N
|
C:PRO297
|
4.1
|
30.6
|
1.0
|
|
CA
|
C:PRO297
|
4.2
|
23.7
|
1.0
|
|
CA
|
C:ASN296
|
4.2
|
26.5
|
1.0
|
|
N
|
C:ASN296
|
4.2
|
28.4
|
1.0
|
|
CB
|
C:ASP301
|
4.3
|
40.9
|
1.0
|
|
N
|
C:GLY299
|
4.3
|
29.6
|
1.0
|
|
CB
|
C:ASN296
|
4.4
|
23.2
|
1.0
|
|
CA
|
B:ASN11
|
4.4
|
30.1
|
1.0
|
|
O
|
B:VAL9
|
4.4
|
42.6
|
1.0
|
|
N
|
B:ASN11
|
4.4
|
39.9
|
1.0
|
|
O
|
C:GLU292
|
4.5
|
53.0
|
1.0
|
|
CA
|
C:GLY299
|
4.5
|
30.4
|
1.0
|
|
CG
|
C:GLN293
|
4.5
|
39.1
|
1.0
|
|
NE2
|
C:GLN293
|
4.6
|
46.9
|
1.0
|
|
C
|
C:PRO297
|
4.6
|
24.9
|
1.0
|
|
CB
|
C:ASP304
|
4.6
|
27.9
|
1.0
|
|
N
|
C:LEU294
|
4.7
|
26.7
|
1.0
|
|
CA
|
B:ALA10
|
4.7
|
31.0
|
1.0
|
|
N
|
C:PHE298
|
4.9
|
30.2
|
1.0
|
|
CB
|
C:GLN293
|
4.9
|
35.8
|
1.0
|
|
OD1
|
C:ASP301
|
4.9
|
48.8
|
1.0
|
|
N
|
B:ALA12
|
4.9
|
48.0
|
1.0
|
|
C
|
B:ASN11
|
5.0
|
34.9
|
1.0
|
|
N
|
C:ASP301
|
5.0
|
35.1
|
1.0
|
|
CA
|
C:LEU294
|
5.0
|
26.4
|
1.0
|
|
Calcium binding site 4 out
of 5 in 9dyj
Go back to
Calcium Binding Sites List in 9dyj
Calcium binding site 4 out
of 5 in the BEST2 + Gaba Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of BEST2 + Gaba Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca601
b:33.4
occ:1.00
|
O
|
D:ASN296
|
2.2
|
40.5
|
1.0
|
|
O
|
D:GLN293
|
2.4
|
43.1
|
1.0
|
|
O
|
C:ALA10
|
2.6
|
39.7
|
1.0
|
|
OD2
|
D:ASP304
|
2.7
|
36.7
|
1.0
|
|
OD2
|
D:ASP301
|
2.8
|
37.9
|
1.0
|
|
OD1
|
D:ASP304
|
2.8
|
43.1
|
1.0
|
|
CG
|
D:ASP304
|
3.1
|
36.4
|
1.0
|
|
C
|
D:ASN296
|
3.3
|
33.9
|
1.0
|
|
C
|
D:GLN293
|
3.5
|
38.7
|
1.0
|
|
C
|
C:ALA10
|
3.7
|
35.3
|
1.0
|
|
CG
|
D:ASP301
|
3.8
|
40.5
|
1.0
|
|
CA
|
D:GLN293
|
4.0
|
38.6
|
1.0
|
|
N
|
D:PRO297
|
4.1
|
31.9
|
1.0
|
|
CA
|
D:PRO297
|
4.2
|
25.8
|
1.0
|
|
CA
|
D:ASN296
|
4.2
|
25.8
|
1.0
|
|
N
|
D:ASN296
|
4.2
|
30.6
|
1.0
|
|
CB
|
D:ASP301
|
4.3
|
41.6
|
1.0
|
|
N
|
D:GLY299
|
4.3
|
31.2
|
1.0
|
|
CB
|
D:ASN296
|
4.4
|
27.2
|
1.0
|
|
CA
|
C:ASN11
|
4.4
|
33.3
|
1.0
|
|
O
|
C:VAL9
|
4.4
|
40.6
|
1.0
|
|
N
|
C:ASN11
|
4.4
|
43.0
|
1.0
|
|
O
|
D:GLU292
|
4.5
|
50.9
|
1.0
|
|
CA
|
D:GLY299
|
4.5
|
33.2
|
1.0
|
|
CG
|
D:GLN293
|
4.5
|
40.0
|
1.0
|
|
NE2
|
D:GLN293
|
4.6
|
50.4
|
1.0
|
|
C
|
D:PRO297
|
4.6
|
25.9
|
1.0
|
|
CB
|
D:ASP304
|
4.6
|
30.2
|
1.0
|
|
N
|
D:LEU294
|
4.7
|
30.4
|
1.0
|
|
CA
|
C:ALA10
|
4.7
|
