Calcium in PDB 8gvw: Cryo-Em Structure of the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2

The structure of Cryo-Em Structure of the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2 also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2 (pdb code 8gvw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2, PDB code: 8gvw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2


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 the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca805 b:69.2 occ:1.00 OD1 A:ASN436 2.5 86.4 1.0 OE2 A:GLU418 2.6 97.8 1.0 OE1 A:GLU421 2.9 111.0 1.0 OD1 A:ASP439 3.0 78.5 1.0 CD A:GLU418 3.3 97.8 1.0 OE1 A:GLU418 3.4 97.8 1.0 CG A:ASN436 3.7 86.4 1.0 CD A:GLU421 3.9 111.0 1.0 NH2 A:ARG492 3.9 50.6 1.0 OE2 A:GLU421 4.0 111.0 1.0 CG A:ASP439 4.0 78.5 1.0 ND2 A:ASN436 4.5 86.4 1.0 CB A:ASP439 4.6 78.5 1.0 OD2 A:ASP433 4.7 101.6 1.0 CB A:ASN436 4.7 86.4 1.0 CA A:ASN436 4.7 86.4 1.0 CG A:GLU418 4.8 97.8 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2


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 the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca805 b:66.1 occ:1.00 OD1 B:ASN436 2.5 87.4 1.0 OE2 B:GLU418 2.6 97.3 1.0 OE1 B:GLU421 2.9 110.4 1.0 OD1 B:ASP439 3.0 79.1 1.0 CD B:GLU418 3.3 97.3 1.0 OE1 B:GLU418 3.4 97.3 1.0 CG B:ASN436 3.7 87.4 1.0 CD B:GLU421 3.9 110.4 1.0 NH2 B:ARG492 3.9 50.9 1.0 OE2 B:GLU421 4.0 110.4 1.0 CG B:ASP439 4.0 79.1 1.0 ND2 B:ASN436 4.5 87.4 1.0 CB B:ASP439 4.6 79.1 1.0 OD2 B:ASP433 4.7 102.9 1.0 CB B:ASN436 4.7 87.4 1.0 CA B:ASN436 4.7 87.4 1.0 CG B:GLU418 4.8 97.3 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2


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 the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca805 b:69.6 occ:1.00 OD1 C:ASN436 2.5 87.9 1.0 OE2 C:GLU418 2.6 98.2 1.0 OE1 C:GLU421 2.9 110.9 1.0 OD1 C:ASP439 3.0 79.0 1.0 CD C:GLU418 3.3 98.2 1.0 OE1 C:GLU418 3.4 98.2 1.0 CG C:ASN436 3.7 87.9 1.0 CD C:GLU421 3.9 110.9 1.0 NH2 C:ARG492 3.9 50.9 1.0 OE2 C:GLU421 4.0 110.9 1.0 CG C:ASP439 4.0 79.0 1.0 ND2 C:ASN436 4.5 87.9 1.0 CB C:ASP439 4.6 79.0 1.0 OD2 C:ASP433 4.7 103.4 1.0 CB C:ASN436 4.7 87.9 1.0 CA C:ASN436 4.7 87.9 1.0 CG C:GLU418 4.8 98.2 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2


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 the Human TRPC5 Ion Channel in Lipid Nanodiscs, CLASS2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca805 b:70.8 occ:1.00 OD1 D:ASN436 2.5 87.3 1.0 OE2 D:GLU418 2.6 97.0 1.0 OE1 D:GLU421 2.9 109.8 1.0 OD1 D:ASP439 3.0 78.9 1.0 CD D:GLU418 3.3 97.0 1.0 OE1 D:GLU418 3.4 97.0 1.0 CG D:ASN436 3.7 87.3 1.0 CD D:GLU421 3.9 109.8 1.0 NH2 D:ARG492 3.9 50.5 1.0 OE2 D:GLU421 4.0 109.8 1.0 CG D:ASP439 4.0 78.9 1.0 ND2 D:ASN436 4.5 87.3 1.0 CB D:ASP439 4.6 78.9 1.0 OD2 D:ASP433 4.7 103.3 1.0 CB D:ASN436 4.7 87.3 1.0 CA D:ASN436 4.7 87.3 1.0 CG D:GLU418 4.8 97.0 1.0

J.Won, J.Kim, H.Jeong, J.Kim, S.Feng, B.Jeong, M.Kwak, J.Ko, W.Im, I.So, H.H.Lee. Molecular Architecture of the G Alpha I -Bound TRPC5 Ion Channel. Nat Commun V. 14 2550 2023.
ISSN: ESSN 2041-1723
PubMed: 37137991
DOI: 10.1038/S41467-023-38281-3