Calcium in PDB 9dyh: BEST2 + Glutamate Open State
Calcium Binding Sites:
The binding sites of Calcium atom in the BEST2 + Glutamate Open State
(pdb code 9dyh). 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 + Glutamate Open State, PDB code: 9dyh:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 9dyh
Go back to
Calcium Binding Sites List in 9dyh
Calcium binding site 1 out
of 5 in the BEST2 + Glutamate 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 + Glutamate Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:97.5
occ:1.00
|
O
|
A:ASN296
|
2.3
|
100.6
|
1.0
|
|
O
|
A:GLN293
|
2.4
|
78.0
|
1.0
|
|
O
|
E:ALA10
|
2.5
|
90.6
|
1.0
|
|
OD2
|
A:ASP304
|
2.6
|
125.0
|
1.0
|
|
OD2
|
A:ASP301
|
2.6
|
138.7
|
1.0
|
|
OD1
|
A:ASP304
|
2.8
|
126.1
|
1.0
|
|
CG
|
A:ASP304
|
3.0
|
125.8
|
1.0
|
|
C
|
A:ASN296
|
3.4
|
100.4
|
1.0
|
|
C
|
A:GLN293
|
3.5
|
68.0
|
1.0
|
|
C
|
E:ALA10
|
3.6
|
76.8
|
1.0
|
|
CG
|
A:ASP301
|
3.7
|
136.3
|
1.0
|
|
CA
|
A:GLN293
|
4.0
|
77.9
|
1.0
|
|
CB
|
A:ASP301
|
4.2
|
123.3
|
1.0
|
|
N
|
A:GLY299
|
4.2
|
83.1
|
1.0
|
|
CA
|
A:PRO297
|
4.2
|
95.7
|
1.0
|
|
N
|
A:PRO297
|
4.2
|
96.9
|
1.0
|
|
CA
|
A:ASN296
|
4.3
|
86.5
|
1.0
|
|
O
|
E:VAL9
|
4.3
|
83.0
|
1.0
|
|
N
|
A:ASN296
|
4.3
|
72.1
|
1.0
|
|
N
|
E:ASN11
|
4.4
|
67.2
|
1.0
|
|
CA
|
E:ASN11
|
4.4
|
71.9
|
1.0
|
|
CA
|
A:GLY299
|
4.4
|
99.2
|
1.0
|
|
CG
|
A:GLN293
|
4.5
|
104.6
|
1.0
|
|
O
|
A:GLU292
|
4.5
|
76.3
|
1.0
|
|
CA
|
E:ALA10
|
4.5
|
80.3
|
1.0
|
|
CB
|
A:ASN296
|
4.5
|
81.8
|
1.0
|
|
CB
|
A:ASP304
|
4.5
|
102.7
|
1.0
|
|
OE1
|
A:GLN293
|
4.6
|
108.8
|
1.0
|
|
N
|
A:LEU294
|
4.6
|
66.5
|
1.0
|
|
C
|
A:PRO297
|
4.7
|
98.9
|
1.0
|
|
OD1
|
A:ASP301
|
4.8
|
134.8
|
1.0
|
|
CB
|
A:GLN293
|
4.8
|
83.2
|
1.0
|
|
N
|
E:ALA12
|
4.8
|
79.2
|
1.0
|
|
N
|
A:PHE298
|
4.8
|
84.6
|
1.0
|
|
C
|
E:ASN11
|
4.9
|
78.7
|
1.0
|
|
N
|
A:ASP301
|
4.9
|
105.4
|
1.0
|
|
Calcium binding site 2 out
of 5 in 9dyh
Go back to
Calcium Binding Sites List in 9dyh
Calcium binding site 2 out
of 5 in the BEST2 + Glutamate 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 + Glutamate Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca601
