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Calcium in PDB 3gn4: Myosin Lever Arm

Protein crystallography data

The structure of Myosin Lever Arm, PDB code: 3gn4 was solved by M.Mukherjea, P.Llinas, H.Kim, M.Travaglia, D.Safer, A.B.Zong, J.Menetrey, C.Franzini-Armstrong, P.R.Selvin, A.Houdusse, H.L.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.52 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.790, 118.390, 182.060, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 26.4

Other elements in 3gn4:

The structure of Myosin Lever Arm also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Myosin Lever Arm (pdb code 3gn4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Myosin Lever Arm, PDB code: 3gn4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3gn4

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Calcium binding site 1 out of 8 in the Myosin Lever Arm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:64.6
occ:1.00
 O B:THR26 2.4 45.4 1.0
OD1 B:ASP22 2.5 51.9 1.0
OD1 B:ASP24 2.7 56.3 1.0
OD1 B:ASP20 2.7 48.7 1.0
OD2 B:ASP24 2.9 58.7 1.0
OD2 B:ASP22 2.9 55.5 1.0
CG B:ASP24 3.0 57.7 1.0
CG B:ASP22 3.1 56.2 1.0
O B:HOH301 3.3 40.9 1.0
OE2 B:GLU31 3.4 59.1 1.0
C B:THR26 3.6 48.0 1.0
CG B:ASP20 4.0 47.5 1.0
N B:THR26 4.3 47.0 1.0
OG1 B:THR26 4.3 46.6 1.0
CB B:ASP24 4.4 48.8 1.0
CA B:THR26 4.5 52.1 1.0
N B:ASP24 4.5 46.6 1.0
N B:ILE27 4.5 47.7 1.0
CA B:ASP20 4.5 43.2 1.0
CB B:ASP22 4.6 44.4 1.0
CB B:ASP20 4.6 41.4 1.0
CA B:ILE27 4.7 45.1 1.0
CD B:GLU31 4.7 55.5 1.0
CG2 B:ILE27 4.7 44.3 1.0
CA B:ASP24 4.8 49.4 1.0
C B:ASP20 4.9 50.5 1.0
N B:GLY25 4.9 51.7 1.0
N B:ASP22 4.9 51.8 1.0
OD2 B:ASP20 4.9 48.3 1.0

Calcium binding site 2 out of 8 in 3gn4

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Calcium binding site 2 out of 8 in the Myosin Lever Arm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:64.2
occ:1.00
 O B:THR62 2.8 52.2 1.0
OD1 B:ASP58 2.8 61.9 1.0
O B:HOH302 2.9 52.6 1.0
OD1 B:ASP56 2.9 56.6 1.0
OD1 B:ASN60 3.0 52.4 1.0
OE1 B:GLU67 3.1 51.8 1.0
OE2 B:GLU67 3.3 55.2 1.0
CG B:ASP58 3.4 63.6 1.0
OD2 B:ASP58 3.4 68.5 1.0
CD B:GLU67 3.5 52.1 1.0
ND2 B:ASN60 3.6 56.5 1.0
CG B:ASN60 3.7 59.0 1.0
C B:THR62 3.9 47.8 1.0
N B:ALA57 4.0 49.4 1.0
CA B:ASP56 4.0 41.6 1.0
CA B:ILE63 4.0 48.1 1.0
CG B:ASP56 4.0 49.3 1.0
N B:ASP58 4.1 50.2 1.0
C B:ASP56 4.1 44.6 1.0
CG2 B:ILE63 4.3 49.8 1.0
N B:ILE63 4.4 45.1 1.0
O B:VAL55 4.6 45.6 1.0
CB B:ASP56 4.6 42.1 1.0
CB B:ASP58 4.6 60.8 1.0
CB B:ILE63 4.7 45.6 1.0
CA B:ALA57 4.9 56.8 1.0
CA B:ASP58 4.9 55.2 1.0
O B:ASP56 4.9 47.6 1.0
CG B:GLU67 5.0 46.0 1.0
C B:ALA57 5.0 56.9 1.0

