Calcium in PDB 4dbq: Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State

The structure of Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State, PDB code: 4dbq was solved by O.Pylypenko, H.L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.310, 107.880, 179.950, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 22.4

The structure of Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Magnesium	(Mg)	1 atom

The binding sites of Calcium atom in the Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State (pdb code 4dbq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State, PDB code: 4dbq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:79.8 occ:1.00 O B:THR26 2.3 58.9 1.0 OD2 B:ASP22 2.5 59.4 1.0 OD2 B:ASP24 2.7 63.7 1.0 OD1 B:ASP22 2.7 63.6 1.0 OD1 B:ASP20 2.7 55.0 1.0 CG B:ASP22 3.0 63.0 1.0 OD1 B:ASP24 3.0 67.4 1.0 OE1 B:GLU31 3.1 86.6 1.0 CG B:ASP24 3.2 64.2 1.0 C B:THR26 3.6 62.3 1.0 CD B:GLU31 3.9 80.0 1.0 CG B:ASP20 4.0 57.5 1.0 OE2 B:GLU31 4.0 76.2 1.0 OG1 B:THR26 4.2 65.5 1.0 N B:THR26 4.4 52.6 1.0 O B:HOH325 4.4 50.2 1.0 CA B:ILE27 4.4 67.5 1.0 N B:ILE27 4.4 64.3 1.0 CB B:ASP22 4.5 56.0 1.0 CA B:THR26 4.5 64.9 1.0 CB B:ASP24 4.6 55.2 1.0 CA B:ASP20 4.6 57.8 1.0 N B:ASP24 4.8 56.4 1.0 CB B:ASP20 4.8 58.0 1.0 OD2 B:ASP20 4.9 54.2 1.0 N B:ASP22 4.9 55.1 1.0 CG2 B:ILE27 4.9 61.3 1.0

Calcium binding site 2 out of 4 in the Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:87.7 occ:1.00 O B:THR62 2.6 61.3 1.0 OD1 B:ASP58 2.7 83.4 1.0 O B:HOH327 2.8 62.8 1.0 OE1 B:GLU67 2.9 71.7 1.0 OD1 B:ASP56 2.9 81.7 1.0 OD1 B:ASN60 3.2 77.5 1.0 OE2 B:GLU67 3.2 63.5 1.0 CD B:GLU67 3.4 69.9 1.0 CG B:ASP58 3.6 83.5 1.0 ND2 B:ASN60 3.7 76.8 1.0 C B:THR62 3.8 64.1 1.0 OD2 B:ASP58 3.8 74.5 1.0 CG B:ASN60 3.8 79.8 1.0 CA B:ILE63 3.9 70.1 1.0 CA B:ASP56 3.9 69.3 1.0 CG2 B:ILE63 3.9 66.3 1.0 CG B:ASP56 3.9 76.5 1.0 N B:ILE63 4.3 64.7 1.0 N B:ALA57 4.4 76.3 1.0 C B:ASP56 4.4 72.6 1.0 CB B:ASP56 4.4 69.6 1.0 CB B:ILE63 4.4 70.1 1.0 N B:ASP58 4.7 78.8 1.0 O B:VAL55 4.7 67.5 1.0 OD2 B:ASP64 4.9 75.1 1.0 CG B:GLU67 4.9 68.7 1.0 OG1 B:THR62 4.9 68.5 1.0 C B:ILE63 4.9 65.7 1.0 N B:ASP56 4.9 70.3 1.0 OD2 B:ASP56 4.9 77.3 1.0 N B:THR62 4.9 71.2 1.0 CA B:THR62 5.0 69.9 1.0 CB B:ASP58 5.0 76.6 1.0