b:97.5
occ:1.00
|
O
|
E:ASN296
|
2.3
|
100.6
|
1.0
|
|
O
|
E:GLN293
|
2.4
|
78.0
|
1.0
|
|
O
|
D:ALA10
|
2.5
|
90.6
|
1.0
|
|
OD2
|
E:ASP304
|
2.6
|
125.0
|
1.0
|
|
OD2
|
E:ASP301
|
2.6
|
138.7
|
1.0
|
|
OD1
|
E:ASP304
|
2.8
|
126.1
|
1.0
|
|
CG
|
E:ASP304
|
3.0
|
125.8
|
1.0
|
|
C
|
E:ASN296
|
3.4
|
100.4
|
1.0
|
|
C
|
E:GLN293
|
3.5
|
68.0
|
1.0
|
|
C
|
D:ALA10
|
3.6
|
76.8
|
1.0
|
|
CG
|
E:ASP301
|
3.7
|
136.3
|
1.0
|
|
CA
|
E:GLN293
|
4.0
|
77.9
|
1.0
|
|
CB
|
E:ASP301
|
4.2
|
123.3
|
1.0
|
|
N
|
E:GLY299
|
4.2
|
83.1
|
1.0
|
|
CA
|
E:PRO297
|
4.2
|
95.7
|
1.0
|
|
N
|
E:PRO297
|
4.2
|
96.9
|
1.0
|
|
CA
|
E:ASN296
|
4.3
|
86.5
|
1.0
|
|
O
|
D:VAL9
|
4.3
|
83.0
|
1.0
|
|
N
|
E:ASN296
|
4.3
|
72.1
|
1.0
|
|
N
|
D:ASN11
|
4.4
|
67.2
|
1.0
|
|
CA
|
D:ASN11
|
4.4
|
71.9
|
1.0
|
|
CA
|
E:GLY299
|
4.4
|
99.2
|
1.0
|
|
CG
|
E:GLN293
|
4.5
|
104.6
|
1.0
|
|
O
|
E:GLU292
|
4.5
|
76.3
|
1.0
|
|
CA
|
D:ALA10
|
4.5
|
80.3
|
1.0
|
|
CB
|
E:ASN296
|
4.5
|
81.8
|
1.0
|
|
CB
|
E:ASP304
|
4.5
|
102.7
|
1.0
|
|
OE1
|
E:GLN293
|
4.6
|
108.8
|
1.0
|
|
N
|
E:LEU294
|
4.6
|
66.5
|
1.0
|
|
C
|
E:PRO297
|
4.7
|
98.9
|
1.0
|
|
OD1
|
E:ASP301
|
4.8
|
134.8
|
1.0
|
|
CB
|
E:GLN293
|
4.8
|
83.2
|
1.0
|
|
N
|
D:ALA12
|
4.8
|
79.2
|
1.0
|
|
N
|
E:PHE298
|
4.8
|
84.6
|
1.0
|
|
N
|
E:ASP301
|
4.9
|
105.4
|
1.0
|
|
C
|
D:ASN11
|
4.9
|
78.7
|
1.0
|
|
Calcium binding site 3 out
of 5 in 9dyh
Go back to
Calcium Binding Sites List in 9dyh
Calcium binding site 3 out
of 5 in the BEST2 + Glutamate 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 + Glutamate Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca601
b:97.5
occ:1.00
|
O
|
D:ASN296
|
2.3
|
100.6
|
1.0
|
|
O
|
D:GLN293
|
2.4
|
78.0
|
1.0
|
|
O
|
C:ALA10
|
2.5
|
90.6
|
1.0
|
|
OD2
|
D:ASP304
|
2.6
|
125.0
|
1.0
|
|
OD2
|
D:ASP301
|
2.6
|
138.7
|
1.0
|
|
OD1
|
D:ASP304
|
2.8
|
126.1
|
1.0
|
|
CG
|
D:ASP304
|
3.0
|
125.8
|
1.0
|
|
C
|
D:ASN296
|
3.4
|
100.4
|
1.0
|
|
C
|
D:GLN293
|
3.5
|
68.0
|
1.0
|
|
C
|
C:ALA10
|
3.6
|
76.8
|
1.0
|
|
CG
|
D:ASP301
|
3.7
|
136.3
|
1.0
|
|
CA
|
D:GLN293
|
4.0
|
