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

The structure of Myosin VI Nucleotide-Free (MDINSERT2-Iq) Crystal Structure, PDB code: 2bki 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 / 2.9
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.781, 250.167, 67.274, 90.00, 90.00, 90.00
R / Rfree (%)	26.4 / 30.4

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

Calcium binding site 1 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2-Iq) 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-Iq) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1148 b:83.9 occ:1.00 O B:THR26 2.4 71.5 1.0 OD1 B:ASP24 2.5 67.1 1.0 OD1 B:ASP22 2.5 65.7 1.0 OD1 B:ASP20 2.6 61.7 1.0 OE1 B:GLU31 3.3 79.6 1.0 CG B:ASP22 3.5 65.5 1.0 C B:THR26 3.6 71.7 1.0 CG B:ASP24 3.6 67.8 1.0 CG B:ASP20 3.7 63.1 1.0 OD2 B:ASP22 3.8 65.2 1.0 OE2 B:GLU31 3.9 79.8 1.0 CD B:GLU31 3.9 79.2 1.0 CA B:ASP20 4.0 64.1 1.0 OD2 B:ASP24 4.1 69.0 1.0 CB B:ASP20 4.2 64.0 1.0 CG2 B:ILE27 4.2 73.2 1.0 N B:THR26 4.4 70.5 1.0 C B:ASP20 4.4 64.5 1.0 CA B:ILE27 4.5 73.2 1.0 N B:ILE27 4.5 72.5 1.0 CA B:THR26 4.6 71.0 1.0 N B:LYS21 4.6 64.9 1.0 N B:ASP22 4.7 65.7 1.0 OD2 B:ASP20 4.7 63.1 1.0 N B:ASP24 4.7 67.1 1.0 CB B:ASP22 4.7 65.7 1.0 CB B:ASP24 4.8 67.6 1.0 N B:GLY23 4.9 66.2 1.0 CB B:ILE27 5.0 73.3 1.0

Calcium binding site 2 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2-Iq) 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-Iq) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1149 b:86.6 occ:1.00 O B:THR62 2.6 79.7 1.0 OD2 B:ASP56 2.9 84.6 1.0 OD1 B:ASN60 3.2 85.6 1.0 OG1 B:THR62 3.5 79.8 1.0 OE1 B:GLU67 3.6 71.5 1.0 C B:THR62 3.8 79.6 1.0 CG B:ASP56 3.9 84.7 1.0 OE2 B:GLU67 4.0 73.2 1.0 CB B:ASP58 4.0 84.9 1.0 OD2 B:ASP58 4.2 84.0 1.0 CD B:GLU67 4.2 72.3 1.0 CG B:ASN60 4.2 83.9 1.0 CG B:ASP58 4.3 84.5 1.0 CB B:THR62 4.4 80.1 1.0 ND2 B:ASN60 4.5 83.3 1.0 CA B:THR62 4.5 80.0 1.0 N B:THR62 4.6 80.4 1.0 OD1 B:ASP56 4.6 84.3 1.0 OD2 B:ASP64 4.6 79.2 1.0 CB B:ASP56 4.7 85.0 1.0 N B:ASP58 4.7 84.9 1.0 CA B:ASP56 4.7 85.2 1.0 N B:ILE63 4.7 78.8 1.0 CA B:ILE63 4.9 78.2 1.0 CA B:ASP58 4.9 84.8 1.0

Calcium binding site 3 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2-Iq) 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-Iq) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1150 b:83.0 occ:1.00 O B:TYR99 2.2 69.2 1.0 OE2 B:GLU104 2.5 74.0 1.0 OD1 B:ASP93 2.5 65.0 1.0 OD1 B:ASN97 3.1 66.4 1.0 OD1 B:ASP95 3.2 69.2 1.0 C B:TYR99 3.2 69.2 1.0 CD B:GLU104 3.3 73.8 1.0 ND2 B:ASN97 3.4 66.4 1.0 CG B:ASN97 3.4 67.2 1.0 CG B:ASP93 3.5 64.6 1.0 OE1 B:GLU104 3.5 74.1 1.0 OD2 B:ASP95 3.8 68.4 1.0 OD2 B:ASP93 3.8 65.0 1.0 N B:TYR99 3.9 68.5 1.0 CG B:ASP95 3.9 67.9 1.0 CA B:TYR99 3.9 68.9 1.0 CB B:TYR99 4.1 69.1 1.0 N B:ASN97 4.2 67.3 1.0 N B:ILE100 4.3 69.4 1.0 CA B:ILE100 4.5 69.5 1.0 CB B:ASP93 4.6 64.1 1.0 N B:GLY96 4.7 67.6 1.0 CB B:ASN97 4.7 67.5 1.0 CG B:GLU104 4.7 72.9 1.0 CA B:ASN97 4.8 67.4 1.0 N B:SER101 4.9 70.0 1.0 C B:ASN97 4.9 67.5 1.0 N B:GLY98 4.9 67.7 1.0 CA B:ASP93 4.9 64.1 1.0

Calcium binding site 4 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2-Iq) 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-Iq) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1151 b:64.0 occ:1.00 O B:GLN135 2.4 66.0 1.0 OD1 B:ASP129 2.4 66.7 1.0 OE1 B:GLU140 2.9 56.6 1.0 OD1 B:ASP131 3.0 69.1 1.0 OD1 B:ASP133 3.0 70.6 1.0 OD2 B:ASP131 3.3 69.1 1.0 OE2 B:GLU140 3.3 57.8 1.0 CG B:ASP129 3.4 66.9 1.0 CG B:ASP131 3.5 69.3 1.0 CD B:GLU140 3.5 58.3 1.0 C B:GLN135 3.6 66.2 1.0 CG B:ASP133 3.7 69.7 1.0 OD2 B:ASP129 3.8 67.1 1.0 OD2 B:ASP133 3.9 69.5 1.0 ND2 B:ASN137 4.0 64.5 1.0 N B:GLN135 4.2 67.2 1.0 N B:ASP133 4.2 69.5 1.0 CB B:ASP129 4.4 67.2 1.0 CA B:ASP129 4.4 67.5 1.0 N B:GLY132 4.5 69.3 1.0 CA B:GLN135 4.5 66.9 1.0 N B:VAL136 4.5 65.6 1.0 N B:ASN137 4.6 63.9 1.0 CA B:VAL136 4.6 65.2 1.0 N B:ASP131 4.6 69.0 1.0 N B:ILE130 4.7 67.6 1.0 CB B:ASP133 4.8 69.4 1.0 C B:ASP129 4.8 67.5 1.0 CB B:ASP131 4.8 69.2 1.0 N B:GLY134 4.9 68.4 1.0 CA B:ASP133 4.9 69.3 1.0 CE2 B:TYR99 4.9 71.0 1.0 CG B:ASN137 4.9 64.1 1.0 CG B:GLU140 5.0 58.4 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