Calcium in PDB 7d7f: Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound State

The binding sites of Calcium atom in the Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound State (pdb code 7d7f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound State, PDB code: 7d7f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound 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 Calcium-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca704 b:30.0 occ:1.00 OE2 B:GLU370 2.4 92.6 1.0 OD1 B:ASN387 2.6 86.0 1.0 OD2 B:ASP390 3.1 78.9 1.0 OE2 B:GLU373 3.1 99.4 1.0 OE1 B:GLU373 3.3 99.4 1.0 CD B:GLU370 3.5 92.6 1.0 CD B:GLU373 3.6 99.4 1.0 CG B:ASN387 3.7 86.0 1.0 OE1 B:GLU370 4.0 92.6 1.0 CE B:LYS455 4.0 77.4 1.0 CG B:ASP390 4.2 78.9 1.0 CA B:ASN387 4.6 86.0 1.0 ND2 B:ASN387 4.6 86.0 1.0 NZ B:LYS455 4.6 77.4 1.0 CB B:ASN387 4.6 86.0 1.0 CB B:ASP390 4.7 78.9 1.0 CG B:GLU370 4.7 92.6 1.0 N B:ASN387 4.8 86.0 1.0 O B:TRP386 5.0 80.4 1.0

Calcium binding site 2 out of 5 in the Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound 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 Calcium-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca704 b:30.0 occ:1.00 OE1 C:GLU370 2.3 92.4 1.0 OD1 C:ASN387 2.5 85.0 1.0 OE2 C:GLU373 2.6 99.5 1.0 OD1 C:ASP390 2.7 77.9 1.0 OE1 C:GLU373 3.0 99.5 1.0 CD C:GLU373 3.0 99.5 1.0 CD C:GLU370 3.4 92.4 1.0 CG C:ASN387 3.7 85.0 1.0 CG C:ASP390 4.0 77.9 1.0 OE2 C:GLU370 4.0 92.4 1.0 CG C:GLU373 4.3 99.5 1.0 ND2 C:ASN387 4.4 85.0 1.0 O C:TRP386 4.4 80.8 1.0 CG C:GLU370 4.6 92.4 1.0 CA C:ASN387 4.7 85.0 1.0 CB C:ASP390 4.7 77.9 1.0 CB C:ASN387 4.8 85.0 1.0 OD2 C:ASP390 4.8 77.9 1.0 CB C:GLU373 5.0 99.5 1.0

Calcium binding site 3 out of 5 in the Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound 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 Calcium-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:30.0 occ:1.00 OD1 D:ASN387 2.0 99.9 1.0 OE1 D:GLU370 2.5 101.1 1.0 OE1 D:GLU373 3.1 105.9 1.0 CG D:ASN387 3.2 99.9 1.0 NZ D:LYS455 3.5 95.3 1.0 OD2 D:ASP390 3.5 96.0 1.0 CD D:GLU370 3.6 101.1 1.0 ND2 D:ASN387 3.9 99.9 1.0 CD D:GLU373 4.1 105.9 1.0 OE2 D:GLU370 4.1 101.1 1.0 CB D:ASN387 4.3 99.9 1.0 CA D:ASN387 4.4 99.9 1.0 CG D:ASP390 4.5 96.0 1.0 CE D:LYS455 4.7 95.3 1.0 CG D:GLU373 4.7 105.9 1.0 CE1 D:TYR381 4.8 107.2 1.0 CG D:GLU370 4.9 101.1 1.0 N D:ASN387 4.9 99.9 1.0 OE2 D:GLU373 4.9 105.9 1.0

Calcium binding site 4 out of 5 in the Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca704 b:83.7 occ:1.00 O D:LEU521 2.9 64.8 1.0 C D:LEU521 4.1 64.8 1.0 CA D:GLY522 4.4 64.5 1.0 O D:GLY522 4.5 64.5 1.0 O A:GLY2066 4.6 64.7 1.0 N D:GLY522 4.7 64.5 1.0 C D:GLY522 4.8 64.5 1.0 CA A:GLY2066 4.8 64.7 1.0

Calcium binding site 5 out of 5 in the Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of PKD1L3-Ctd/PKD2L1 in Calcium-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca705 b:95.8 occ:1.00 O D:LEU117 3.6 79.6 1.0 CB D:MET121 3.7 81.1 1.0 N D:MET121 4.0 81.1 1.0 OE2 D:GLU356 4.1 90.2 1.0 CA D:MET121 4.1 81.1 1.0 C D:GLY120 4.2 77.8 1.0 O D:GLY120 4.4 77.8 1.0 C D:LEU117 4.8 79.6 1.0 CD1 D:LEU117 4.8 79.6 1.0 CA D:GLY120 4.9 77.8 1.0 CG D:MET121 5.0 81.1 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