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Calcium in PDB 8d1l: HBEST1 CA2+-Bound Partially Open Aperture State

Other elements in 8d1l:

The structure of HBEST1 CA2+-Bound Partially Open Aperture State also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the HBEST1 CA2+-Bound Partially Open Aperture State (pdb code 8d1l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the HBEST1 CA2+-Bound Partially Open Aperture State, PDB code: 8d1l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 8d1l

Go back to Calcium Binding Sites List in 8d1l
Calcium binding site 1 out of 5 in the HBEST1 CA2+-Bound Partially Open Aperture State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of HBEST1 CA2+-Bound Partially Open Aperture State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:37.6
occ:1.00
 O B:ASN296 2.3 38.4 1.0
OD2 B:ASP301 2.4 43.5 1.0
OD2 B:ASP304 2.5 40.5 1.0
O B:GLN293 2.5 43.5 1.0
O A:ALA10 2.5 41.2 1.0
OD1 B:ASP304 2.7 40.5 1.0
CG B:ASP304 2.9 40.5 1.0
C B:ASN296 3.5 38.4 1.0
CG B:ASP301 3.5 43.5 1.0
C B:GLN293 3.6 43.5 1.0
C A:ALA10 3.7 41.2 1.0
CB B:ASP301 4.1 43.5 1.0
CA B:GLN293 4.1 43.5 1.0
CA B:PRO297 4.3 36.8 1.0
N B:GLY299 4.3 40.2 1.0
N B:PRO297 4.3 36.8 1.0
CA A:ASN11 4.4 44.4 1.0
CA B:ASN296 4.4 38.4 1.0
CA B:GLY299 4.4 40.2 1.0
N A:ASN11 4.4 44.4 1.0
O A:VAL9 4.4 41.7 1.0
CB B:ASP304 4.4 40.5 1.0
N B:ASN296 4.4 38.4 1.0
OD1 B:ASP301 4.5 43.5 1.0
CB B:ASN296 4.5 38.4 1.0
O B:GLU292 4.6 45.0 1.0
CG B:GLN293 4.6 43.5 1.0
C B:PRO297 4.6 36.8 1.0
CA A:ALA10 4.7 41.2 1.0
N B:LEU294 4.7 39.4 1.0
N B:ASP301 4.7 43.5 1.0
N B:PHE298 4.9 37.4 1.0
C A:ASN11 4.9 44.4 1.0
N A:ALA12 5.0 47.3 1.0
CB B:GLN293 5.0 43.5 1.0

Calcium binding site 2 out of 5 in 8d1l

Go back to Calcium Binding Sites List in 8d1l
Calcium binding site 2 out of 5 in the HBEST1 CA2+-Bound Partially Open Aperture State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of HBEST1 CA2+-Bound Partially Open Aperture State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:37.6
occ:1.00
 O C:ASN296 2.3 38.4 1.0
OD2 C:ASP301 2.4 43.5 1.0
OD2 C:ASP304 2.5 40.5 1.0
O C:GLN293 2.5 43.5 1.0
O B:ALA10 2.5 41.2 1.0
OD1 C:ASP304 2.7 40.5 1.0
CG C:ASP304 2.9 40.5 1.0
C C:ASN296 3.5 38.4 1.0
CG C:ASP301 3.5 43.5 1.0
C C:GLN293 3.6 43.5 1.0
C B:ALA10 3.7 41.2 1.0
CB C:ASP301 4.1 43.5 1.0
CA C:GLN293 4.1 43.5 1.0
CA C:PRO297 4.3 36.8 1.0
N C:GLY299 4.3 40.2 1.0
N C:PRO297 4.3 36.8 1.0
CA B:ASN11 4.3 44.4 1.0
CA C:ASN296 4.4 38.4 1.0
N B:ASN11 4.4 44.4 1.0
CA C:GLY299 4.4 40.2 1.0
O B:VAL9 4.4 41.7 1.0
CB C:ASP304 4.4 40.5 1.0
N C:ASN296 4.4 38.4 1.0
OD1 C:ASP301 4.5 43.5 1.0
CB C:ASN296 4.5 38.4 1.0
O C:GLU292 4.6 45.0 1.0
CG C:GLN293 4.6 43.5 1.0
C C:PRO297 4.6 36.8 1.0
CA B:ALA10 4.7 41.2 1.0
N C:LEU294 4.7 39.4 1.0
N C:ASP301 4.7 43.5 1.0
C B:ASN11 4.9 44.4 1.0
N C:PHE298 4.9 37.4 1.0
N B:ALA12 5.0 47.3 1.0
CB C:GLN293 5.0 43.5 1.0

