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

Other elements in 9kca:

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

Calcium binding site 1 out of 5 in 9kca

Go back to Calcium Binding Sites List in 9kca
Calcium binding site 1 out of 5 in the Cryo-Em Structure of Docked 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 Docked Mouse Bestrophin-1 in A Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:39.8
occ:1.00
 O B:ALA10 2.5 68.7 1.0
O A:ASN296 2.5 47.4 1.0
OD2 A:ASP304 2.8 57.0 1.0
O A:GLN293 2.9 39.1 1.0
OD2 A:ASP301 3.3 68.0 1.0
OD1 A:ASP304 3.3 57.9 1.0
CG A:ASP304 3.4 58.9 1.0
C A:ASN296 3.6 39.7 1.0
C B:ALA10 3.6 69.2 1.0
C A:GLN293 4.0 35.9 1.0
CG A:ASP301 4.3 72.0 1.0
CA A:ASN296 4.3 37.5 1.0
N A:ASN296 4.4 39.5 1.0
CB A:ASN296 4.4 41.2 1.0
CB A:ASP301 4.5 67.5 1.0
O B:VAL9 4.5 63.5 1.0
N B:ASN11 4.5 69.4 1.0
CA A:GLN293 4.5 38.0 1.0
N A:GLY299 4.5 48.4 1.0
CA B:ASN11 4.5 65.4 1.0
CA B:ALA10 4.5 59.2 1.0
N A:PRO297 4.6 32.0 1.0
CA A:GLY299 4.6 49.9 1.0
CA A:PRO297 4.7 32.8 1.0
CB A:ASP304 4.9 54.9 1.0
CG A:GLN293 4.9 50.5 1.0

Calcium binding site 2 out of 5 in 9kca

Go back to Calcium Binding Sites List in 9kca
Calcium binding site 2 out of 5 in the Cryo-Em Structure of Docked 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 Docked Mouse Bestrophin-1 in A Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:43.6
occ:1.00
 O C:ALA10 2.5 68.2 1.0
O B:ASN296 2.5 49.6 1.0
OD2 B:ASP304 2.7 59.4 1.0
O B:GLN293 3.0 43.1 1.0
OD2 B:ASP301 3.2 72.2 1.0
OD1 B:ASP304 3.2 60.2 1.0
CG B:ASP304 3.3 61.2 1.0
C B:ASN296 3.7 42.0 1.0
C C:ALA10 3.7 70.3 1.0
C B:GLN293 4.0 39.4 1.0
CG B:ASP301 4.2 74.9 1.0
CB B:ASP301 4.4 66.8 1.0
CA B:ASN296 4.4 39.6 1.0
N B:ASN296 4.4 41.4 1.0
CB B:ASN296 4.5 43.1 1.0
N B:GLY299 4.5 47.8 1.0
N C:ASN11 4.5 73.6 1.0
CA B:GLN293 4.5 42.6 1.0
CA C:ASN11 4.5 68.3 1.0
CA B:GLY299 4.5 50.8 1.0
O C:VAL9 4.6 65.0 1.0
CA C:ALA10 4.6 62.0 1.0
N B:PRO297 4.6 34.3 1.0
CA B:PRO297 4.7 34.5 1.0
CB B:ASP304 4.8 56.7 1.0
CG B:GLN293 5.0 52.8 1.0
C B:PRO297 5.0 42.2 1.0

Calcium binding site 3 out of 5 in 9kca

Go back to Calcium Binding Sites List in 9kca
Calcium binding site 3 out of 5 in the Cryo-Em Structure of Docked 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 Docked Mouse Bestrophin-1 in A Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:42.5
occ:1.00
 O C:ASN296 2.5 48.0 1.0
O D:ALA10 2.5 64.9 1.0
OD2 C:ASP304 2.7 58.1 1.0
O C:GLN293 2.9 43.3 1.0
OD2 C:ASP301 3.0 67.0 1.0
OD1 C:ASP304 3.3 55.0 1.0
CG C:ASP304 3.4 58.1 1.0
C C:ASN296 3.6 40.9 1.0
C D:ALA10 3.7 67.9 1.0
C C:GLN293 4.0 38.8 1.0
CG C:ASP301 4.1 70.5 1.0
CA C:ASN296 4.4 38.7 1.0
N C:ASN296 4.4 39.8 1.0
CB C:ASN296 4.4 44.4 1.0
CB C:ASP301 4.5 66.7 1.0
CA C:GLN293 4.5 40.4 1.0
N C:GLY299 4.5 47.9 1.0
O D:VAL9 4.5 62.4 1.0
CA C:GLY299 4.6 50.6 1.0
N C:PRO297 4.6 33.9 1.0
N D:ASN11 4.6 70.4 1.0
CA D:ASN11 4.6 65.0 1.0
CA D:ALA10 4.6 60.4 1.0
CA C:PRO297 4.6 34.4 1.0
CB C:ASP304 4.8 54.9 1.0
CG C:GLN293 4.9 52.2 1.0
C C:PRO297 5.0 40.4 1.0
O C:GLU292 5.0 57.4 1.0

