Calcium in PDB 4dbp: Myosin VI Nucleotide-Free (MDINSERT2) D179Y Crystal Structure

The structure of Myosin VI Nucleotide-Free (MDINSERT2) D179Y Crystal Structure, PDB code: 4dbp 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)	19.89 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.600, 104.390, 90.020, 90.00, 91.15, 90.00
R / Rfree (%)	16.3 / 21.8

The binding sites of Calcium atom in the Myosin VI Nucleotide-Free (MDINSERT2) D179Y Crystal Structure (pdb code 4dbp). 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) D179Y Crystal Structure, PDB code: 4dbp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) D179Y 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) D179Y Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:50.4 occ:1.00 OD2 C:ASP24 2.7 39.0 1.0 O C:THR26 2.8 52.9 1.0 OE2 C:GLU31 2.9 60.7 1.0 OD1 C:ASP20 2.9 49.1 1.0 OD2 C:ASP22 2.9 59.3 1.0 OE1 C:GLU31 2.9 59.5 1.0 O C:HOH303 3.0 42.2 1.0 CD C:GLU31 3.3 58.8 1.0 OD1 C:ASP22 3.3 64.7 1.0 CG C:ASP22 3.4 56.5 1.0 CG C:ASP24 3.5 49.7 1.0 OD1 C:ASP24 3.9 47.6 1.0 C C:THR26 3.9 47.3 1.0 CG C:ASP20 4.0 45.5 1.0 OG1 C:THR26 4.2 54.2 1.0 N C:ASP24 4.5 38.0 1.0 N C:THR26 4.5 31.2 1.0 CA C:ASP20 4.5 41.2 1.0 N C:ASP22 4.7 53.0 1.0 CB C:ASP24 4.7 39.1 1.0 CB C:ASP20 4.7 36.2 1.0 CA C:THR26 4.7 52.9 1.0 CA C:ILE27 4.7 43.9 1.0 CG2 C:THR28 4.7 50.9 1.0 N C:ILE27 4.7 42.3 1.0 C C:ASP20 4.8 43.2 1.0 OD2 C:ASP20 4.8 41.4 1.0 CG C:GLU31 4.8 44.6 1.0 N C:GLY23 4.8 50.0 1.0 CB C:ASP22 4.8 55.1 1.0 N C:LYS21 4.9 53.5 1.0 N C:THR28 4.9 47.3 1.0

Calcium binding site 2 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) D179Y 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) D179Y Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:55.9 occ:1.00 O C:THR62 2.7 36.4 1.0 OD2 C:ASP56 2.8 40.1 1.0 OE1 C:GLU67 2.9 50.3 1.0 OD1 C:ASP58 2.9 75.8 1.0 OD1 C:ASN60 3.0 62.7 1.0 OE2 C:GLU67 3.0 53.1 1.0 O C:HOH313 3.2 54.3 1.0 CD C:GLU67 3.3 50.1 1.0 CG C:ASN60 3.4 61.6 1.0 ND2 C:ASN60 3.4 55.9 1.0 CG C:ASP58 3.5 71.6 1.0 OD2 C:ASP58 3.5 65.8 1.0 C C:THR62 3.9 46.1 1.0 CG C:ASP56 4.0 65.8 1.0 N C:ASN60 4.2 58.3 1.0 OD2 C:ASP64 4.2 60.5 1.0 N C:THR62 4.4 50.6 1.0 CA C:ASP56 4.5 50.7 1.0 CB C:ASN60 4.5 59.6 1.0 N C:GLY61 4.6 60.5 1.0 N C:ASP64 4.6 46.1 1.0 CA C:ILE63 4.6 40.6 1.0 N C:GLY59 4.7 69.9 1.0 C C:ASP56 4.7 52.4 1.0 OG1 C:THR62 4.7 46.3 1.0 N C:ASP58 4.7 68.8 1.0 N C:ILE63 4.7 45.8 1.0 OD1 C:ASP56 4.7 76.5 1.0 CB C:ASP56 4.8 57.3 1.0 CA C:ASN60 4.8 62.1 1.0 CA C:THR62 4.8 48.5 1.0 CG C:GLU67 4.8 47.2 1.0 CB C:ASP58 4.8 67.5 1.0 N C:ALA57 4.9 59.5 1.0 CG C:ASP64 4.9 55.4 1.0 O C:HOH323 5.0 56.4 1.0

