Calcium in PDB 2vas: Myosin VI (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State

The structure of Myosin VI (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State, PDB code: 2vas was solved by J.Menetrey, P.Llinas, J.Cicolari, G.Squires, X.Liu, A.Li, H.L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.28 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.420, 100.470, 174.070, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.6

The structure of Myosin VI (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 (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State (pdb code 2vas). 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 (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State, PDB code: 2vas:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Myosin VI (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 (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1148 b:62.9 occ:1.00 O B:THR26 2.3 50.0 1.0 OD1 B:ASP20 2.4 38.6 1.0 OD2 B:ASP22 2.6 42.9 1.0 OD2 B:ASP24 2.6 45.2 1.0 OD1 B:ASP22 3.3 42.6 1.0 CG B:ASP22 3.3 42.6 1.0 C B:THR26 3.4 49.9 1.0 CG B:ASP24 3.5 45.3 1.0 CG B:ASP20 3.7 37.7 1.0 OD1 B:ASP24 3.7 44.5 1.0 OE1 B:GLU31 3.8 55.2 1.0 CA B:THR26 3.9 49.3 1.0 N B:THR26 4.0 48.8 1.0 CG2 B:THR26 4.0 48.7 1.0 CB B:THR26 4.1 49.3 1.0 N B:ILE27 4.5 50.7 1.0 OD2 B:ASP20 4.5 35.6 1.0 CA B:ASP20 4.5 38.6 1.0 CB B:ASP20 4.5 38.5 1.0 N B:ASP24 4.7 45.1 1.0 CB B:ASP22 4.8 42.5 1.0 CB B:ASP24 4.9 45.4 1.0 CD B:GLU31 4.9 54.5 1.0 N B:GLY23 4.9 43.3 1.0 CA B:ILE27 4.9 51.5 1.0 N B:ASP22 5.0 41.7 1.0 C B:ASP20 5.0 39.3 1.0

Calcium binding site 2 out of 4 in the Myosin VI (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 (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1149 b:0.6 occ:1.00 OD2 B:ASP56 2.4 67.4 1.0 O B:THR62 2.8 61.0 1.0 OD1 B:ASP58 2.9 68.6 1.0 OD1 B:ASN60 3.6 65.5 1.0 CG B:ASP56 3.6 67.8 1.0 CG B:ASP58 3.6 68.1 1.0 CG2 B:THR62 3.7 62.1 1.0 C B:THR62 3.7 61.0 1.0 OD2 B:ASP58 3.8 68.5 1.0 O B:ASP58 3.9 67.6 1.0 OE1 B:GLU67 4.0 56.2 1.0 CA B:ASP56 4.0 67.8 1.0 CB B:ASP56 4.3 67.8 1.0 N B:THR62 4.4 62.4 1.0 N B:ALA57 4.5 68.1 1.0 CA B:THR62 4.5 61.6 1.0 C B:ASP56 4.5 68.0 1.0 N B:ASP58 4.5 67.8 1.0 O B:VAL55 4.5 67.8 1.0 CG B:ASN60 4.5 65.7 1.0 OD1 B:ASP56 4.6 67.4 1.0 N B:ILE63 4.6 60.2 1.0 CB B:THR62 4.7 61.7 1.0 ND2 B:ASN60 4.7 65.3 1.0 C B:ASP58 4.8 67.5 1.0 CB B:ASP58 4.8 67.8 1.0 CD B:GLU67 4.9 56.5 1.0 CA B:ILE63 4.9 59.4 1.0 OE2 B:GLU67 4.9 57.5 1.0 CA B:ASP58 5.0 67.7 1.0

