Calcium in PDB 2bkh: Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure

The structure of Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure, PDB code: 2bkh was solved by J.Menetrey, A.Bahloul, C.Yengo, A.Wells, C.Morris, H.L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.4
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.570, 104.437, 90.284, 90.00, 91.26, 90.00
R / Rfree (%)	20.6 / 25.4

The binding sites of Calcium atom in the Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure (pdb code 2bkh). 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 Nucleotide-Free (MDINSERT2) Crystal Structure, PDB code: 2bkh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1148 b:65.9 occ:1.00 O B:THR26 2.1 69.3 1.0 OD1 B:ASP20 2.3 61.5 1.0 OD2 B:ASP22 2.4 65.0 1.0 OD2 B:ASP24 2.6 66.2 1.0 OE2 B:GLU31 2.7 78.6 1.0 CG B:ASP24 3.2 66.5 1.0 OE1 B:GLU31 3.2 78.0 1.0 OD1 B:ASP24 3.3 67.3 1.0 C B:THR26 3.3 69.6 1.0 CG B:ASP22 3.3 65.3 1.0 CD B:GLU31 3.3 78.1 1.0 OD1 B:ASP22 3.4 66.6 1.0 CG B:ASP20 3.5 62.2 1.0 N B:THR26 4.1 68.3 1.0 CA B:THR26 4.2 69.0 1.0 OD2 B:ASP20 4.2 60.8 1.0 N B:ILE27 4.3 70.3 1.0 CG2 B:THR26 4.3 68.8 1.0 N B:ASP24 4.3 65.8 1.0 CB B:ASP20 4.3 62.4 1.0 CA B:ILE27 4.4 70.9 1.0 CB B:ASP24 4.4 66.4 1.0 CA B:ASP20 4.4 62.5 1.0 CB B:THR26 4.7 69.0 1.0 N B:THR28 4.7 72.5 1.0 CA B:ASP24 4.7 66.2 1.0 CB B:ASP22 4.8 65.2 1.0 C B:ASP20 4.8 63.2 1.0 CG B:GLU31 4.8 77.7 1.0 N B:GLY23 4.9 65.4 1.0 CG2 B:THR28 4.9 73.2 1.0 N B:GLY25 5.0 66.8 1.0 C B:ASP24 5.0 66.3 1.0 N B:ASP22 5.0 64.9 1.0 C B:ILE27 5.0 71.5 1.0 N B:LYS21 5.0 64.1 1.0

Calcium binding site 2 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1149 b:71.5 occ:1.00 O B:THR62 2.1 69.8 1.0 OE1 B:GLU67 2.3 62.6 1.0 OD2 B:ASP56 2.3 75.7 1.0 OD1 B:ASN60 2.3 72.5 1.0 OD1 B:ASP58 2.7 77.0 1.0 OE2 B:GLU67 2.8 65.4 1.0 CD B:GLU67 2.9 64.5 1.0 C B:THR62 3.3 70.2 1.0 OD2 B:ASP58 3.4 77.2 1.0 CG B:ASP56 3.4 75.6 1.0 CG B:ASP58 3.4 76.2 1.0 CG B:ASN60 3.5 72.6 1.0 OD2 B:ASP64 3.9 70.9 1.0 OD1 B:ASP56 4.1 75.0 1.0 ND2 B:ASN60 4.1 72.8 1.0 N B:ILE63 4.1 69.9 1.0 N B:THR62 4.2 70.8 1.0 CA B:ILE63 4.2 69.6 1.0 CA B:THR62 4.2 70.3 1.0 N B:ASP64 4.3 68.9 1.0 CA B:ASP56 4.4 76.2 1.0 CG B:GLU67 4.4 66.0 1.0 CG2 B:THR62 4.4 70.2 1.0 N B:ASN60 4.4 73.1 1.0 CB B:ASP56 4.4 76.1 1.0 CB B:ASN60 4.7 72.8 1.0 CG B:ASP64 4.7 69.8 1.0 N B:GLY59 4.7 74.3 1.0 C B:ASP56 4.8 76.3 1.0 C B:ILE63 4.8 69.3 1.0 CB B:THR62 4.8 70.2 1.0 N B:ASP58 4.8 75.9 1.0 CB B:ASP58 4.8 75.8 1.0 N B:ALA57 4.9 76.2 1.0 CA B:ASN60 4.9 72.8 1.0