31.4
|
1.0
|
|
N
|
D:PHE298
|
4.9
|
30.4
|
1.0
|
|
CB
|
D:GLN293
|
4.9
|
36.7
|
1.0
|
|
OD1
|
D:ASP301
|
4.9
|
47.6
|
1.0
|
|
N
|
C:ALA12
|
4.9
|
49.2
|
1.0
|
|
C
|
C:ASN11
|
5.0
|
38.3
|
1.0
|
|
N
|
D:ASP301
|
5.0
|
34.3
|
1.0
|
|
CA
|
D:LEU294
|
5.0
|
28.2
|
1.0
|
|
Calcium binding site 5 out
of 5 in 9dyj
Go back to
Calcium Binding Sites List in 9dyj
Calcium binding site 5 out
of 5 in the BEST2 + Gaba Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of BEST2 + Gaba Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:36.0
occ:1.00
|
O
|
A:ASN296
|
2.2
|
37.2
|
1.0
|
|
O
|
A:GLN293
|
2.4
|
38.6
|
1.0
|
|
O
|
E:ALA10
|
2.6
|
37.3
|
1.0
|
|
OD2
|
A:ASP304
|
2.7
|
37.9
|
1.0
|
|
OD2
|
A:ASP301
|
2.8
|
35.5
|
1.0
|
|
OD1
|
A:ASP304
|
2.8
|
44.3
|
1.0
|
|
CG
|
A:ASP304
|
3.1
|
35.6
|
1.0
|
|
C
|
A:ASN296
|
3.3
|
35.1
|
1.0
|
|
C
|
A:GLN293
|
3.5
|
35.4
|
1.0
|
|
C
|
E:ALA10
|
3.7
|
35.1
|
1.0
|
|
CG
|
A:ASP301
|
3.8
|
39.3
|
1.0
|
|
CA
|
A:GLN293
|
4.0
|
36.3
|
1.0
|
|
N
|
A:PRO297
|
4.1
|
30.6
|
1.0
|
|
CA
|
A:PRO297
|
4.2
|
23.9
|
1.0
|
|
CA
|
A:ASN296
|
4.2
|
26.0
|
1.0
|
|
N
|
A:ASN296
|
4.2
|
31.8
|
1.0
|
|
CB
|
A:ASP301
|
4.3
|
39.1
|
1.0
|
|
N
|
A:GLY299
|
4.3
|
27.4
|
1.0
|
|
CB
|
A:ASN296
|
4.4
|
24.2
|
1.0
|
|
CA
|
E:ASN11
|
4.4
|
32.0
|
1.0
|
|
O
|
E:VAL9
|
4.4
|
44.5
|
1.0
|
|
N
|
E:ASN11
|
4.4
|
44.1
|
1.0
|
|
O
|
A:GLU292
|
4.4
|
53.7
|
1.0
|
|
CA
|
A:GLY299
|
4.5
|
30.6
|
1.0
|
|
CG
|
A:GLN293
|
4.5
|
37.4
|
1.0
|
|
NE2
|
A:GLN293
|
4.6
|
45.8
|
1.0
|
|
C
|
A:PRO297
|
4.6
|
26.9
|
1.0
|
|
CB
|
A:ASP304
|
4.6
|
29.0
|
1.0
|
|
N
|
A:LEU294
|
4.7
|
29.6
|
1.0
|
|
CA
|
E:ALA10
|
4.7
|
30.2
|
1.0
|
|
N
|
A:PHE298
|
4.9
|
28.0
|
1.0
|
|
CB
|
A:GLN293
|
4.9
|
35.9
|
1.0
|
|
OD1
|
A:ASP301
|
4.9
|
49.3
|
1.0
|
|
N
|
E:ALA12
|
4.9
|
49.0
|
1.0
|
|
C
|
E:ASN11
|
5.0
|
36.7
|
1.0
|
|
N
|
A:ASP301
|
5.0
|
34.2
|
1.0
|
|
CA
|
A:LEU294
|
5.0
|
29.0
|
1.0
|
|
Reference:
A.P.Owji,
J.Dong,
A.Kittredge,
J.Wang,
Y.Zhang,
T.Yang.
Neurotransmitter-Bound Bestrophin Channel Structures Reveal Small Molecule Drug Targeting Sites For Disease Treatment. Nat Commun V. 15 10766 2024.
ISSN: ESSN 2041-1723
PubMed: 39737942
DOI: 10.1038/S41467-024-54938-Z
Page generated: Sat Feb 8 16:20:59 2025
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