Ruthenium in PDB 8s8z: Cryo-Em Structure of Octameric Human CALHM1 (I109W) in Complex with Ruthenium Red

The binding sites of Ruthenium atom in the Cryo-Em Structure of Octameric Human CALHM1 (I109W) in Complex with Ruthenium Red (pdb code 8s8z). 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 Octameric Human CALHM1 (I109W) in Complex with Ruthenium Red, PDB code: 8s8z:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in the Cryo-Em Structure of Octameric Human CALHM1 (I109W) in Complex with 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 Octameric Human CALHM1 (I109W) in Complex with Ruthenium Red within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru402 b:362.9 occ:1.00 RU2 A:R2R402 0.0 362.9 1.0 O06 A:R2R402 1.7 281.7 1.0 O13 A:R2R402 1.7 250.6 1.0 N05 A:R2R402 1.8 244.9 1.0 N04 A:R2R402 1.8 264.8 1.0 N03 A:R2R402 1.8 251.2 1.0 N01 A:R2R402 1.8 267.0 1.0 RU1 A:R2R402 3.1 307.5 1.0 RU3 A:R2R402 3.1 311.9 1.0 N16 A:R2R402 3.1 272.1 1.0 N19 A:R2R402 3.1 279.0 1.0 N12 A:R2R402 3.1 270.4 1.0 N10 A:R2R402 3.4 262.3 1.0 N11 A:R2R402 3.6 246.7 1.0 N18 A:R2R402 3.9 274.4 1.0 N15 A:R2R402 4.0 255.5 1.0 N08 A:R2R402 4.1 267.6 1.0 N17 A:R2R402 4.7 248.1 1.0 N09 A:R2R402 4.8 229.4 1.0

Ruthenium binding site 2 out of 3 in the Cryo-Em Structure of Octameric Human CALHM1 (I109W) in Complex with 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 Octameric Human CALHM1 (I109W) in Complex with Ruthenium Red within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru402 b:311.9 occ:1.00 RU3 A:R2R402 0.0 311.9 1.0 O06 A:R2R402 1.8 281.7 1.0 N11 A:R2R402 1.8 246.7 1.0 N08 A:R2R402 1.8 267.6 1.0 N09 A:R2R402 1.8 229.4 1.0 N10 A:R2R402 1.8 262.3 1.0 N12 A:R2R402 1.8 270.4 1.0 N05 A:R2R402 3.0 244.9 1.0 RU2 A:R2R402 3.1 362.9 1.0 N03 A:R2R402 3.1 251.2 1.0 N01 A:R2R402 3.9 267.0 1.0 N04 A:R2R402 4.1 264.8 1.0 O13 A:R2R402 4.6 250.6 1.0

Ruthenium binding site 3 out of 3 in the Cryo-Em Structure of Octameric Human CALHM1 (I109W) in Complex with 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 Octameric Human CALHM1 (I109W) in Complex with Ruthenium Red within 5.0Å range: probe atom residue distance (Å) B Occ A:Ru402 b:307.5 occ:1.00 RU1 A:R2R402 0.0 307.5 1.0 O13 A:R2R402 1.7 250.6 1.0 N18 A:R2R402 1.8 274.4 1.0 N19 A:R2R402 1.8 279.0 1.0 N16 A:R2R402 1.8 272.1 1.0 N15 A:R2R402 1.8 255.5 1.0 N17 A:R2R402 1.8 248.1 1.0 RU2 A:R2R402 3.1 362.9 1.0 N01 A:R2R402 3.1 267.0 1.0 N05 A:R2R402 3.3 244.9 1.0 N04 A:R2R402 3.6 264.8 1.0 N03 A:R2R402 4.0 251.2 1.0 O06 A:R2R402 4.7 281.7 1.0

J.L.Syrjanen, M.Epstein, R.Gomez, H.Furukawa. Structure of Human CALHM1 Reveals Key Locations For Channel Regulation and Blockade By Ruthenium Red Nat Commun V. 14 3821 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-39388-3