Calcium binding site 4 out of 5 in 9kca

Go back to Calcium Binding Sites List in 9kca
Calcium binding site 4 out of 5 in the Cryo-Em Structure of Docked 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 Docked Mouse Bestrophin-1 in A Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:38.5
occ:1.00
 O D:ASN296 2.5 45.3 1.0
O E:ALA10 2.5 63.6 1.0
OD2 D:ASP304 2.8 54.0 1.0
O D:GLN293 2.9 39.6 1.0
OD2 D:ASP301 3.0 64.2 1.0
OD1 D:ASP304 3.2 54.5 1.0
CG D:ASP304 3.4 55.9 1.0
C D:ASN296 3.6 36.8 1.0
C E:ALA10 3.7 66.7 1.0
C D:GLN293 4.0 37.7 1.0
CG D:ASP301 4.0 68.3 1.0
CA D:ASN296 4.4 35.9 1.0
N D:ASN296 4.4 39.5 1.0
CB D:ASP301 4.4 65.7 1.0
CB D:ASN296 4.4 41.3 1.0
CA D:GLN293 4.5 40.5 1.0
N D:GLY299 4.5 47.2 1.0
O E:VAL9 4.5 63.3 1.0
N E:ASN11 4.6 69.2 1.0
CA D:GLY299 4.6 50.5 1.0
N D:PRO297 4.6 30.0 1.0
CA E:ASN11 4.6 63.6 1.0
CA E:ALA10 4.6 57.7 1.0
CA D:PRO297 4.6 32.6 1.0
CB D:ASP304 4.9 52.5 1.0
CG D:GLN293 4.9 53.6 1.0
C D:PRO297 5.0 39.9 1.0
O D:GLU292 5.0 59.6 1.0

Calcium binding site 5 out of 5 in 9kca

Go back to Calcium Binding Sites List in 9kca
Calcium binding site 5 out of 5 in the Cryo-Em Structure of Docked 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 Docked Mouse Bestrophin-1 in A Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca702

b:43.6
occ:1.00
 O E:ASN296 2.5 47.3 1.0
O A:ALA10 2.6 67.1 1.0
OD2 E:ASP304 2.7 59.2 1.0
O E:GLN293 2.9 39.9 1.0
OD1 E:ASP304 3.2 56.6 1.0
OD2 E:ASP301 3.2 68.7 1.0
CG E:ASP304 3.3 59.5 1.0
C E:ASN296 3.6 40.0 1.0
C A:ALA10 3.7 68.0 1.0
C E:GLN293 4.0 37.0 1.0
CG E:ASP301 4.2 73.0 1.0
CB E:ASP301 4.4 68.5 1.0
N E:ASN296 4.4 38.8 1.0
CA E:ASN296 4.4 37.2 1.0
CA E:GLN293 4.5 40.2 1.0
CB E:ASN296 4.5 41.8 1.0
N E:GLY299 4.5 47.5 1.0
N E:PRO297 4.5 33.6 1.0
O A:VAL9 4.6 64.9 1.0
CA E:PRO297 4.6 34.3 1.0
N A:ASN11 4.6 69.2 1.0
CA A:ASN11 4.6 66.2 1.0
CA E:GLY299 4.6 51.8 1.0
CA A:ALA10 4.6 60.1 1.0
CB E:ASP304 4.8 57.1 1.0
CG E:GLN293 4.9 52.8 1.0
C E:PRO297 5.0 42.4 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 10:09:10 2025

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