Vanadium in PDB 8qyu: Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil

The structure of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil, PDB code: 8qyu was solved by J.Robert-Paganin, C.Kikuti, D.Auguin, S.Rety, A.David, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.63 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.996, 122.503, 187.463, 90, 90, 90
R / Rfree (%)	19.1 / 23.5

The structure of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Vanadium atom in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil (pdb code 8qyu). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil, PDB code: 8qyu:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil within 5.0Å range: probe atom residue distance (Å) B Occ A:V902 b:25.7 occ:1.00 V A:VO4902 0.0 25.7 1.0 O4 A:VO4902 1.5 21.8 1.0 O3 A:VO4902 1.6 25.0 1.0 O1 A:VO4902 1.6 35.5 1.0 O2 A:VO4902 1.6 19.6 1.0 O3B A:ADP901 2.3 20.1 1.0 PB A:ADP901 3.5 22.7 1.0 O2B A:ADP901 3.6 17.2 1.0 MG A:MG903 3.7 22.7 1.0 OG A:SER241 3.8 18.6 1.0 N A:SER242 3.9 21.8 1.0 CA A:SER180 4.0 14.8 1.0 N A:GLY464 4.0 20.3 1.0 ND2 A:ASN238 4.0 24.2 1.0 O A:HOH1024 4.0 18.9 1.0 O A:HOH1064 4.1 20.8 1.0 OG A:SER180 4.1 26.3 1.0 NZ A:LYS184 4.1 6.0 1.0 N A:GLY181 4.2 17.1 1.0 CB A:SER180 4.3 15.2 1.0 O1B A:ADP901 4.3 19.6 1.0 CA A:SER241 4.3 23.0 1.0 O A:SER242 4.4 21.1 1.0 O A:HOH1052 4.4 16.1 1.0 CB A:SER241 4.5 21.1 1.0 CB A:SER242 4.6 20.1 1.0 CE A:LYS184 4.6 6.0 1.0 C A:SER241 4.6 27.9 1.0 O3A A:ADP901 4.6 22.2 1.0 C A:SER180 4.6 19.9 1.0 CA A:ALA463 4.7 16.8 1.0 OG A:SER242 4.7 27.5 1.0 CA A:SER242 4.7 17.6 1.0 CA A:GLY464 4.8 19.3 1.0 C A:ALA463 4.9 19.6 1.0

Vanadium binding site 2 out of 2 in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil within 5.0Å range: probe atom residue distance (Å) B Occ B:V902 b:26.5 occ:1.00 V B:VO4902 0.0 26.5 1.0 O4 B:VO4902 1.5 16.8 1.0 O2 B:VO4902 1.6 20.2 1.0 O3 B:VO4902 1.6 24.1 1.0 O1 B:VO4902 1.7 30.1 1.0 O1B B:ADP901 2.2 17.3 1.0 PB B:ADP901 3.4 23.2 1.0 O3B B:ADP901 3.6 19.0 1.0 MG B:MG903 3.6 17.6 1.0 N B:SER242 3.8 23.6 1.0 OG B:SER180 3.8 19.3 1.0 OG B:SER241 3.9 22.0 1.0 CA B:SER180 3.9 18.6 1.0 N B:GLY464 4.0 18.5 1.0 ND2 B:ASN238 4.0 13.8 1.0 O B:HOH1008 4.0 19.6 1.0 O B:HOH1039 4.1 17.8 1.0 N B:GLY181 4.1 27.7 1.0 NZ B:LYS184 4.2 7.5 1.0 O2B B:ADP901 4.2 20.7 1.0 CA B:SER241 4.2 22.9 1.0 CB B:SER180 4.3 15.3 1.0 O B:HOH1015 4.3 17.2 1.0 O B:SER242 4.4 23.1 1.0 CB B:SER241 4.5 21.7 1.0 C B:SER241 4.5 26.1 1.0 CB B:SER242 4.5 24.1 1.0 CE B:LYS184 4.5 16.6 1.0 C B:SER180 4.6 27.2 1.0 O3A B:ADP901 4.6 20.9 1.0 CA B:ALA463 4.6 24.8 1.0 OG B:SER242 4.6 31.9 1.0 CA B:SER242 4.7 21.3 1.0 CA B:GLY464 4.8 15.6 1.0 C B:ALA463 4.8 19.9 1.0 N B:SER180 4.9 22.4 1.0 CG B:ASN238 5.0 23.0 1.0

D.Auguin, J.Robert-Paganin, S.Rety, C.Kikuti, A.David, G.Theumer, A.W.Schmidt, H.J.Knolker, A.Houdusse. Omecamtiv Mecarbil and Mavacamten Target the Same Myosin Pocket Despite Antagonistic Effects in Heart Contraction. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 38014327
DOI: 10.1101/2023.11.15.567213