Calcium in PDB 9kp6: Cryo-Em Structure of Mouse Bestrophin-1 in A Closed State

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

Chlorine

(Cl)

10 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Mouse Bestrophin-1 in A Closed State (pdb code 9kp6). 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 Mouse Bestrophin-1 in A Closed State, PDB code: 9kp6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Cryo-Em Structure of Mouse Bestrophin-1 in A Closed 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 Mouse Bestrophin-1 in A Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:52.3 occ:1.00 OD2 A:ASP304 2.6 78.4 1.0 O A:ASN296 2.6 63.1 1.0 O B:ALA10 2.7 75.0 1.0 O A:GLN293 2.9 48.5 1.0 OD1 A:ASP304 3.2 73.5 1.0 CG A:ASP304 3.3 77.2 1.0 OD2 A:ASP301 3.3 84.6 1.0 C A:ASN296 3.7 57.7 1.0 C B:ALA10 3.9 82.2 1.0 C A:GLN293 4.0 47.7 1.0 CG A:ASP301 4.2 84.6 1.0 CB A:ASP301 4.3 74.8 1.0 CB A:ASN296 4.4 60.3 1.0 CA A:ASN296 4.4 52.8 1.0 N A:ASN296 4.4 55.0 1.0 CA A:GLN293 4.6 51.0 1.0 CA A:GLY299 4.6 66.7 1.0 N A:PRO297 4.6 48.8 1.0 CA B:ASN11 4.6 82.5 1.0 N B:ASN11 4.7 87.5 1.0 O B:VAL9 4.7 83.2 1.0 CA A:PRO297 4.7 48.0 1.0 N A:GLY299 4.7 62.3 1.0 CB A:ASP304 4.8 72.3 1.0 CA B:ALA10 4.8 77.7 1.0 C A:PRO297 4.9 55.1 1.0 O A:GLU292 5.0 62.6 1.0

Calcium binding site 2 out of 5 in the Cryo-Em Structure of Mouse Bestrophin-1 in A Closed 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 Mouse Bestrophin-1 in A Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:55.8 occ:1.00 OD2 B:ASP304 2.6 79.0 1.0 O C:ALA10 2.6 83.1 1.0 O B:ASN296 2.7 63.7 1.0 O B:GLN293 2.9 52.3 1.0 OD1 B:ASP301 3.2 87.4 1.0 OD1 B:ASP304 3.2 74.2 1.0 CG B:ASP304 3.3 78.1 1.0 C B:ASN296 3.7 59.4 1.0 C C:ALA10 3.8 88.6 1.0 C B:GLN293 4.1 49.7 1.0 CG B:ASP301 4.1 90.1 1.0 CB B:ASP301 4.2 79.9 1.0 CB B:ASN296 4.4 64.1 1.0 CA B:ASN296 4.4 57.2 1.0 N B:ASN296 4.5 57.1 1.0 CA B:GLY299 4.6 67.3 1.0 CA C:ASN11 4.6 89.0 1.0 CA B:GLN293 4.6 52.4 1.0 N C:ASN11 4.6 92.1 1.0 N B:PRO297 4.7 49.1 1.0 O C:VAL9 4.7 88.4 1.0 N B:GLY299 4.7 61.5 1.0 CA B:PRO297 4.7 50.1 1.0 CB B:ASP304 4.7 74.7 1.0 CA C:ALA10 4.8 83.5 1.0 C B:PRO297 4.9 56.9 1.0

