Calcium in PDB 3l9i: Myosin VI Nucleotide-Free (MDINSERT2) L310G Mutant Crystal Structure

The structure of Myosin VI Nucleotide-Free (MDINSERT2) L310G Mutant Crystal Structure, PDB code: 3l9i was solved by O.Pylypenko, L.Song, L.H.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.540, 104.400, 90.330, 90.00, 91.09, 90.00
R / Rfree (%)	18.5 / 23.5

The binding sites of Calcium atom in the Myosin VI Nucleotide-Free (MDINSERT2) L310G Mutant Crystal Structure (pdb code 3l9i). 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) L310G Mutant Crystal Structure, PDB code: 3l9i:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) L310G Mutant 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) L310G Mutant Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1148 b:67.2 occ:1.00 O C:THR26 2.3 66.6 1.0 OD2 C:ASP22 2.3 67.1 1.0 OD1 C:ASP20 2.3 66.5 1.0 OD2 C:ASP24 2.3 66.6 1.0 OE2 C:GLU31 2.4 70.1 1.0 O C:HOH620 2.5 62.3 1.0 CG C:ASP24 3.1 66.4 1.0 CD C:GLU31 3.1 73.9 1.0 OE1 C:GLU31 3.1 74.1 1.0 OD1 C:ASP24 3.4 68.1 1.0 CG C:ASP22 3.4 69.3 1.0 CG C:ASP20 3.4 63.8 1.0 C C:THR26 3.5 66.6 1.0 OD1 C:ASP22 3.8 70.6 1.0 CA C:ASP20 4.1 64.4 1.0 N C:THR26 4.2 65.2 1.0 CB C:ASP20 4.2 64.3 1.0 CA C:THR26 4.3 66.2 1.0 OD2 C:ASP20 4.3 62.9 1.0 N C:ASP24 4.4 66.2 1.0 CB C:ASP24 4.4 66.0 1.0 CG2 C:THR26 4.4 66.1 1.0 N C:ILE27 4.5 67.1 1.0 C C:ASP20 4.5 65.6 1.0 CB C:THR26 4.6 66.3 1.0 CA C:ILE27 4.6 67.8 1.0 CG C:GLU31 4.6 73.3 1.0 N C:GLY23 4.7 67.8 1.0 N C:ASP22 4.7 68.5 1.0 CB C:ASP22 4.8 68.8 1.0 CA C:ASP24 4.8 65.6 1.0 N C:GLY25 4.9 64.4 1.0 N C:LYS21 4.9 67.3 1.0 O C:ASP20 4.9 66.0 1.0

Calcium binding site 2 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) L310G Mutant 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) L310G Mutant Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1149 b:70.6 occ:1.00 OE2 C:GLU67 2.3 69.3 1.0 OD2 C:ASP56 2.3 71.6 1.0 OD1 C:ASN60 2.3 71.6 1.0 OE1 C:GLU67 2.3 68.6 1.0 O C:THR62 2.3 69.4 1.0 OD1 C:ASP58 2.3 72.3 1.0 CD C:GLU67 2.6 66.2 1.0 CG C:ASP58 3.3 74.4 1.0 CG C:ASN60 3.3 73.7 1.0 O C:HOH545 3.3 77.6 1.0 CG C:ASP56 3.4 73.2 1.0 C C:THR62 3.6 69.2 1.0 OD2 C:ASP58 3.6 75.6 1.0 ND2 C:ASN60 3.8 74.5 1.0 CG C:GLU67 4.2 64.9 1.0 OD1 C:ASP56 4.2 73.4 1.0 N C:THR62 4.2 70.7 1.0 N C:ASN60 4.3 73.4 1.0 CA C:ASP56 4.4 73.3 1.0 CB C:ASP56 4.4 73.2 1.0 N C:ILE63 4.5 68.1 1.0 CA C:ILE63 4.5 67.4 1.0 CA C:THR62 4.5 69.6 1.0 N C:ASP64 4.6 65.5 1.0 OD2 C:ASP64 4.6 71.8 1.0 CB C:ASN60 4.6 73.2 1.0 N C:GLY59 4.6 74.3 1.0 CB C:ASP58 4.6 74.6 1.0 CD1 C:ILE63 4.6 68.2 1.0 N C:GLY61 4.7 72.7 1.0 C C:ASP56 4.8 73.4 1.0 CA C:ASN60 4.8 73.4 1.0 N C:ASP58 4.8 74.5 1.0 OG1 C:THR62 4.8 68.2 1.0 C C:ASN60 4.9 73.2 1.0 CG C:ASP64 4.9 66.8 1.0 C C:ILE63 5.0 66.5 1.0