Calcium binding site 3 out of 4 in the Myosin VI (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 (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1150 b:28.0 occ:1.00 OD1 B:ASP93 2.3 38.8 1.0 O B:PHE99 2.3 28.9 1.0 OD1 B:ASN97 2.4 35.0 1.0 OD1 B:ASP95 2.5 36.8 1.0 OE1 B:GLU104 2.5 25.4 1.0 OE2 B:GLU104 2.6 23.1 1.0 CD B:GLU104 2.9 24.5 1.0 CG B:ASP93 3.3 38.3 1.0 CG B:ASN97 3.5 34.5 1.0 CG B:ASP95 3.6 36.6 1.0 C B:PHE99 3.6 29.1 1.0 O B:HOH2003 4.0 29.0 1.0 OD2 B:ASP95 4.0 37.0 1.0 OD2 B:ASP93 4.1 38.5 1.0 ND2 B:ASN97 4.1 33.9 1.0 CA B:ASP93 4.2 37.8 1.0 CB B:ASP93 4.2 38.0 1.0 N B:PHE99 4.2 30.6 1.0 N B:ASN97 4.3 34.3 1.0 CG B:GLU104 4.4 24.5 1.0 CA B:PHE99 4.4 29.8 1.0 C B:ASP93 4.5 37.8 1.0 N B:ASP95 4.5 37.3 1.0 N B:ILE100 4.5 28.1 1.0 N B:LYS94 4.6 37.7 1.0 CB B:ASN97 4.6 34.2 1.0 CA B:ILE100 4.6 27.5 1.0 N B:GLY96 4.7 35.9 1.0 N B:SER101 4.7 26.4 1.0 CB B:ASP95 4.8 36.6 1.0 CA B:ASN97 4.8 33.8 1.0 N B:GLY98 4.9 32.7 1.0 CB B:PHE99 4.9 30.1 1.0 CA B:ASP95 5.0 36.8 1.0 C B:ASP95 5.0 36.4 1.0

Calcium binding site 4 out of 4 in the Myosin VI (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 (Md-INSERT2-Cam, Delta-INSERT1) Post-Rigor State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1151 b:37.4 occ:1.00 O B:GLN135 2.3 36.2 1.0 OD2 B:ASP129 2.3 32.5 1.0 OD2 B:ASP131 2.3 41.0 1.0 OD2 B:ASP133 2.6 40.1 1.0 OE2 B:GLU140 2.8 41.4 1.0 OE1 B:GLU140 2.8 40.5 1.0 CG B:ASP131 3.0 40.0 1.0 OD1 B:ASP131 3.1 40.2 1.0 CD B:GLU140 3.1 41.0 1.0 CG B:ASP133 3.4 39.1 1.0 C B:GLN135 3.4 36.1 1.0 CG B:ASP129 3.5 35.0 1.0 OD1 B:ASP133 3.8 40.4 1.0 N B:ASP133 4.1 37.9 1.0 N B:GLN135 4.2 35.6 1.0 N B:VAL136 4.3 36.4 1.0 CA B:VAL136 4.3 36.5 1.0 OD1 B:ASP129 4.3 32.3 1.0 CA B:GLN135 4.3 35.8 1.0 CB B:ASP133 4.3 37.9 1.0 CB B:ASP129 4.4 36.8 1.0 CA B:ASP129 4.4 37.2 1.0 N B:ASN137 4.4 38.1 1.0 CB B:ASP131 4.5 39.9 1.0 N B:GLY132 4.5 39.3 1.0 N B:ASP131 4.5 39.6 1.0 CA B:ASP133 4.6 37.8 1.0 CG B:GLU140 4.7 40.5 1.0 CB B:GLN135 4.7 35.7 1.0 C B:ASP129 4.7 37.8 1.0 N B:GLY134 4.8 36.5 1.0 N B:ILE130 4.8 38.7 1.0 C B:VAL136 4.8 37.1 1.0 C B:ASP133 4.9 37.2 1.0 CA B:ASP131 4.9 39.7 1.0 ND2 B:ASN137 4.9 39.8 1.0 CG B:ASN137 5.0 39.9 1.0

J.Menetrey, P.Llinas, J.Cicolari, G.Squires, X.Liu, A.Li, H.L.Sweeney, A.Houdusse. The Post-Rigor Structure of Myosin VI and Implications For the Recovery Stroke. Embo J. V. 27 244 2008.
ISSN: ISSN 0261-4189
PubMed: 18046460
DOI: 10.1038/SJ.EMBOJ.7601937