Calcium binding site 3 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) D179Y 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) D179Y Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:74.7 occ:1.00 OD1 C:ASP93 3.0 75.3 1.0 O C:PHE99 3.0 82.1 1.0 OD1 C:ASP95 3.0 79.6 1.0 OD1 C:ASN97 3.1 78.6 1.0 OE2 C:GLU104 3.1 95.6 1.0 CD C:GLU104 3.2 88.7 1.0 ND2 C:ASN97 3.4 63.1 1.0 CG C:ASP95 3.5 82.0 1.0 OD2 C:ASP95 3.5 78.2 1.0 CG C:ASN97 3.6 71.2 1.0 OE1 C:GLU104 3.6 91.1 1.0 CG C:GLU104 3.7 78.0 1.0 CG C:ASP93 3.7 74.1 1.0 C C:PHE99 4.2 79.6 1.0 CA C:ASP93 4.2 70.6 1.0 N C:ASP95 4.3 86.6 1.0 OD2 C:ASP93 4.3 72.8 1.0 N C:LYS94 4.4 61.2 1.0 N C:SER101 4.4 68.2 1.0 CB C:GLU104 4.5 71.3 1.0 C C:ASP93 4.5 65.8 1.0 CB C:ASP93 4.5 71.3 1.0 CB C:ASP95 4.7 86.6 1.0 CA C:ILE100 4.7 68.7 1.0 CB C:SER101 4.7 67.0 1.0 N C:ASN97 4.8 68.3 1.0 CA C:ASP95 4.9 86.3 1.0 N C:ILE100 4.9 75.8 1.0 CB C:ASN97 4.9 74.2 1.0 C C:ILE100 4.9 63.7 1.0 N C:GLY96 4.9 77.0 1.0 OG C:SER101 5.0 62.5 1.0

Calcium binding site 4 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) D179Y 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) D179Y Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca204 b:84.7 occ:1.00 O C:GLN135 2.9 71.2 1.0 OE1 C:GLU140 3.0 94.3 1.0 OD2 C:ASP131 3.2 84.7 1.0 OE2 C:GLU140 3.2 92.9 1.0 OD2 C:ASP129 3.2 89.8 1.0 OD1 C:ASP133 3.2 93.5 1.0 OD1 C:ASP131 3.3 74.9 1.0 CG C:ASP129 3.3 93.2 1.0 CD C:GLU140 3.4 93.8 1.0 CG C:ASP131 3.5 81.4 1.0 OD1 C:ASP129 3.5 95.7 1.0 CA C:VAL136 3.9 57.6 1.0 CA C:ASP129 4.0 86.3 1.0 C C:GLN135 4.0 73.0 1.0 CB C:ASP129 4.1 91.3 1.0 N C:ASN137 4.1 69.6 1.0 CG C:ASP133 4.2 89.8 1.0 N C:ILE130 4.3 84.2 1.0 ND2 C:ASN137 4.4 66.4 1.0 N C:VAL136 4.4 62.1 1.0 N C:ASP131 4.5 0.3 1.0 C C:VAL136 4.5 63.2 1.0 CG C:ASN137 4.5 73.0 1.0 OD2 C:ASP133 4.5 81.7 1.0 C C:ASP129 4.5 87.3 1.0 N C:GLY132 4.7 98.6 1.0 CB C:ASP131 4.7 85.8 1.0 OD1 C:ASN137 4.8 72.2 1.0 CG C:GLU140 4.9 92.8 1.0 CB C:VAL136 4.9 80.7 1.0 CB C:ASN137 5.0 77.8 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.