Calcium binding site 3 out of 5 in the Cryo-Em Structure of Mouse Bestrophin-1 in A Closed 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 Mouse Bestrophin-1 in A Closed State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:57.9 occ:1.00 O D:ALA10 2.6 78.8 1.0 OD2 C:ASP304 2.6 74.7 1.0 O C:ASN296 2.6 64.3 1.0 O C:GLN293 3.0 52.1 1.0 OD2 C:ASP301 3.3 86.4 1.0 OD1 C:ASP304 3.3 74.4 1.0 CG C:ASP304 3.3 76.9 1.0 C C:ASN296 3.7 57.6 1.0 C D:ALA10 3.8 81.7 1.0 C C:GLN293 4.1 50.1 1.0 CG C:ASP301 4.2 87.0 1.0 CB C:ASP301 4.3 78.7 1.0 CB C:ASN296 4.4 58.5 1.0 CA C:ASN296 4.4 54.0 1.0 N C:ASN296 4.4 56.6 1.0 CA D:ASN11 4.6 77.7 1.0 CA C:GLY299 4.6 67.6 1.0 N D:ASN11 4.6 84.6 1.0 CA C:GLN293 4.6 51.7 1.0 O D:VAL9 4.6 83.2 1.0 N C:PRO297 4.6 47.6 1.0 CA D:ALA10 4.7 75.9 1.0 N C:GLY299 4.7 64.0 1.0 CA C:PRO297 4.7 47.9 1.0 CB C:ASP304 4.8 73.0 1.0 C C:PRO297 4.9 52.8 1.0

Calcium binding site 4 out of 5 in the Cryo-Em Structure of Mouse Bestrophin-1 in A Closed 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 Mouse Bestrophin-1 in A Closed State within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:54.6 occ:1.00 OD2 D:ASP304 2.6 77.2 1.0 O D:ASN296 2.6 62.4 1.0 O E:ALA10 2.7 74.4 1.0 O D:GLN293 2.9 52.0 1.0 OD1 D:ASP304 3.2 71.5 1.0 CG D:ASP304 3.3 75.9 1.0 OD2 D:ASP301 3.3 85.8 1.0 C D:ASN296 3.7 58.3 1.0 C E:ALA10 3.8 80.4 1.0 C D:GLN293 4.0 48.4 1.0 CG D:ASP301 4.2 86.3 1.0 CB D:ASP301 4.2 78.6 1.0 CB D:ASN296 4.4 60.4 1.0 CA D:ASN296 4.4 54.7 1.0 N D:ASN296 4.5 54.2 1.0 CA D:GLN293 4.6 48.7 1.0 CA E:ASN11 4.6 83.1 1.0 CA D:GLY299 4.6 63.1 1.0 N D:PRO297 4.6 50.0 1.0 N E:ASN11 4.7 86.8 1.0 CA D:PRO297 4.7 48.4 1.0 O E:VAL9 4.7 81.2 1.0 CB D:ASP304 4.7 70.4 1.0 N D:GLY299 4.7 59.6 1.0 CA E:ALA10 4.8 75.7 1.0 C D:PRO297 4.9 54.6 1.0

Calcium binding site 5 out of 5 in the Cryo-Em Structure of Mouse Bestrophin-1 in A Closed 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 Mouse Bestrophin-1 in A Closed State within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca702 b:54.1 occ:1.00 O A:ALA10 2.6 78.1 1.0 O E:ASN296 2.6 61.9 1.0 OD2 E:ASP304 2.6 76.5 1.0 O E:GLN293 2.9 52.3 1.0 OD1 E:ASP304 3.3 73.1 1.0 OD2 E:ASP301 3.3 87.6 1.0 CG E:ASP304 3.4 77.4 1.0 C E:ASN296 3.7 57.6 1.0 C A:ALA10 3.8 82.2 1.0 C E:GLN293 4.1 48.9 1.0 CG E:ASP301 4.2 89.7 1.0 CB E:ASN296 4.3 60.4 1.0 CB E:ASP301 4.3 80.6 1.0 CA E:ASN296 4.4 54.7 1.0 N E:ASN296 4.4 56.2 1.0 CA A:ASN11 4.5 81.5 1.0 N A:ASN11 4.6 86.1 1.0 CA E:GLY299 4.6 69.1 1.0 CA E:GLN293 4.6 49.9 1.0 O A:VAL9 4.6 84.0 1.0 N E:PRO297 4.6 48.8 1.0 CA A:ALA10 4.7 78.7 1.0 N E:GLY299 4.7 64.0 1.0 CA E:PRO297 4.8 49.2 1.0 CB E:ASP304 4.8 73.9 1.0 C E:PRO297 4.9 55.5 1.0

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