Ruthenium in PDB 7s8b: Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red

The structure of Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Ruthenium atom in the Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red (pdb code 7s8b). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red, PDB code: 7s8b:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru813 b:20.0 occ:1.00 RU2 A:R2R813 0.0 20.0 1.0 O06 A:R2R813 1.8 20.0 1.0 O13 A:R2R813 1.8 20.0 1.0 N01 A:R2R813 2.0 20.0 1.0 N05 A:R2R813 2.0 20.0 1.0 N03 A:R2R813 2.0 20.0 1.0 N04 A:R2R813 2.0 20.0 1.0 RU1 A:R2R813 3.7 20.0 1.0 RU3 A:R2R813 3.7 20.0 1.0 N11 A:R2R813 4.2 20.0 1.0 N10 A:R2R813 4.2 20.0 1.0 N12 A:R2R813 4.2 20.0 1.0 N18 A:R2R813 4.2 20.0 1.0 N19 A:R2R813 4.2 20.0 1.0 N17 A:R2R813 4.2 20.0 1.0 N09 A:R2R813 4.2 20.0 1.0 N16 A:R2R813 4.2 20.0 1.0 O C:THR539 4.2 24.7 1.0 O D:THR539 4.3 21.9 1.0 O A:THR539 4.3 0.0 1.0 O B:THR539 4.3 1.8 1.0 OG1 D:THR539 4.5 21.9 1.0 OG1 C:THR539 4.5 24.7 1.0 OG1 A:THR539 4.5 0.0 1.0 OG1 B:THR539 4.6 1.8 1.0

Ruthenium binding site 2 out of 3 in the Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru813 b:20.0 occ:1.00 RU3 A:R2R813 0.0 20.0 1.0 O06 A:R2R813 1.8 20.0 1.0 N12 A:R2R813 2.0 20.0 1.0 N10 A:R2R813 2.0 20.0 1.0 N08 A:R2R813 2.0 20.0 1.0 N09 A:R2R813 2.0 20.0 1.0 N11 A:R2R813 2.0 20.0 1.0 RU2 A:R2R813 3.7 20.0 1.0 OD1 D:ASP542 4.1 23.7 1.0 OD1 A:ASP542 4.2 18.5 1.0 OD1 B:ASP542 4.2 13.9 1.0 N03 A:R2R813 4.2 20.0 1.0 N04 A:R2R813 4.2 20.0 1.0 N05 A:R2R813 4.2 20.0 1.0 N01 A:R2R813 4.2 20.0 1.0 OD1 C:ASP542 4.2 16.6 1.0 O C:THR539 4.5 24.7 1.0 O D:THR539 4.5 21.9 1.0 O A:THR539 4.6 0.0 1.0 O B:THR539 4.6 1.8 1.0 CA A:CA812 4.7 0.0 1.0

Ruthenium binding site 3 out of 3 in the Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Cryo-Em Structure of Human TRPV6 in Complex with Channel Blocker Ruthenium Red within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru813 b:20.0 occ:1.00 RU1 A:R2R813 0.0 20.0 1.0 O13 A:R2R813 1.8 20.0 1.0 N17 A:R2R813 2.0 20.0 1.0 N18 A:R2R813 2.0 20.0 1.0 N19 A:R2R813 2.0 20.0 1.0 N15 A:R2R813 2.0 20.0 1.0 N16 A:R2R813 2.0 20.0 1.0 RU2 A:R2R813 3.7 20.0 1.0 N01 A:R2R813 4.2 20.0 1.0 N05 A:R2R813 4.2 20.0 1.0 N04 A:R2R813 4.2 20.0 1.0 N03 A:R2R813 4.2 20.0 1.0

A.Neuberger, K.D.Nadezhdin, A.I.Sobolevsky. Structural Mechanisms of TRPV6 Inhibition By Ruthenium Red and Econazole. Nat Commun V. 12 6284 2021.
ISSN: ESSN 2041-1723
PubMed: 34725357
DOI: 10.1038/S41467-021-26608-X