Calcium binding site 3 out of 8 in 3gn4

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Calcium binding site 3 out of 8 in the Myosin Lever Arm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:57.2
occ:1.00
 O B:PHE99 2.5 43.8 1.0
OE1 B:GLU104 2.5 50.4 1.0
OD1 B:ASP95 2.5 46.9 1.0
OD1 B:ASP93 2.6 47.9 1.0
OD1 B:ASN97 2.7 48.7 1.0
OE2 B:GLU104 2.9 45.6 1.0
CD B:GLU104 3.0 49.0 1.0
CG B:ASN97 3.1 47.8 1.0
CG B:ASP95 3.1 52.2 1.0
OD2 B:ASP95 3.2 52.2 1.0
ND2 B:ASN97 3.2 43.8 1.0
C B:PHE99 3.7 49.6 1.0
CG B:ASP93 3.8 42.9 1.0
N B:ASN97 4.0 41.4 1.0
CB B:ASN97 4.2 43.4 1.0
CA B:ASP93 4.2 43.0 1.0
CG B:GLU104 4.4 43.3 1.0
N B:PHE99 4.4 45.4 1.0
CB B:ASP95 4.5 48.9 1.0
CB B:ASP93 4.5 43.9 1.0
N B:ASP95 4.5 49.1 1.0
N B:GLY96 4.5 43.0 1.0
CA B:ASN97 4.6 44.0 1.0
CA B:PHE99 4.6 48.4 1.0
N B:ILE100 4.7 51.5 1.0
OD2 B:ASP93 4.7 48.4 1.0
CA B:ILE100 4.7 49.5 1.0
C B:ASP95 4.7 45.4 1.0
C B:ASP93 4.7 43.9 1.0
CA B:ASP95 4.8 46.0 1.0
N B:GLY98 4.9 42.0 1.0
N B:SER101 4.9 46.8 1.0
CB B:PHE99 5.0 56.9 1.0

Calcium binding site 4 out of 8 in 3gn4

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Calcium binding site 4 out of 8 in the Myosin Lever Arm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:66.8
occ:1.00
 OE1 B:GLU140 2.1 56.5 1.0
OD1 B:ASP131 2.5 49.2 1.0
O B:GLN135 2.5 62.3 1.0
OD1 B:ASP133 2.6 58.2 1.0
OD1 B:ASP129 2.6 55.8 1.0
O B:HOH303 2.6 53.1 1.0
CG B:ASP133 3.1 62.1 1.0
OD2 B:ASP133 3.2 62.4 1.0
C B:GLN135 3.2 56.4 1.0
CD B:GLU140 3.3 61.2 1.0
CG B:ASP131 3.4 60.0 1.0
OD2 B:ASP131 3.5 59.9 1.0
CG B:ASP129 3.6 53.2 1.0
N B:VAL136 3.8 54.0 1.0
CA B:VAL136 3.9 51.0 1.0
N B:GLN135 4.0 48.5 1.0
OE2 B:GLU140 4.0 59.0 1.0
CA B:GLN135 4.0 50.3 1.0
N B:ASN137 4.1 48.0 1.0
N B:ASP133 4.1 58.1 1.0
OD2 B:ASP129 4.3 49.2 1.0
CB B:GLN135 4.3 60.1 1.0
CB B:ASP133 4.3 57.1 1.0
CG B:GLU140 4.3 55.4 1.0
CA B:ASP129 4.4 52.7 1.0
CB B:ASP129 4.4 52.1 1.0
C B:VAL136 4.5 51.4 1.0
CA B:ASP133 4.6 51.3 1.0
N B:GLY132 4.7 53.2 1.0
N B:GLY134 4.7 53.0 1.0
CB B:ASP131 4.8 56.0 1.0
C B:ASP129 4.8 52.2 1.0
C B:ASP133 4.9 54.7 1.0
N B:ASP131 4.9 63.0 1.0

