Magnesium 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:

Vanadium	(V)	2 atoms
Fluorine	(F)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Omecamtiv Mecarbil, PDB code: 8qyu:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg903 b:22.7 occ:1.00 OG A:SER242 1.9 27.5 1.0 OG1 A:THR185 2.0 23.1 1.0 O A:HOH1024 2.1 18.9 1.0 O4 A:VO4902 2.1 21.8 1.0 O A:HOH1052 2.2 16.1 1.0 O2B A:ADP901 2.4 17.2 1.0 CB A:SER242 2.9 20.1 1.0 CB A:THR185 3.2 22.8 1.0 V A:VO4902 3.7 25.7 1.0 N A:SER242 3.7 21.8 1.0 PB A:ADP901 3.7 22.7 1.0 CA A:SER242 3.9 17.6 1.0 O3B A:ADP901 3.9 20.1 1.0 CG2 A:THR185 4.1 10.2 1.0 OD2 A:ASP461 4.1 41.1 1.0 OD1 A:ASP461 4.1 40.9 1.0 N A:THR185 4.1 16.6 1.0 CA A:THR185 4.2 16.7 1.0 O2A A:ADP901 4.3 23.1 1.0 O A:HOH1028 4.4 24.0 1.0 O1 A:VO4902 4.4 35.5 1.0 O3 A:VO4902 4.4 25.0 1.0 CG A:ASP461 4.5 40.2 1.0 O3A A:ADP901 4.6 22.2 1.0 O A:ASN240 4.6 25.8 1.0 O A:ILE462 4.7 22.4 1.0 O A:HOH1148 4.7 28.4 1.0 O1B A:ADP901 4.8 19.6 1.0 C A:SER241 4.8 27.9 1.0 ND2 A:ASN232 4.8 16.3 1.0 O2 A:VO4902 4.8 19.6 1.0 PA A:ADP901 4.9 21.3 1.0 O1A A:ADP901 5.0 18.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg903 b:17.6 occ:1.00 OG1 B:THR185 2.0 17.5 1.0 O3B B:ADP901 2.1 19.0 1.0 O B:HOH1039 2.1 17.8 1.0 O B:HOH1015 2.1 17.2 1.0 O2 B:VO4902 2.1 20.2 1.0 OG B:SER242 2.2 31.9 1.0 CB B:THR185 3.1 23.4 1.0 CB B:SER242 3.2 24.1 1.0 PB B:ADP901 3.5 23.2 1.0 V B:VO4902 3.6 26.5 1.0 O1B B:ADP901 3.8 17.3 1.0 N B:SER242 3.8 23.6 1.0 N B:THR185 3.9 21.9 1.0 OD1 B:ASP461 4.0 27.5 1.0 CA B:THR185 4.1 19.6 1.0 CA B:SER242 4.1 21.3 1.0 O1A B:ADP901 4.1 35.4 1.0 OD2 B:ASP461 4.1 29.8 1.0 CG2 B:THR185 4.1 16.9 1.0 O4 B:VO4902 4.3 16.8 1.0 O3A B:ADP901 4.4 20.9 1.0 O B:HOH1011 4.5 19.2 1.0 CG B:ASP461 4.5 30.1 1.0 O1 B:VO4902 4.5 30.1 1.0 O2B B:ADP901 4.5 20.7 1.0 O B:ASN240 4.6 29.4 1.0 O3 B:VO4902 4.6 24.1 1.0 PA B:ADP901 4.7 26.0 1.0 O B:ILE462 4.7 27.4 1.0 O2A B:ADP901 4.8 21.9 1.0 ND2 B:ASN232 4.9 13.7 1.0 C B:SER241 4.9 26.1 1.0 ND2 B:ASN238 4.9 13.8 1.0 C B:LYS184 4.9 24.3 1.0 CB B:LYS184 5.0 16.0 1.0 O B:HOH1045 5.0 29.1 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