Calcium in PDB 7d7e: Structure of PKD1L3-Ctd/PKD2L1 in Apo State

The binding sites of Calcium atom in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State (pdb code 7d7e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State, PDB code: 7d7e:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of PKD1L3-Ctd/PKD2L1 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca704 b:30.0 occ:1.00 ND2 B:ASN387 2.6 100.5 1.0 OD1 B:ASP390 2.7 92.6 1.0 OE1 B:GLU373 2.8 115.0 1.0 OE2 B:GLU370 3.4 107.9 1.0 NZ B:LYS455 3.4 92.4 1.0 CD B:GLU373 3.6 115.0 1.0 OE1 B:GLU370 3.6 107.9 1.0 OE2 B:GLU373 3.7 115.0 1.0 CG B:ASN387 3.9 100.5 1.0 CD B:GLU370 3.9 107.9 1.0 CG B:ASP390 3.9 92.6 1.0 CA B:ASN387 4.6 100.5 1.0 CB B:ASN387 4.6 100.5 1.0 CB B:ASP390 4.7 92.6 1.0 OD1 B:ASN387 4.7 100.5 1.0 CE B:LYS455 4.8 92.4 1.0 OD2 B:ASP390 4.8 92.6 1.0 N B:ASN387 4.9 100.5 1.0

Calcium binding site 2 out of 3 in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of PKD1L3-Ctd/PKD2L1 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca704 b:30.0 occ:1.00 OE2 C:GLU373 2.4 105.2 1.0 OE2 C:GLU370 2.5 100.2 1.0 OD1 C:ASP390 2.5 89.4 1.0 OD1 C:ASN387 2.7 96.8 1.0 NZ C:LYS455 3.0 88.6 1.0 CD C:GLU373 3.3 105.2 1.0 CD C:GLU370 3.6 100.2 1.0 CG C:ASP390 3.6 89.4 1.0 OE1 C:GLU373 3.6 105.2 1.0 CG C:ASN387 3.9 96.8 1.0 OE1 C:GLU370 3.9 100.2 1.0 CE C:LYS455 4.1 88.6 1.0 CB C:ASP390 4.2 89.4 1.0 OD2 C:ASP390 4.5 89.4 1.0 CA C:ASN387 4.6 96.8 1.0 CG C:GLU373 4.6 105.2 1.0 OE1 C:GLU369 4.7 98.8 1.0 ND2 C:ASN387 4.7 96.8 1.0 CB C:ASN387 4.8 96.8 1.0 CG C:GLU370 4.8 100.2 1.0

Calcium binding site 3 out of 3 in the Structure of PKD1L3-Ctd/PKD2L1 in Apo State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of PKD1L3-Ctd/PKD2L1 in Apo State within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca803 b:30.0 occ:1.00 OD1 D:ASN387 1.9 119.9 1.0 OD2 D:ASP390 2.7 115.1 1.0 OE2 D:GLU373 2.8 123.0 1.0 OE1 D:GLU370 3.0 120.8 1.0 CG D:ASN387 3.1 119.9 1.0 OE2 D:GLU370 3.4 120.8 1.0 CD D:GLU370 3.6 120.8 1.0 ND2 D:ASN387 3.8 119.9 1.0 CG D:ASP390 3.8 115.1 1.0 NZ D:LYS455 4.0 109.1 1.0 CD D:GLU373 4.0 123.0 1.0 CB D:ASN387 4.2 119.9 1.0 CA D:ASN387 4.2 119.9 1.0 N D:ASN387 4.5 119.9 1.0 CB D:ASP390 4.6 115.1 1.0 OE1 D:GLU373 4.6 123.0 1.0 O D:TRP386 4.7 116.6 1.0 OD1 D:ASP390 4.7 115.1 1.0 C D:TRP386 4.7 116.6 1.0 CE D:LYS455 5.0 109.1 1.0

Q.Su, M.Chen, Y.Wang, B.Li, D.Jing, X.Zhan, Y.Yu, Y.Shi. Structural Basis For Ca 2+ Activation of the Heteromeric PKD1L3/PKD2L1 Channel. Nat Commun V. 12 4871 2021.
ISSN: ESSN 2041-1723
PubMed: 34381056
DOI: 10.1038/S41467-021-25216-Z