Calcium binding site 3 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1150 b:91.5 occ:1.00 O B:PHE99 2.4 68.1 1.0 OD1 B:ASP93 2.4 80.5 1.0 OD1 B:ASP95 2.6 81.8 1.0 OE2 B:GLU104 2.6 82.6 1.0 OE1 B:GLU104 2.7 82.1 1.0 OD1 B:ASN97 2.9 71.7 1.0 CD B:GLU104 3.0 81.7 1.0 CG B:ASP93 3.4 81.7 1.0 CG B:ASN97 3.5 71.8 1.0 C B:PHE99 3.6 68.2 1.0 ND2 B:ASN97 3.7 70.7 1.0 CG B:ASP95 3.8 80.6 1.0 N B:GLY96 4.0 77.0 1.0 N B:ASN97 4.0 73.3 1.0 OD2 B:ASP93 4.1 82.9 1.0 CA B:ASP93 4.1 81.4 1.0 N B:PHE99 4.3 67.5 1.0 OD2 B:ASP95 4.4 81.4 1.0 CB B:ASP93 4.4 81.5 1.0 N B:ASP95 4.4 80.0 1.0 CA B:PHE99 4.5 67.0 1.0 N B:ILE100 4.5 69.3 1.0 C B:ASP93 4.5 81.3 1.0 CG B:GLU104 4.5 80.6 1.0 N B:LYS94 4.5 81.1 1.0 CA B:ILE100 4.6 70.4 1.0 CA B:GLY96 4.6 75.9 1.0 CB B:ASN97 4.7 72.3 1.0 C B:ASP95 4.8 78.5 1.0 C B:GLY96 4.8 74.7 1.0 CA B:ASN97 4.8 72.3 1.0 CB B:ASP95 4.9 79.7 1.0 CA B:ASP95 4.9 79.5 1.0

Calcium binding site 4 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1151 b:90.5 occ:1.00 OD2 B:ASP129 2.2 84.9 1.0 O B:GLN135 2.6 84.9 1.0 OE1 B:GLU140 2.6 84.2 1.0 OD2 B:ASP133 2.8 86.7 1.0 OD2 B:ASP131 3.2 84.8 1.0 CG B:ASP129 3.3 85.3 1.0 OD1 B:ASP131 3.4 83.9 1.0 CD B:GLU140 3.6 84.6 1.0 CG B:ASP131 3.6 84.8 1.0 CG B:ASP133 3.6 85.9 1.0 C B:GLN135 3.6 84.8 1.0 OE2 B:GLU140 3.8 83.3 1.0 OD1 B:ASP133 3.8 86.1 1.0 N B:ASN137 3.9 85.0 1.0 ND2 B:ASN137 4.0 85.1 1.0 OD1 B:ASP129 4.0 84.3 1.0 CA B:VAL136 4.1 84.6 1.0 CG B:ASN137 4.2 85.4 1.0 N B:VAL136 4.3 84.6 1.0 CB B:ASP129 4.3 85.4 1.0 CE2 B:PHE99 4.4 58.4 1.0 CA B:ASP129 4.5 85.5 1.0 C B:VAL136 4.5 84.7 1.0 CB B:ASN137 4.6 85.3 1.0 OD1 B:ASN137 4.6 84.7 1.0 N B:GLN135 4.7 84.8 1.0 CA B:GLN135 4.7 84.7 1.0 N B:ASP131 4.8 85.2 1.0 CD2 B:PHE99 4.8 60.0 1.0 CB B:ASP133 4.9 85.5 1.0 N B:ASP133 4.9 85.3 1.0 N B:ILE130 4.9 85.3 1.0 C B:ASP129 4.9 85.4 1.0 CB B:ASP131 4.9 84.8 1.0 CA B:ASN137 4.9 85.3 1.0 CG B:GLU140 5.0 84.7 1.0

J.Menetrey, A.Bahloul, A.Wells, C.Yengo, C.Morris, H.L.Sweeney, A.Houdusse. The Structure of the Myosin VI Motor Reveals the Mechanism of Directionality Reversal Nature V. 435 779 2005.
ISSN: ISSN 0028-0836
PubMed: 15944696
DOI: 10.1038/NATURE03592