77.9
|
1.0
|
|
CB
|
D:ASP301
|
4.2
|
123.3
|
1.0
|
|
N
|
D:GLY299
|
4.2
|
83.1
|
1.0
|
|
CA
|
D:PRO297
|
4.2
|
95.7
|
1.0
|
|
N
|
D:PRO297
|
4.2
|
96.9
|
1.0
|
|
CA
|
D:ASN296
|
4.3
|
86.5
|
1.0
|
|
O
|
C:VAL9
|
4.3
|
83.0
|
1.0
|
|
N
|
D:ASN296
|
4.3
|
72.1
|
1.0
|
|
N
|
C:ASN11
|
4.4
|
67.2
|
1.0
|
|
CA
|
C:ASN11
|
4.4
|
71.9
|
1.0
|
|
CA
|
D:GLY299
|
4.4
|
99.2
|
1.0
|
|
CG
|
D:GLN293
|
4.5
|
104.6
|
1.0
|
|
O
|
D:GLU292
|
4.5
|
76.3
|
1.0
|
|
CB
|
D:ASN296
|
4.5
|
81.8
|
1.0
|
|
CA
|
C:ALA10
|
4.5
|
80.3
|
1.0
|
|
CB
|
D:ASP304
|
4.5
|
102.7
|
1.0
|
|
OE1
|
D:GLN293
|
4.6
|
108.8
|
1.0
|
|
N
|
D:LEU294
|
4.6
|
66.5
|
1.0
|
|
C
|
D:PRO297
|
4.7
|
98.9
|
1.0
|
|
OD1
|
D:ASP301
|
4.8
|
134.8
|
1.0
|
|
N
|
C:ALA12
|
4.8
|
79.2
|
1.0
|
|
CB
|
D:GLN293
|
4.8
|
83.2
|
1.0
|
|
N
|
D:PHE298
|
4.8
|
84.6
|
1.0
|
|
C
|
C:ASN11
|
4.9
|
78.7
|
1.0
|
|
N
|
D:ASP301
|
4.9
|
105.4
|
1.0
|
|
Calcium binding site 4 out
of 5 in 9dyh
Go back to
Calcium Binding Sites List in 9dyh
Calcium binding site 4 out
of 5 in the BEST2 + Glutamate 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 + Glutamate Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:97.5
occ:1.00
|
O
|
B:ASN296
|
2.3
|
100.6
|
1.0
|
|
O
|
B:GLN293
|
2.4
|
78.0
|
1.0
|
|
O
|
A:ALA10
|
2.5
|
90.6
|
1.0
|
|
OD2
|
B:ASP304
|
2.6
|
125.0
|
1.0
|
|
OD2
|
B:ASP301
|
2.6
|
138.7
|
1.0
|
|
OD1
|
B:ASP304
|
2.8
|
126.1
|
1.0
|
|
CG
|
B:ASP304
|
3.0
|
125.8
|
1.0
|
|
C
|
B:ASN296
|
3.4
|
100.4
|
1.0
|
|
C
|
B:GLN293
|
3.5
|
68.0
|
1.0
|
|
C
|
A:ALA10
|
3.6
|
76.8
|
1.0
|
|
CG
|
B:ASP301
|
3.7
|
136.3
|
1.0
|
|
CA
|
B:GLN293
|
4.0
|
77.9
|
1.0
|
|
CB
|
B:ASP301
|
4.2
|
123.3
|
1.0
|
|
N
|
B:GLY299
|
4.2
|
83.1
|
1.0
|
|
CA
|
B:PRO297
|
4.2
|
95.7
|
1.0
|
|
N
|
B:PRO297
|
4.2
|
96.9
|
1.0
|
|
CA
|
B:ASN296
|
4.3
|
86.5
|
1.0
|
|
O
|
A:VAL9
|
4.3
|
83.0
|
1.0
|
|
N
|
B:ASN296
|
4.3
|
72.1
|
1.0
|
|
N
|
A:ASN11
|
4.4
|
67.2
|
1.0
|
|
CA
|
A:ASN11
|
4.4
|
71.9
|
1.0
|
|
CA
|
B:GLY299
|
4.4
|
99.2
|
1.0
|
|
CG
|
B:GLN293
|
4.5
|
104.6
|
1.0
|
|
O
|
B:GLU292
|
4.5
|
76.3
|
1.0
|
|
CB
|
B:ASN296
|
4.5
|
81.8
|
1.0
|
|
CA
|
A:ALA10