Calcium binding site 3 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) L310G Mutant 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) L310G Mutant Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1151 b:88.3 occ:1.00 O C:GLN135 2.3 87.9 1.0 OE1 C:GLU140 2.3 88.3 1.0 OD2 C:ASP129 2.3 87.1 1.0 OD2 C:ASP133 2.3 88.9 1.0 OE2 C:GLU140 2.8 89.3 1.0 CD C:GLU140 2.9 89.1 1.0 OD2 C:ASP131 3.3 88.5 1.0 CG C:ASP133 3.3 90.1 1.0 CG C:ASP129 3.5 85.1 1.0 ND2 C:ASN137 3.5 88.7 1.0 C C:GLN135 3.5 88.2 1.0 OD1 C:ASP131 3.5 87.3 1.0 CG C:ASP131 3.6 88.8 1.0 OD1 C:ASP133 3.7 92.4 1.0 CA C:ASP129 3.8 84.5 1.0 CB C:ASP129 4.0 84.5 1.0 N C:GLN135 4.2 88.5 1.0 CG C:ASN137 4.2 89.1 1.0 CA C:VAL136 4.3 88.3 1.0 C C:ASP129 4.3 85.2 1.0 N C:ILE130 4.3 86.1 1.0 N C:VAL136 4.3 88.2 1.0 N C:ASN137 4.4 88.5 1.0 CG C:GLU140 4.4 89.7 1.0 OD1 C:ASP129 4.5 84.8 1.0 CA C:GLN135 4.5 88.2 1.0 N C:ASP133 4.5 89.7 1.0 N C:ASP131 4.5 88.5 1.0 CB C:ASP133 4.5 89.8 1.0 N C:GLY134 4.6 89.3 1.0 OD1 C:ASN137 4.6 89.3 1.0 CB C:ASP131 4.8 88.8 1.0 N C:GLY132 4.8 89.5 1.0 C C:VAL136 4.8 88.4 1.0 CA C:ASP133 5.0 89.7 1.0

Calcium binding site 4 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) L310G Mutant 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) L310G Mutant Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1150 b:86.5 occ:1.00 OD1 C:ASP93 2.3 87.2 1.0 OE2 C:GLU104 2.3 85.2 1.0 OD1 C:ASN97 2.3 85.8 1.0 OE1 C:GLU104 2.3 85.7 1.0 OD1 C:ASP95 2.3 87.8 1.0 O C:PHE99 2.4 85.9 1.0 CD C:GLU104 2.6 85.1 1.0 CG C:ASP95 3.3 89.3 1.0 CG C:ASP93 3.3 87.7 1.0 CG C:ASN97 3.3 86.3 1.0 C C:PHE99 3.6 86.1 1.0 ND2 C:ASN97 3.7 83.7 1.0 OD2 C:ASP95 3.8 89.4 1.0 OD2 C:ASP93 3.9 87.0 1.0 CG C:GLU104 4.1 85.1 1.0 CA C:ASP93 4.2 87.7 1.0 N C:ASN97 4.2 87.4 1.0 N C:GLY96 4.2 88.5 1.0 N C:ASP95 4.3 89.0 1.0 CB C:ASP93 4.3 87.5 1.0 C C:ASP93 4.4 87.9 1.0 N C:PHE99 4.4 86.3 1.0 N C:LYS94 4.5 88.4 1.0 CA C:PHE99 4.5 86.1 1.0 CB C:ASP95 4.5 88.8 1.0 N C:ILE100 4.5 85.7 1.0 N C:SER101 4.6 84.5 1.0 CB C:ASN97 4.6 87.1 1.0 CA C:ILE100 4.6 85.5 1.0 CA C:ASP95 4.8 88.9 1.0 CA C:ASN97 4.9 87.3 1.0 O C:ASP93 4.9 87.9 1.0 CB C:GLU104 4.9 84.7 1.0 CB C:PHE99 5.0 86.4 1.0

O.Pylypenko, L.Song, G.Squires, X.Liu, A.B.Zong, A.Houdusse, L.H.Sweeney. Role of Insert I of Myosin VI in Modulating Nucleotide Affinity To Be Published.