Calcium in PDB 8w41: Cryo-Em Structure of Myosin VI in the Autoinhibited State

The structure of Cryo-Em Structure of Myosin VI in the Autoinhibited State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Cryo-Em Structure of Myosin VI in the Autoinhibited State (pdb code 8w41). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Myosin VI in the Autoinhibited State, PDB code: 8w41:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Myosin VI in the Autoinhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Myosin VI in the Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:116.6 occ:1.00 O B:GLN136 2.3 107.3 1.0 OD1 B:ASP134 2.3 112.7 1.0 OE2 B:GLU141 2.4 104.5 1.0 OE1 B:GLU141 2.4 104.5 1.0 OD1 B:ASP130 2.5 115.6 1.0 CD B:GLU141 2.7 104.5 1.0 CG B:ASP134 3.1 112.7 1.0 OD2 B:ASP134 3.1 112.7 1.0 ND2 B:ASN138 3.2 104.2 1.0 CG B:ASP130 3.3 115.6 1.0 C B:GLN136 3.3 107.3 1.0 OD2 B:ASP130 3.4 115.6 1.0 CA B:VAL137 3.5 103.6 1.0 N B:ASN138 3.7 104.2 1.0 N B:VAL137 3.9 103.6 1.0 C B:VAL137 3.9 103.6 1.0 CG B:ASN138 4.1 104.2 1.0 CG B:GLU141 4.2 104.5 1.0 N B:GLN136 4.5 107.3 1.0 CB B:ASP132 4.5 115.1 1.0 CB B:ASP134 4.5 112.7 1.0 N B:ASP134 4.5 112.7 1.0 CB B:ASN138 4.5 104.2 1.0 CA B:GLN136 4.6 107.3 1.0 CB B:ASP130 4.6 115.6 1.0 CA B:ASN138 4.7 104.2 1.0 CB B:VAL137 4.8 103.6 1.0 OD2 B:ASP132 4.8 115.1 1.0 CE2 B:TYR100 4.8 105.2 1.0 O B:VAL137 4.8 103.6 1.0 OD1 B:ASN138 4.9 104.2 1.0 N B:GLY133 4.9 111.8 1.0 CB B:GLU141 5.0 104.5 1.0 CA B:ASP130 5.0 115.6 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Myosin VI in the Autoinhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Myosin VI in the Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:115.3 occ:1.00 OD1 B:ASP94 2.3 103.2 1.0 OD1 B:ASN98 2.3 104.0 1.0 OD1 B:ASP96 2.4 101.9 1.0 OE1 B:GLU105 2.5 104.2 1.0 OE2 B:GLU105 2.5 104.2 1.0 O B:TYR100 2.5 105.2 1.0 CD B:GLU105 2.8 104.2 1.0 OD2 B:ASP96 2.9 101.9 1.0 CG B:ASP96 2.9 101.9 1.0 CG B:ASN98 3.2 104.0 1.0 CG B:ASP94 3.4 103.2 1.0 C B:TYR100 3.7 105.2 1.0 ND2 B:ASN98 3.8 104.0 1.0 OD2 B:ASP94 3.8 103.2 1.0 CG B:GLU105 4.3 104.2 1.0 CA B:ILE101 4.3 102.2 1.0 CB B:ASP96 4.3 101.9 1.0 CB B:ASN98 4.4 104.0 1.0 N B:ILE101 4.5 102.2 1.0 N B:SER102 4.5 105.1 1.0 N B:ASN98 4.5 104.0 1.0 N B:TYR100 4.6 105.2 1.0 CB B:ASP94 4.7 103.2 1.0 N B:ASP96 4.7 101.9 1.0 CA B:TYR100 4.8 105.2 1.0 CA B:ASP94 4.9 103.2 1.0 C B:ILE101 4.9 102.2 1.0 CA B:ASN98 4.9 104.0 1.0 N B:GLY97 5.0 104.9 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Myosin VI in the Autoinhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Myosin VI in the Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:98.4 occ:1.00 O B:THR27 2.7 99.0 1.0 OD1 B:ASP25 3.0 102.4 1.0 OD2 B:ASP23 3.1 104.1 1.0 OD1 B:ASP23 3.5 104.1 1.0 CG B:ASP23 3.6 104.1 1.0 CG B:ASP25 3.9 102.4 1.0 C B:THR27 3.9 99.0 1.0 CG1 B:ILE28 3.9 92.8 1.0 OD1 B:ASP21 3.9 98.6 1.0 OD2 B:ASP25 4.1 102.4 1.0 CA B:ILE28 4.1 92.8 1.0 N B:ILE28 4.5 92.8 1.0 CB B:ILE28 4.5 92.8 1.0 CB B:ASP23 4.9 104.1 1.0 CG B:ASP21 4.9 98.6 1.0 CG2 B:ILE28 5.0 92.8 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Myosin VI in the Autoinhibited State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Myosin VI in the Autoinhibited State within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:96.7 occ:1.00 OD1 B:ASN61 2.3 96.3 1.0 OG1 B:THR63 2.4 97.4 1.0 O B:THR63 2.5 97.4 1.0 CG B:ASN61 2.9 96.3 1.0 ND2 B:ASN61 2.9 96.3 1.0 C B:THR63 3.2 97.4 1.0 OD1 B:ASP59 3.3 96.5 1.0 OD2 B:ASP59 3.3 96.5 1.0 OD1 B:ASP57 3.5 97.9 1.0 CB B:THR63 3.6 97.4 1.0 CG B:ASP59 3.7 96.5 1.0 CA B:THR63 3.8 97.4 1.0 N B:THR63 3.9 97.4 1.0 N B:ILE64 4.2 92.8 1.0 CB B:ASN61 4.2 96.3 1.0 OE1 B:GLU68 4.6 89.7 1.0 CG B:ASP57 4.6 97.9 1.0 CA B:ILE64 4.6 92.8 1.0 CG2 B:THR63 4.7 97.4 1.0 N B:ASP65 4.7 92.0 1.0 OE2 B:GLU68 4.7 89.7 1.0 CG2 B:THR27 4.8 99.0 1.0 C B:ILE64 5.0 92.8 1.0

F.Niu, L.Li, L.Wang, J.Xiao, S.Xu, Y.Liu, L.Lin, C.Yu, Z.Wei. Autoinhibition and Activation of Myosin VI Revealed By Its Cryo-Em Structure Nat Commun V. 15 1187 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-45424-7