|
4.5
|
80.3
|
1.0
|
|
CB
|
B:ASP304
|
4.5
|
102.7
|
1.0
|
|
OE1
|
B:GLN293
|
4.6
|
108.8
|
1.0
|
|
N
|
B:LEU294
|
4.6
|
66.5
|
1.0
|
|
C
|
B:PRO297
|
4.7
|
98.9
|
1.0
|
|
OD1
|
B:ASP301
|
4.8
|
134.8
|
1.0
|
|
CB
|
B:GLN293
|
4.8
|
83.2
|
1.0
|
|
N
|
A:ALA12
|
4.8
|
79.2
|
1.0
|
|
N
|
B:PHE298
|
4.8
|
84.6
|
1.0
|
|
N
|
B:ASP301
|
4.9
|
105.4
|
1.0
|
|
C
|
A:ASN11
|
4.9
|
78.7
|
1.0
|
|
Calcium binding site 5 out
of 5 in 9dyh
Go back to
Calcium Binding Sites List in 9dyh
Calcium binding site 5 out
of 5 in the BEST2 + Glutamate 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 + Glutamate Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca601
b:97.5
occ:1.00
|
O
|
C:ASN296
|
2.3
|
100.6
|
1.0
|
|
O
|
C:GLN293
|
2.4
|
78.0
|
1.0
|
|
O
|
B:ALA10
|
2.5
|
90.6
|
1.0
|
|
OD2
|
C:ASP304
|
2.6
|
125.0
|
1.0
|
|
OD2
|
C:ASP301
|
2.6
|
138.7
|
1.0
|
|
OD1
|
C:ASP304
|
2.8
|
126.1
|
1.0
|
|
CG
|
C:ASP304
|
3.0
|
125.8
|
1.0
|
|
C
|
C:ASN296
|
3.4
|
100.4
|
1.0
|
|
C
|
C:GLN293
|
3.5
|
68.0
|
1.0
|
|
C
|
B:ALA10
|
3.6
|
76.8
|
1.0
|
|
CG
|
C:ASP301
|
3.7
|
136.3
|
1.0
|
|
CA
|
C:GLN293
|
4.0
|
77.9
|
1.0
|
|
CB
|
C:ASP301
|
4.2
|
123.3
|
1.0
|
|
N
|
C:GLY299
|
4.2
|
83.1
|
1.0
|
|
CA
|
C:PRO297
|
4.2
|
95.7
|
1.0
|
|
N
|
C:PRO297
|
4.2
|
96.9
|
1.0
|
|
CA
|
C:ASN296
|
4.3
|
86.5
|
1.0
|
|
O
|
B:VAL9
|
4.3
|
83.0
|
1.0
|
|
N
|
C:ASN296
|
4.3
|
72.1
|
1.0
|
|
N
|
B:ASN11
|
4.4
|
67.2
|
1.0
|
|
CA
|
B:ASN11
|
4.4
|
71.9
|
1.0
|
|
CA
|
C:GLY299
|
4.4
|
99.2
|
1.0
|
|
CG
|
C:GLN293
|
4.5
|
104.6
|
1.0
|
|
O
|
C:GLU292
|
4.5
|
76.3
|
1.0
|
|
CB
|
C:ASN296
|
4.5
|
81.8
|
1.0
|
|
CA
|
B:ALA10
|
4.5
|
80.3
|
1.0
|
|
CB
|
C:ASP304
|
4.5
|
102.7
|
1.0
|
|
OE1
|
C:GLN293
|
4.6
|
108.8
|
1.0
|
|
N
|
C:LEU294
|
4.6
|
66.5
|
1.0
|
|
C
|
C:PRO297
|
4.7
|
98.9
|
1.0
|
|
OD1
|
C:ASP301
|
4.8
|
134.8
|
1.0
|
|
CB
|
C:GLN293
|
4.8
|
83.2
|
1.0
|
|
N
|
B:ALA12
|
4.8
|
79.2
|
1.0
|
|
N
|
C:PHE298
|
4.8
|
84.6
|
1.0
|
|
N
|
C:ASP301
|
4.9
|
105.4
|
1.0
|
|
C
|
B:ASN11
|
4.9
|
78.7
|
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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