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Calcium in PDB 9dym: BEST1 + Paba Intermediate State

Other elements in 9dym:

The structure of BEST1 + Paba Intermediate State also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the BEST1 + Paba Intermediate State (pdb code 9dym). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the BEST1 + Paba Intermediate State, PDB code: 9dym:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 9dym

Go back to Calcium Binding Sites List in 9dym
Calcium binding site 1 out of 5 in the BEST1 + Paba Intermediate State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of BEST1 + Paba Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:34.5
occ:1.00
OD2 D:ASP301 2.2 54.7 1.0
O E:ALA10 2.4 35.4 1.0
O D:ASN296 2.4 42.8 1.0
O D:GLN293 2.6 38.5 1.0
OD2 D:ASP304 2.6 46.1 1.0
OD1 D:ASP304 3.0 52.9 1.0
CG D:ASP304 3.2 50.3 1.0
CG D:ASP301 3.4 52.8 1.0
C E:ALA10 3.5 40.7 1.0
C D:ASN296 3.5 31.4 1.0
C D:GLN293 3.7 38.8 1.0
CA D:GLN293 4.1 40.6 1.0
CB D:ASP301 4.1 52.5 1.0
N E:ASN11 4.2 49.3 1.0
CA E:ASN11 4.2 44.2 1.0
CA D:ASN296 4.3 35.4 1.0
N D:ASN296 4.3 40.3 1.0
O E:VAL9 4.4 31.6 1.0
N D:PRO297 4.4 29.3 1.0
OD1 D:ASP301 4.4 68.8 1.0
CA D:PRO297 4.4 30.8 1.0
N D:GLY299 4.4 45.7 1.0
CB D:ASN296 4.5 35.6 1.0
CA E:ALA10 4.5 35.7 1.0
O D:GLU292 4.5 61.0 1.0
CA D:GLY299 4.6 51.2 1.0
CG D:GLN293 4.6 60.7 1.0
CB D:ASP304 4.7 44.7 1.0
C E:ASN11 4.8 46.2 1.0
N D:LEU294 4.8 35.6 1.0
C D:PRO297 4.8 34.9 1.0
N E:ALA12 4.8 46.3 1.0
N D:ASP301 4.9 57.9 1.0
OD1 E:ASN11 5.0 81.1 1.0
N D:PHE298 5.0 41.0 1.0

Calcium binding site 2 out of 5 in 9dym

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Calcium binding site 2 out of 5 in the BEST1 + Paba Intermediate State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of BEST1 + Paba Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:39.0
occ:1.00
O B:ASN296 2.3 37.5 1.0
OD2 B:ASP301 2.3 62.0 1.0
O C:ALA10 2.4 43.0 1.0
OD2 B:ASP304 2.5 36.7 1.0
O B:GLN293 2.6 45.1 1.0
OD1 B:ASP304 2.9 51.6 1.0
CG B:ASP304 3.0 43.8 1.0
C B:ASN296 3.4 31.9 1.0
C C:ALA10 3.5 38.6 1.0
CG B:ASP301 3.5 60.0 1.0
C B:GLN293 3.8 38.5 1.0
CB B:ASP301 4.2 55.5 1.0
CA B:ASN296 4.2 31.9 1.0
N B:PRO297 4.3 32.6 1.0
N B:GLY299 4.3 39.2 1.0
CA C:ASN11 4.3 45.0 1.0
CA B:PRO297 4.3 32.8 1.0
CA B:GLN293 4.3 40.4 1.0
N B:ASN296 4.3 36.0 1.0
N C:ASN11 4.3 47.5 1.0
O C:VAL9 4.3 41.8 1.0
CB B:ASN296 4.4 32.8 1.0
CA B:GLY299 4.4 39.8 1.0
CA C:ALA10 4.5 31.4 1.0
OD1 B:ASP301 4.5 79.5 1.0
CB B:ASP304 4.5 38.0 1.0
O B:GLU292 4.7 63.6 1.0
C B:PRO297 4.7 31.8 1.0
CG B:GLN293 4.7 59.9 1.0
N B:LEU294 4.8 37.0 1.0
N B:PHE298 4.9 33.8 1.0
C C:ASN11 4.9 51.8 1.0
N B:ASP301 4.9 45.8 1.0
OD1 C:ASN11 4.9 66.0 1.0
N C:ALA12 5.0 57.6 1.0
CG B:ASN296 5.0 33.6 1.0

Calcium binding site 3 out of 5 in 9dym

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Calcium binding site 3 out of 5 in the BEST1 + Paba Intermediate State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of BEST1 + Paba Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca601

