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Calcium in PDB 9kc9: Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State

Other elements in 9kc9:

The structure of Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State (pdb code 9kc9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State, PDB code: 9kc9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 9kc9

Go back to Calcium Binding Sites List in 9kc9
Calcium binding site 1 out of 5 in the Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:51.5
occ:1.00
 O A:ASN296 2.5 52.4 1.0
OD2 A:ASP301 2.6 69.6 1.0
OD2 A:ASP304 2.6 65.6 1.0
O B:ALA10 2.7 66.7 1.0
O A:GLN293 2.9 47.0 1.0
OD1 A:ASP304 3.1 64.0 1.0
CG A:ASP304 3.2 65.0 1.0
C A:ASN296 3.6 48.3 1.0
CG A:ASP301 3.6 68.1 1.0
C B:ALA10 3.9 68.2 1.0
C A:GLN293 4.0 46.5 1.0
CB A:ASP301 4.2 64.5 1.0
CA A:ASN296 4.4 47.0 1.0
N A:ASN296 4.4 47.5 1.0
CB A:ASN296 4.4 51.1 1.0
N A:PRO297 4.6 42.8 1.0
OD1 A:ASP301 4.6 71.5 1.0
CA A:GLN293 4.6 47.3 1.0
CA A:PRO297 4.6 42.8 1.0
CB A:ASP304 4.7 62.1 1.0
CA A:GLY299 4.7 58.8 1.0
CA B:ASN11 4.7 69.1 1.0
N B:ASN11 4.7 70.8 1.0
O B:VAL9 4.8 64.3 1.0
CA B:ALA10 4.8 63.0 1.0
N A:GLY299 4.8 55.4 1.0
C A:PRO297 4.8 49.1 1.0
CG A:GLN293 4.9 62.9 1.0

Calcium binding site 2 out of 5 in 9kc9

Go back to Calcium Binding Sites List in 9kc9
Calcium binding site 2 out of 5 in the Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:51.5
occ:1.00
 O E:ASN296 2.5 52.4 1.0
OD2 E:ASP301 2.6 69.6 1.0
OD2 E:ASP304 2.6 65.6 1.0
O A:ALA10 2.7 66.7 1.0
O E:GLN293 2.9 47.0 1.0
OD1 E:ASP304 3.1 64.0 1.0
CG E:ASP304 3.2 65.0 1.0
C E:ASN296 3.6 48.3 1.0
CG E:ASP301 3.6 68.1 1.0
C A:ALA10 3.9 68.2 1.0
C E:GLN293 4.0 46.5 1.0
CB E:ASP301 4.2 64.5 1.0
CA E:ASN296 4.4 47.0 1.0
N E:ASN296 4.4 47.5 1.0
CB E:ASN296 4.4 51.1 1.0
N E:PRO297 4.6 42.8 1.0
OD1 E:ASP301 4.6 71.5 1.0
CA E:GLN293 4.6 47.3 1.0
CA E:PRO297 4.6 42.8 1.0
CB E:ASP304 4.7 62.1 1.0
CA E:GLY299 4.7 58.8 1.0
CA A:ASN11 4.7 69.1 1.0
N A:ASN11 4.7 70.8 1.0
O A:VAL9 4.8 64.3 1.0
CA A:ALA10 4.8 63.0 1.0
N E:GLY299 4.8 55.4 1.0
C E:PRO297 4.8 49.1 1.0
CG E:GLN293 4.9 62.9 1.0

Calcium binding site 3 out of 5 in 9kc9

Go back to Calcium Binding Sites List in 9kc9
Calcium binding site 3 out of 5 in the Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:51.5
occ:1.00
 O B:ASN296 2.5 52.4 1.0
OD2 B:ASP301 2.6 69.6 1.0
OD2 B:ASP304 2.6 65.6 1.0
O C:ALA10 2.7 66.7 1.0
O B:GLN293 2.9 47.0 1.0
OD1 B:ASP304 3.1 64.0 1.0
CG B:ASP304 3.2 65.0 1.0
C B:ASN296 3.6 48.3 1.0
CG B:ASP301 3.6 68.1 1.0
C C:ALA10 3.9 68.2 1.0
C B:GLN293 4.0 46.5 1.0
CB B:ASP301 4.2 64.5 1.0
CA B:ASN296 4.4 47.0 1.0
N B:ASN296 4.4 47.5 1.0
CB B:ASN296 4.4 51.1 1.0
N B:PRO297 4.6 42.8 1.0
OD1 B:ASP301 4.6 71.5 1.0
CA B:GLN293 4.6 47.3 1.0
CA B:PRO297 4.6 42.8 1.0
CB B:ASP304 4.7 62.1 1.0
CA B:GLY299 4.7 58.8 1.0
CA C:ASN11 4.7 69.1 1.0
N C:ASN11 4.7 70.8 1.0
O C:VAL9 4.8 64.3 1.0
CA C:ALA10 4.8 63.0 1.0
N B:GLY299 4.8 55.4 1.0
C B:PRO297 4.8 49.1 1.0
CG B:GLN293 4.9 62.9 1.0

