Calcium in PDB 8d1n: BBEST2_345 CA2+-Bound Open State
Other elements in 8d1n:
The structure of BBEST2_345 CA2+-Bound Open State also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the BBEST2_345 CA2+-Bound Open State
(pdb code 8d1n). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
BBEST2_345 CA2+-Bound Open State, PDB code: 8d1n:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 8d1n
Go back to
Calcium Binding Sites List in 8d1n
Calcium binding site 1 out
of 5 in the BBEST2_345 CA2+-Bound Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of BBEST2_345 CA2+-Bound Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca401
b:2.0
occ:1.00
|
O
|
D:HOH538
|
2.4
|
10.0
|
1.0
|
|
OD2
|
E:ASP301
|
2.4
|
2.0
|
1.0
|
|
O
|
E:GLN293
|
2.4
|
1.1
|
1.0
|
|
O
|
E:ASN296
|
2.5
|
0.8
|
1.0
|
|
OD2
|
E:ASP304
|
2.5
|
1.4
|
1.0
|
|
OD1
|
E:ASP304
|
2.6
|
1.4
|
1.0
|
|
O
|
D:ALA10
|
2.7
|
1.3
|
1.0
|
|
CG
|
E:ASP304
|
2.9
|
1.4
|
1.0
|
|
C
|
E:ASN296
|
3.5
|
0.8
|
1.0
|
|
C
|
E:GLN293
|
3.5
|
1.1
|
1.0
|
|
CG
|
E:ASP301
|
3.5
|
2.0
|
1.0
|
|
C
|
D:ALA10
|
3.7
|
1.3
|
1.0
|
|
CA
|
E:GLN293
|
4.0
|
1.1
|
1.0
|
|
CB
|
E:ASP301
|
4.1
|
2.0
|
1.0
|
|
CA
|
E:PRO297
|
4.2
|
0.8
|
1.0
|
|
N
|
E:PRO297
|
4.3
|
0.8
|
1.0
|
|
CA
|
E:ASN296
|
4.4
|
0.8
|
1.0
|
|
N
|
E:GLY299
|
4.4
|
1.3
|
1.0
|
|
N
|
E:ASN296
|
4.4
|
0.8
|
1.0
|
|
O
|
E:GLU292
|
4.4
|
1.8
|
1.0
|
|
CB
|
E:ASP304
|
4.4
|
1.4
|
1.0
|
|
CG
|
E:GLN293
|
4.5
|
1.1
|
1.0
|
|
N
|
D:LYS11
|
4.5
|
2.6
|
1.0
|
|
CA
|
D:LYS11
|
4.5
|
2.6
|
1.0
|
|
CB
|
E:ASN296
|
4.5
|
0.8
|
1.0
|
|
O
|
D:VAL9
|
4.5
|
1.2
|
1.0
|
|
OD1
|
E:ASP301
|
4.6
|
2.0
|
1.0
|
|
OE1
|
E:GLN293
|
4.6
|
1.1
|
1.0
|
|
CA
|
E:GLY299
|
4.6
|
1.3
|
1.0
|
|
N
|
E:LEU294
|
4.6
|
0.8
|
1.0
|
|
C
|
E:PRO297
|
4.7
|
0.8
|
1.0
|
|
CA
|
D:ALA10
|
4.7
|
1.3
|
1.0
|
|
N
|
E:ASP301
|
4.8
|
2.0
|
1.0
|
|
CB
|
E:GLN293
|
4.8
|
1.1
|
1.0
|
|
N
|
D:ALA12
|
4.9
|
3.1
|
1.0
|
|
N
|
E:PHE298
|
4.9
|
0.8
|
1.0
|
|
Calcium binding site 2 out
of 5 in 8d1n
Go back to
Calcium Binding Sites List in 8d1n
Calcium binding site 2 out
of 5 in the BBEST2_345 CA2+-Bound Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of BBEST2_345 CA2+-Bound Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca401