b:37.9
occ:1.00
OD2 E:ASP301 2.3 53.2 1.0
O E:ASN296 2.4 40.1 1.0
O A:ALA10 2.4 37.3 1.0
OD2 E:ASP304 2.6 41.2 1.0
O E:GLN293 2.7 34.7 1.0
OD1 E:ASP304 3.1 51.3 1.0
CG E:ASP304 3.2 43.1 1.0
C A:ALA10 3.4 38.6 1.0
CG E:ASP301 3.5 55.5 1.0
C E:ASN296 3.5 31.9 1.0
C E:GLN293 3.8 39.2 1.0
CA A:ASN11 4.1 47.4 1.0
N A:ASN11 4.2 45.9 1.0
CB E:ASP301 4.2 52.1 1.0
O A:VAL9 4.2 42.9 1.0
CA E:GLN293 4.3 47.7 1.0
CA E:ASN296 4.3 35.2 1.0
N E:GLY299 4.3 44.8 1.0
N E:ASN296 4.3 40.7 1.0
CB E:ASN296 4.4 35.3 1.0
N E:PRO297 4.4 31.8 1.0
CA E:GLY299 4.4 43.4 1.0
OD1 E:ASP301 4.4 66.5 1.0
CA E:PRO297 4.4 35.6 1.0
CA A:ALA10 4.5 38.0 1.0
O E:GLU292 4.6 56.1 1.0
C A:ASN11 4.6 48.1 1.0
CB E:ASP304 4.7 38.9 1.0
N A:ALA12 4.7 53.1 1.0
CG E:GLN293 4.8 61.4 1.0
C E:PRO297 4.9 39.0 1.0
N E:ASP301 4.9 56.5 1.0
N E:LEU294 4.9 37.4 1.0
OD1 A:ASN11 4.9 76.7 1.0
N E:PHE298 5.0 40.4 1.0
CG E:ASN296 5.0 36.2 1.0

Calcium binding site 4 out of 5 in 9dym

Go back to Calcium Binding Sites List in 9dym
Calcium binding site 4 out of 5 in the BEST1 + Paba Intermediate State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of BEST1 + Paba Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:41.5
occ:1.00
O A:ASN296 2.3 35.0 1.0
OD2 A:ASP301 2.3 51.7 1.0
O B:ALA10 2.4 51.3 1.0
OD2 A:ASP304 2.5 43.1 1.0
O A:GLN293 2.6 44.8 1.0
OD1 A:ASP304 2.8 46.1 1.0
CG A:ASP304 3.0 47.3 1.0
C A:ASN296 3.4 28.8 1.0
C B:ALA10 3.5 47.8 1.0
CG A:ASP301 3.5 54.0 1.0
C A:GLN293 3.6 40.0 1.0
CA A:GLN293 4.1 44.2 1.0
CB A:ASP301 4.2 51.8 1.0
CA A:ASN296 4.3 32.0 1.0
N A:PRO297 4.3 31.1 1.0
N A:GLY299 4.3 37.5 1.0
CA A:PRO297 4.3 30.5 1.0
CA B:ASN11 4.3 45.8 1.0
N A:ASN296 4.3 34.2 1.0
N B:ASN11 4.3 51.8 1.0
O B:VAL9 4.4 51.3 1.0
CA A:GLY299 4.5 42.0 1.0
CB A:ASN296 4.5 33.2 1.0
CA B:ALA10 4.5 40.6 1.0
OD1 A:ASP301 4.5 64.3 1.0
O A:GLU292 4.5 50.6 1.0
CB A:ASP304 4.6 41.8 1.0
CG A:GLN293 4.6 60.8 1.0
C A:PRO297 4.7 30.2 1.0
N A:LEU294 4.7 37.6 1.0
C B:ASN11 4.8 48.2 1.0
N A:PHE298 4.9 32.0 1.0
N A:ASP301 4.9 45.4 1.0
N B:ALA12 4.9 50.9 1.0

Calcium binding site 5 out of 5 in 9dym

Go back to Calcium Binding Sites List in 9dym
Calcium binding site 5 out of 5 in the BEST1 + Paba Intermediate State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of BEST1 + Paba Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca601

b:35.6
occ:1.00
O C:ASN296 2.2 39.9 1.0
OD2 C:ASP301 2.4 54.0 1.0
O D:ALA10 2.4 38.1 1.0
OD2 C:ASP304 2.6 35.8 1.0
O C:GLN293 2.7 44.7 1.0
OD1 C:ASP304 2.9 47.3 1.0
CG C:ASP304 3.1 39.4 1.0
C C:ASN296 3.3 32.2 1.0
CG C:ASP301 3.5 51.2 1.0
C D:ALA10 3.5 41.0 1.0
C C:GLN293 3.7 41.3 1.0
CA C:ASN296 4.2 35.6 1.0
CB C:ASP301 4.2 46.3 1.0
CA C:GLN293 4.2 43.7 1.0
N C:ASN296 4.2 37.1 1.0
N C:GLY299 4.2 38.3 1.0
N C:PRO297 4.2 32.1 1.0
O D:VAL9 4.3 35.2 1.0
CA C:PRO297 4.3 33.4 1.0
CA D:ASN11 4.3 48.2 1.0
N D:ASN11 4.3 52.6 1.0
CB C:ASN296 4.3 37.3 1.0
CA C:GLY299 4.4 38.3 1.0
CA D:ALA10 4.5 36.6 1.0
OD1 C:ASP301 4.5 64.8 1.0
O C:GLU292 4.6 43.4 1.0
CB C:ASP304 4.6 34.5 1.0
C C:PRO297 4.7 31.7 1.0
CG C:GLN293 4.8 57.6 1.0
N C:LEU294 4.8 40.5 1.0
C D:ASN11 4.8 52.3 1.0
N C:PHE298 4.9 31.8 1.0
N D:ALA12 4.9 57.0 1.0
CG C:ASN296 4.9 41.5 1.0
N C:ASP301 5.0 43.5 1.0

Reference:

A.P.Owji, J.Dong, A.Kittredge, J.Wang, Y.Zhang, T.Yang. Neurotransmitter-Bound Bestrophin Channel Structures Reveal Small Molecule Drug Targeting Sites For Disease Treatment. Nat Commun V. 15 10766 2024.
ISSN: ESSN 2041-1723
PubMed: 39737942
DOI: 10.1038/S41467-024-54938-Z
Page generated: Thu Jul 10 09:26:00 2025

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