Calcium binding site 3 out of 4 in the Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:52.4 occ:1.00 O B:PHE99 2.3 53.6 1.0 OD1 B:ASP95 2.4 55.2 1.0 OD1 B:ASP93 2.4 56.5 1.0 OD1 B:ASN97 2.5 57.5 1.0 OE1 B:GLU104 2.5 51.8 1.0 OE2 B:GLU104 2.7 54.4 1.0 O B:HOH305 2.7 50.7 1.0 CD B:GLU104 3.0 53.4 1.0 CG B:ASN97 3.4 58.4 1.0 CG B:ASP95 3.4 61.5 1.0 C B:PHE99 3.5 51.5 1.0 CG B:ASP93 3.6 55.3 1.0 OD2 B:ASP95 3.9 58.7 1.0 ND2 B:ASN97 3.9 53.6 1.0 O B:HOH311 4.0 53.4 1.0 CA B:ASP93 4.1 54.7 1.0 N B:PHE99 4.3 54.3 1.0 N B:ASP95 4.3 56.7 1.0 N B:ASN97 4.3 50.0 1.0 CB B:ASP93 4.3 56.4 1.0 C B:ASP93 4.4 56.2 1.0 CG B:GLU104 4.4 45.3 1.0 CA B:PHE99 4.4 50.5 1.0 OD2 B:ASP93 4.5 55.7 1.0 N B:ILE100 4.5 51.4 1.0 CB B:ASN97 4.5 58.8 1.0 CA B:ILE100 4.5 47.6 1.0 CB B:ASP95 4.5 54.3 1.0 O B:HOH320 4.5 43.1 1.0 N B:SER101 4.5 49.0 1.0 N B:LYS94 4.6 50.2 1.0 N B:GLY96 4.8 47.4 1.0 CA B:ASN97 4.8 53.4 1.0 CA B:ASP95 4.8 59.2 1.0 CB B:PHE99 4.8 53.4 1.0 O B:ASP93 4.9 56.2 1.0 C B:ILE100 4.9 46.1 1.0 C B:ASP95 4.9 55.0 1.0 N B:GLY98 4.9 56.3 1.0 OG B:SER101 5.0 40.5 1.0

Calcium binding site 4 out of 4 in the Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Myosin VI D179Y (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:52.8 occ:1.00 OD2 B:ASP129 2.5 51.3 1.0 O B:GLN135 2.5 52.7 1.0 OD1 B:ASP133 2.5 59.1 1.0 OD1 B:ASP131 2.6 64.5 1.0 OE1 B:GLU140 2.6 52.2 1.0 O B:HOH323 2.7 52.7 1.0 OE2 B:GLU140 2.8 53.9 1.0 CD B:GLU140 3.0 57.4 1.0 CG B:ASP131 3.3 61.1 1.0 CG B:ASP133 3.4 56.0 1.0 CG B:ASP129 3.5 56.0 1.0 OD2 B:ASP131 3.6 54.5 1.0 C B:GLN135 3.6 47.2 1.0 OD2 B:ASP133 3.9 55.8 1.0 N B:ASP133 4.2 46.9 1.0 CA B:ASP129 4.2 51.7 1.0 N B:GLN135 4.3 45.9 1.0 CB B:ASP129 4.3 52.7 1.0 CA B:VAL136 4.3 47.3 1.0 N B:ASN137 4.4 51.0 1.0 N B:ASP131 4.4 56.2 1.0 N B:VAL136 4.4 43.4 1.0 OD1 B:ASP129 4.4 53.6 1.0 CB B:ASP133 4.5 50.5 1.0 N B:GLY132 4.5 58.5 1.0 CG B:GLU140 4.5 53.4 1.0 CA B:GLN135 4.5 48.9 1.0 C B:ASP129 4.6 54.5 1.0 CB B:ASP131 4.6 56.7 1.0 N B:GLY134 4.6 50.9 1.0 N B:ILE130 4.7 56.9 1.0 CA B:ASP133 4.7 48.3 1.0 ND2 B:ASN137 4.7 49.4 1.0 C B:VAL136 4.8 49.8 1.0 CA B:ASP131 4.8 55.9 1.0 CG B:GLN135 4.8 53.3 1.0 C B:ASP131 4.9 58.1 1.0 CG B:ASN137 4.9 54.3 1.0 C B:ASP133 4.9 54.6 1.0

L.Song, O.Pylypenko, Z.Yang, A.Houdusse, L.H.Sweeney. Mutations in Myosin VI That Cause A Loss of Coordination Between Heads Provide Insights Into the Structural Changes Underlying Force Generation and the Importance of Gating To Be Published.