Calcium binding site 4 out of 5 in 9kc9

Go back to Calcium Binding Sites List in 9kc9
Calcium binding site 4 out of 5 in the Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:51.5
occ:1.00
 O C:ASN296 2.5 52.4 1.0
OD2 C:ASP301 2.6 69.6 1.0
OD2 C:ASP304 2.6 65.6 1.0
O D:ALA10 2.7 66.7 1.0
O C:GLN293 2.9 47.0 1.0
OD1 C:ASP304 3.1 64.0 1.0
CG C:ASP304 3.2 65.0 1.0
C C:ASN296 3.6 48.3 1.0
CG C:ASP301 3.6 68.1 1.0
C D:ALA10 3.9 68.2 1.0
C C:GLN293 4.0 46.5 1.0
CB C:ASP301 4.2 64.5 1.0
CA C:ASN296 4.4 47.0 1.0
N C:ASN296 4.4 47.5 1.0
CB C:ASN296 4.4 51.1 1.0
N C:PRO297 4.6 42.8 1.0
OD1 C:ASP301 4.6 71.5 1.0
CA C:GLN293 4.6 47.3 1.0
CA C:PRO297 4.6 42.8 1.0
CB C:ASP304 4.7 62.1 1.0
CA C:GLY299 4.7 58.8 1.0
CA D:ASN11 4.7 69.1 1.0
N D:ASN11 4.7 70.8 1.0
O D:VAL9 4.8 64.3 1.0
CA D:ALA10 4.8 63.0 1.0
N C:GLY299 4.8 55.4 1.0
C C:PRO297 4.8 49.1 1.0
CG C:GLN293 4.9 62.9 1.0

Calcium binding site 5 out of 5 in 9kc9

Go back to Calcium Binding Sites List in 9kc9
Calcium binding site 5 out of 5 in the Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of Docked Mouse Bestrophin-1 in A Partial Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:51.5
occ:1.00
 O D:ASN296 2.5 52.4 1.0
OD2 D:ASP301 2.6 69.6 1.0
OD2 D:ASP304 2.6 65.6 1.0
O E:ALA10 2.7 66.7 1.0
O D:GLN293 2.9 47.0 1.0
OD1 D:ASP304 3.1 64.0 1.0
CG D:ASP304 3.2 65.0 1.0
C D:ASN296 3.6 48.3 1.0
CG D:ASP301 3.6 68.1 1.0
C E:ALA10 3.9 68.2 1.0
C D:GLN293 4.0 46.5 1.0
CB D:ASP301 4.2 64.5 1.0
CA D:ASN296 4.4 47.0 1.0
N D:ASN296 4.4 47.5 1.0
CB D:ASN296 4.4 51.1 1.0
N D:PRO297 4.6 42.8 1.0
OD1 D:ASP301 4.6 71.5 1.0
CA D:GLN293 4.6 47.3 1.0
CA D:PRO297 4.6 42.8 1.0
CB D:ASP304 4.7 62.1 1.0
CA D:GLY299 4.7 58.8 1.0
CA E:ASN11 4.7 69.1 1.0
N E:ASN11 4.7 70.8 1.0
O E:VAL9 4.8 64.3 1.0
CA E:ALA10 4.8 63.0 1.0
N D:GLY299 4.8 55.4 1.0
C D:PRO297 4.8 49.1 1.0
CG D:GLN293 4.9 62.9 1.0

Reference:

K.W.Kim, E.Lee, A.Ko, J.Hwang, K.Park, B.C.Lee, K.W.Kim, W.J.Oh, K.Kim, H.H.Lim. Cryo-Em Structures of Mouse Bestrophin 1 Channel in Closed and Partially Open Conformations. Mol.Cells 00208 2025.
ISSN: ISSN 1016-8478
PubMed: 40043778
DOI: 10.1016/J.MOCELL.2025.100208
Page generated: Thu Jul 10 10:08:18 2025

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