Calcium binding site 3 out of 5 in 8d1l

Go back to Calcium Binding Sites List in 8d1l
Calcium binding site 3 out of 5 in the HBEST1 CA2+-Bound Partially Open Aperture State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of HBEST1 CA2+-Bound Partially Open Aperture State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:37.6
occ:1.00
 O A:ASN296 2.3 38.4 1.0
OD2 A:ASP301 2.4 43.5 1.0
OD2 A:ASP304 2.5 40.5 1.0
O A:GLN293 2.5 43.5 1.0
O E:ALA10 2.5 41.2 1.0
OD1 A:ASP304 2.7 40.5 1.0
CG A:ASP304 2.9 40.5 1.0
C A:ASN296 3.5 38.4 1.0
CG A:ASP301 3.5 43.5 1.0
C A:GLN293 3.6 43.5 1.0
C E:ALA10 3.7 41.2 1.0
CB A:ASP301 4.1 43.5 1.0
CA A:GLN293 4.1 43.5 1.0
CA A:PRO297 4.3 36.8 1.0
N A:GLY299 4.3 40.2 1.0
N A:PRO297 4.3 36.8 1.0
CA E:ASN11 4.4 44.4 1.0
CA A:ASN296 4.4 38.4 1.0
CA A:GLY299 4.4 40.2 1.0
N E:ASN11 4.4 44.4 1.0
CB A:ASP304 4.4 40.5 1.0
O E:VAL9 4.4 41.7 1.0
N A:ASN296 4.4 38.4 1.0
OD1 A:ASP301 4.5 43.5 1.0
CB A:ASN296 4.5 38.4 1.0
O A:GLU292 4.6 45.0 1.0
CG A:GLN293 4.6 43.5 1.0
C A:PRO297 4.6 36.8 1.0
CA E:ALA10 4.7 41.2 1.0
N A:LEU294 4.7 39.4 1.0
N A:ASP301 4.7 43.5 1.0
N A:PHE298 4.9 37.4 1.0
C E:ASN11 4.9 44.4 1.0
N E:ALA12 5.0 47.3 1.0
CB A:GLN293 5.0 43.5 1.0

Calcium binding site 4 out of 5 in 8d1l

Go back to Calcium Binding Sites List in 8d1l
Calcium binding site 4 out of 5 in the HBEST1 CA2+-Bound Partially Open Aperture State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of HBEST1 CA2+-Bound Partially Open Aperture State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:37.6
occ:1.00
 O D:ASN296 2.3 38.4 1.0
OD2 D:ASP301 2.4 43.5 1.0
OD2 D:ASP304 2.5 40.5 1.0
O D:GLN293 2.5 43.5 1.0
O C:ALA10 2.5 41.2 1.0
OD1 D:ASP304 2.7 40.5 1.0
CG D:ASP304 2.9 40.5 1.0
C D:ASN296 3.5 38.4 1.0
CG D:ASP301 3.5 43.5 1.0
C D:GLN293 3.6 43.5 1.0
C C:ALA10 3.7 41.2 1.0
CB D:ASP301 4.1 43.5 1.0
CA D:GLN293 4.1 43.5 1.0
CA D:PRO297 4.3 36.8 1.0
N D:GLY299 4.3 40.2 1.0
N D:PRO297 4.3 36.8 1.0
CA C:ASN11 4.3 44.4 1.0
CA D:ASN296 4.4 38.4 1.0
N C:ASN11 4.4 44.4 1.0
CA D:GLY299 4.4 40.2 1.0
CB D:ASP304 4.4 40.5 1.0
O C:VAL9 4.4 41.7 1.0
N D:ASN296 4.4 38.4 1.0
OD1 D:ASP301 4.5 43.5 1.0
CB D:ASN296 4.5 38.4 1.0
O D:GLU292 4.6 45.0 1.0
CG D:GLN293 4.6 43.5 1.0
C D:PRO297 4.6 36.8 1.0
CA C:ALA10 4.7 41.2 1.0
N D:LEU294 4.7 39.4 1.0
N D:ASP301 4.7 43.5 1.0
C C:ASN11 4.9 44.4 1.0
N D:PHE298 4.9 37.4 1.0
N C:ALA12 5.0 47.3 1.0
CB D:GLN293 5.0 43.5 1.0

Calcium binding site 5 out of 5 in 8d1l

Go back to Calcium Binding Sites List in 8d1l
Calcium binding site 5 out of 5 in the HBEST1 CA2+-Bound Partially Open Aperture State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of HBEST1 CA2+-Bound Partially Open Aperture State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca602

b:37.6
occ:1.00
 O E:ASN296 2.3 38.4 1.0
OD2 E:ASP301 2.4 43.5 1.0
OD2 E:ASP304 2.5 40.5 1.0
O E:GLN293 2.5 43.5 1.0
O D:ALA10 2.5 41.2 1.0
OD1 E:ASP304 2.7 40.5 1.0
CG E:ASP304 2.9 40.5 1.0
C E:ASN296 3.5 38.4 1.0
CG E:ASP301 3.5 43.5 1.0
C E:GLN293 3.6 43.5 1.0
C D:ALA10 3.7 41.2 1.0
CB E:ASP301 4.1 43.5 1.0
CA E:GLN293 4.1 43.5 1.0
CA E:PRO297 4.3 36.8 1.0
N E:GLY299 4.3 40.2 1.0
N E:PRO297 4.3 36.8 1.0
CA D:ASN11 4.3 44.4 1.0
CA E:ASN296 4.4 38.4 1.0
N D:ASN11 4.4 44.4 1.0
CA E:GLY299 4.4 40.2 1.0
O D:VAL9 4.4 41.7 1.0
CB E:ASP304 4.4 40.5 1.0
N E:ASN296 4.4 38.4 1.0
OD1 E:ASP301 4.5 43.5 1.0
CB E:ASN296 4.5 38.4 1.0
O E:GLU292 4.6 45.0 1.0
CG E:GLN293 4.6 43.5 1.0
C E:PRO297 4.6 36.8 1.0
CA D:ALA10 4.7 41.2 1.0
N E:LEU294 4.7 39.4 1.0
N E:ASP301 4.7 43.5 1.0
C D:ASN11 4.9 44.4 1.0
N E:PHE298 4.9 37.4 1.0
N D:ALA12 5.0 47.3 1.0
CB E:GLN293 5.0 43.5 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 07:48:38 2024

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