b:2.0
occ:1.00
|
O
|
C:HOH538
|
2.4
|
10.0
|
1.0
|
|
OD2
|
D:ASP301
|
2.4
|
2.0
|
1.0
|
|
O
|
D:GLN293
|
2.4
|
1.1
|
1.0
|
|
O
|
D:ASN296
|
2.5
|
0.8
|
1.0
|
|
OD2
|
D:ASP304
|
2.5
|
1.4
|
1.0
|
|
OD1
|
D:ASP304
|
2.6
|
1.4
|
1.0
|
|
O
|
C:ALA10
|
2.6
|
1.3
|
1.0
|
|
CG
|
D:ASP304
|
2.9
|
1.4
|
1.0
|
|
C
|
D:ASN296
|
3.5
|
0.8
|
1.0
|
|
C
|
D:GLN293
|
3.5
|
1.1
|
1.0
|
|
CG
|
D:ASP301
|
3.5
|
2.0
|
1.0
|
|
C
|
C:ALA10
|
3.7
|
1.3
|
1.0
|
|
CA
|
D:GLN293
|
4.0
|
1.1
|
1.0
|
|
CB
|
D:ASP301
|
4.1
|
2.0
|
1.0
|
|
CA
|
D:PRO297
|
4.2
|
0.8
|
1.0
|
|
N
|
D:PRO297
|
4.3
|
0.8
|
1.0
|
|
CA
|
D:ASN296
|
4.4
|
0.8
|
1.0
|
|
N
|
D:GLY299
|
4.4
|
1.3
|
1.0
|
|
N
|
D:ASN296
|
4.4
|
0.8
|
1.0
|
|
O
|
D:GLU292
|
4.4
|
1.8
|
1.0
|
|
CB
|
D:ASP304
|
4.4
|
1.4
|
1.0
|
|
N
|
C:LYS11
|
4.4
|
2.6
|
1.0
|
|
CA
|
C:LYS11
|
4.5
|
2.6
|
1.0
|
|
CG
|
D:GLN293
|
4.5
|
1.1
|
1.0
|
|
CB
|
D:ASN296
|
4.5
|
0.8
|
1.0
|
|
O
|
C:VAL9
|
4.5
|
1.2
|
1.0
|
|
OD1
|
D:ASP301
|
4.6
|
2.0
|
1.0
|
|
OE1
|
D:GLN293
|
4.6
|
1.1
|
1.0
|
|
CA
|
D:GLY299
|
4.6
|
1.3
|
1.0
|
|
N
|
D:LEU294
|
4.6
|
0.8
|
1.0
|
|
CA
|
C:ALA10
|
4.6
|
1.3
|
1.0
|
|
C
|
D:PRO297
|
4.7
|
0.8
|
1.0
|
|
N
|
D:ASP301
|
4.8
|
2.0
|
1.0
|
|
CB
|
D:GLN293
|
4.8
|
1.1
|
1.0
|
|
N
|
C:ALA12
|
4.9
|
3.1
|
1.0
|
|
N
|
D:PHE298
|
4.9
|
0.8
|
1.0
|
|
C
|
C:LYS11
|
5.0
|
2.6
|
1.0
|
|
Calcium binding site 3 out
of 5 in 8d1n
Go back to
Calcium Binding Sites List in 8d1n
Calcium binding site 3 out
of 5 in the BBEST2_345 CA2+-Bound Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of BBEST2_345 CA2+-Bound Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:2.0
occ:1.00
|
O
|
E:HOH538
|
2.4
|
10.0
|
1.0
|
|
OD2
|
A:ASP301
|
2.4
|
2.0
|
1.0
|
|
O
|
A:GLN293
|
2.4
|
1.1
|
1.0
|
|
O
|
A:ASN296
|
2.5
|
0.8
|
1.0
|
|
OD2
|
A:ASP304
|
2.5
|
1.4
|
1.0
|
|
OD1
|
A:ASP304
|
2.6
|
1.4
|
1.0
|
|
O
|
E:ALA10
|
2.7
|
1.3
|
1.0
|
|
CG
|
A:ASP304
|
2.9
|
1.4
|
1.0
|
|
C
|
A:ASN296
|
3.5
|
0.8
|
1.0
|
|
C
|
A:GLN293
|
3.5
|
1.1
|
1.0
|
|
CG
|
A:ASP301
|
3.5
|
2.0
|
1.0
|
|
C
|
E:ALA10
|
3.7
|
1.3
|
1.0
|
|
CA
|
A:GLN293
|
4.0
|
1.1
|
1.0
|
|
CB
|
A:ASP301
|
4.1
|
2.0
|
1.0
|
|
CA
|
A:PRO297
|
4.2
|
0.8
|
1.0
|
|
N
|
A:PRO297
|
4.3
|
0.8
|
1.0
|
|
CA
|
A:ASN296
|
4.4
|
0.8
|
1.0
|
|
N
|
A:GLY299
|
4.4
|
1.3
|
1.0
|
|
N
|
A:ASN296
|
4.4
|
0.8
|
1.0
|
|
O
|
A:GLU292
|
4.4
|
1.8
|
1.0
|
|
CB
|
A:ASP304
|
4.4
|
1.4
|
1.0
|
|
CG
|
A:GLN293
|
4.5
|
1.1
|
1.0
|
|
N
|
E:LYS11
|
4.5
|
2.6
|
1.0
|
|
CA
|
E:LYS11
|
4.5
|
2.6
|
1.0
|
|
CB
|
A:ASN296
|
4.5
|
0.8
|
1.0
|
|
O
|
E:VAL9
|
4.5
|
1.2
|
1.0
|
|
OD1
|
A:ASP301
|
4.6
|
2.0
|
1.0
|
|
OE1
|
A:GLN293
|
4.6
|
1.1
|
1.0
|
|
CA
|
A:GLY299
|
4.6
|
1.3
|
1.0
|
|
N
|
A:LEU294
|
4.6
|
0.8
|
1.0
|
|
C
|
A:PRO297
|
4.7
|
0.8
|
1.0
|
|
CA
|
E:ALA10
|
4.7
|
1.3
|
1.0
|
|
N
|
A:ASP301
|
4.8
|
2.0
|
1.0
|
|
CB
|
A:GLN293
|
4.8
|
1.1
|
1.0
|
|
N
|
E:ALA12
|
4.9
|
3.1
|
1.0
|
|
N
|
A:PHE298
|
4.9
|
0.8
|
1.0
|
|
Calcium binding site 4 out
of 5 in 8d1n
Go back to
Calcium Binding Sites List in 8d1n
Calcium binding site 4 out
of 5 in the BBEST2_345 CA2+-Bound Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of BBEST2_345 CA2+-Bound Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca401
b:2.0
occ:1.00
|
O
|
B:HOH538
|
2.4
|
10.0
|
1.0
|
|
OD2
|
C:ASP301
|
2.4
|
2.0
|
1.0
|
|
O
|
C:GLN293
|
2.4
|
1.1
|
1.0
|
|
O
|
C:ASN296
|
2.5
|
0.8
|
1.0
|
|
OD2
|
C:ASP304
|
2.5
|
1.4
|
1.0
|
|
OD1
|
C:ASP304
|
2.6
|
1.4
|
1.0
|
|
O
|
B:ALA10
|
2.7
|
1.3
|
1.0
|
|
CG
|
C:ASP304
|
2.9
|
1.4
|
1.0
|
|
C
|
C:ASN296
|
3.5
|
0.8
|
1.0
|
|
C
|
C:GLN293
|
3.5
|
1.1
|
1.0
|
|
CG
|
C:ASP301
|
3.5
|
2.0
|
1.0
|
|
C
|
B:ALA10
|
3.7
|
1.3
|
1.0
|
|
CA
|
C:GLN293
|
4.0
|
1.1
|
1.0
|
|
CB
|
C:ASP301
|
4.1
|
2.0
|
1.0
|
|
CA
|
C:PRO297
|
4.2
|
0.8
|
1.0
|
|
N
|
C:PRO297
|
4.3
|
0.8
|
1.0
|
|
CA
|
C:ASN296
|
4.4
|
0.8
|
1.0
|
|
N
|
C:GLY299
|
4.4
|
1.3
|
1.0
|
|
N
|
C:ASN296
|
4.4
|
0.8
|
1.0
|
|
O
|
C:GLU292
|
4.4
|
1.8
|
1.0
|
|
CB
|
C:ASP304
|
4.4
|
1.4
|
1.0
|
|
N
|
B:LYS11
|
4.5
|
2.6
|
1.0
|
|
CA
|
B:LYS11
|
4.5
|
2.6
|
1.0
|
|
CG
|
C:GLN293
|
4.5
|
1.1
|
1.0
|
|
CB
|
C:ASN296
|
4.5
|
0.8
|
1.0
|
|
O
|
B:VAL9
|
4.5
|
1.2
|
1.0
|
|
OD1
|
C:ASP301
|
4.6
|
2.0
|
1.0
|
|
OE1
|
C:GLN293
|
4.6
|
1.1
|
1.0
|
|
CA
|
C:GLY299
|
4.6
|
1.3
|
1.0
|
|
N
|
C:LEU294
|
4.6
|
0.8
|
1.0
|
|
CA
|
B:ALA10
|
4.7
|
1.3
|
1.0
|
|
C
|
C:PRO297
|
4.7
|
0.8
|
1.0
|
|
N
|
C:ASP301
|
4.8
|
2.0
|
1.0
|
|
CB
|
C:GLN293
|
4.8
|
1.1
|
1.0
|
|
N
|
B:ALA12
|
4.9
|
3.1
|
1.0
|
|
N
|
C:PHE298
|
4.9
|
0.8
|
1.0
|
|
C
|
B:LYS11
|
5.0
|
2.6
|
1.0
|
|
Calcium binding site 5 out
of 5 in 8d1n
Go back to
Calcium Binding Sites List in 8d1n
Calcium binding site 5 out
of 5 in the BBEST2_345 CA2+-Bound Open State
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of BBEST2_345 CA2+-Bound Open State within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:2.0
occ:1.00
|
O
|
A:HOH538
|
2.4
|
10.0
|
1.0
|
|
OD2
|
B:ASP301
|
2.4
|
2.0
|
1.0
|
|
O
|
B:GLN293
|
2.4
|
1.1
|
1.0
|
|
O
|
B:ASN296
|
2.5
|
0.8
|
1.0
|
|
OD2
|
B:ASP304
|
2.5
|
1.4
|
1.0
|
|
OD1
|
B:ASP304
|
2.6
|
1.4
|
1.0
|
|
O
|
A:ALA10
|
2.7
|
1.3
|
1.0
|
|
CG
|
B:ASP304
|
2.9
|
1.4
|
1.0
|
|
C
|
B:ASN296
|
3.5
|
0.8
|
1.0
|
|
C
|
B:GLN293
|
3.5
|
1.1
|
1.0
|
|
CG
|
B:ASP301
|
3.5
|
2.0
|
1.0
|
|
C
|
A:ALA10
|
3.7
|
1.3
|
1.0
|
|
CA
|
B:GLN293
|
4.0
|
1.1
|
1.0
|
|
CB
|
B:ASP301
|
4.1
|
2.0
|
1.0
|
|
CA
|
B:PRO297
|
4.2
|
0.8
|
1.0
|
|
N
|
B:PRO297
|
4.3
|
0.8
|
1.0
|
|
CA
|
B:ASN296
|
4.4
|
0.8
|
1.0
|
|
N
|
B:GLY299
|
4.4
|
1.3
|
1.0
|
|
N
|
B:ASN296
|
4.4
|
0.8
|
1.0
|
|
O
|
B:GLU292
|
4.4
|
1.8
|
1.0
|
|
CB
|
B:ASP304
|
4.4
|
1.4
|
1.0
|
|
N
|
A:LYS11
|
4.5
|
2.6
|
1.0
|
|
CA
|
A:LYS11
|
4.5
|
2.6
|
1.0
|
|
CG
|
B:GLN293
|
4.5
|
1.1
|
1.0
|
|
CB
|
B:ASN296
|
4.5
|
0.8
|
1.0
|
|
O
|
A:VAL9
|
4.5
|
1.2
|
1.0
|
|
OD1
|
B:ASP301
|
4.6
|
2.0
|
1.0
|
|
OE1
|
B:GLN293
|
4.6
|
1.1
|
1.0
|
|
CA
|
B:GLY299
|
4.6
|
1.3
|
1.0
|
|
N
|
B:LEU294
|
4.6
|
0.8
|
1.0
|
|
CA
|
A:ALA10
|
4.6
|
1.3
|
1.0
|
|
C
|
B:PRO297
|
4.7
|
0.8
|
1.0
|
|
N
|
B:ASP301
|
4.8
|
2.0
|
1.0
|
|
CB
|
B:GLN293
|
4.8
|
1.1
|
1.0
|
|
N
|
A:ALA12
|
4.9
|
3.1
|
1.0
|
|
N
|
B:PHE298
|
4.9
|
0.8
|
1.0
|
|
C
|
A:LYS11
|
5.0
|
2.6
|
1.0
|
|
Reference:
A.P.Owji,
J.Wang,
A.Kittredge,
Z.Clark,
Y.Zhang,
W.A.Hendrickson,
T.Yang.
Structures and Gating Mechanisms of Human Bestrophin Anion Channels. Nat Commun V. 13 3836 2022.
ISSN: ESSN 2041-1723
PubMed: 35789156
DOI: 10.1038/S41467-022-31437-7
Page generated: Fri Jul 19 07:49:10 2024
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