Calcium binding site 5 out of 8 in 3gn4

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Calcium binding site 5 out of 8 in the Myosin Lever Arm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:64.2
occ:1.00
 O F:THR26 2.2 54.7 1.0
OD1 F:ASP20 2.5 45.5 1.0
OD1 F:ASP22 2.6 47.1 1.0
OD1 F:ASP24 2.9 47.6 1.0
OE2 F:GLU31 3.0 49.7 1.0
OD2 F:ASP22 3.1 55.7 1.0
CG F:ASP22 3.2 53.7 1.0
C F:THR26 3.5 50.6 1.0
CG F:ASP20 3.5 49.7 1.0
CG F:ASP24 3.6 50.6 1.0
O F:HOH301 3.6 49.9 1.0
OD2 F:ASP24 3.7 51.3 1.0
CA F:ASP20 3.9 41.2 1.0
CB F:ASP20 4.0 44.0 1.0
CG2 F:ILE27 4.1 39.1 1.0
CD F:GLU31 4.2 48.5 1.0
N F:THR26 4.3 42.5 1.0
C F:ASP20 4.3 45.5 1.0
N F:ILE27 4.3 42.9 1.0
CA F:ILE27 4.4 43.8 1.0
CA F:THR26 4.4 48.9 1.0
OD2 F:ASP20 4.6 47.8 1.0
CB F:ASP22 4.6 53.8 1.0
N F:ASP22 4.6 52.5 1.0
N F:LYS21 4.6 45.3 1.0
N F:ASP24 4.7 48.9 1.0
OG1 F:THR26 4.7 32.3 1.0
CB F:ILE27 4.8 43.9 1.0
CB F:ASP24 4.8 44.9 1.0
CG F:GLU31 4.8 39.5 1.0
O F:ASP20 4.9 42.6 1.0
N F:GLY23 5.0 44.5 1.0
CA F:ASP22 5.0 50.8 1.0

Calcium binding site 6 out of 8 in 3gn4

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Calcium binding site 6 out of 8 in the Myosin Lever Arm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca202

b:68.1
occ:1.00
 OD1 F:ASP58 2.7 58.5 1.0
OD1 F:ASP56 2.7 50.3 1.0
O F:THR62 2.7 46.2 1.0
O F:HOH302 3.0 48.8 1.0
OD1 F:ASN60 3.1 53.7 1.0
OD2 F:ASP58 3.1 61.0 1.0
CG F:ASP58 3.2 62.8 1.0
OE1 F:GLU67 3.3 46.1 1.0
ND2 F:ASN60 3.4 56.1 1.0
CG F:ASN60 3.6 57.2 1.0
C F:THR62 3.9 47.0 1.0
CG F:ASP56 3.9 49.0 1.0
CA F:ILE63 4.2 44.5 1.0
CA F:ASP56 4.2 42.6 1.0
N F:ASP58 4.3 59.1 1.0
CD F:GLU67 4.3 47.5 1.0
N F:ALA57 4.4 55.2 1.0
C F:ASP56 4.4 50.3 1.0
CB F:ASP58 4.4 57.9 1.0
N F:ILE63 4.5 41.8 1.0
OE2 F:GLU67 4.5 50.4 1.0
CG2 F:ILE63 4.6 42.0 1.0
OG1 F:THR62 4.6 45.5 1.0
CB F:ASP56 4.6 44.6 1.0
CA F:ASP58 4.8 56.4 1.0
OD2 F:ASP56 4.9 50.6 1.0
CB F:ASN60 4.9 47.9 1.0
CB F:ILE63 5.0 42.7 1.0

Calcium binding site 7 out of 8 in 3gn4

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Calcium binding site 7 out of 8 in the Myosin Lever Arm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca203

b:75.8
occ:1.00
 OE1 F:GLU104 2.5 54.9 1.0
O F:PHE99 2.6 59.1 1.0
OD1 F:ASP95 2.7 69.5 1.0
OD1 F:ASN97 2.8 60.7 1.0
OD2 F:ASP95 2.9 68.1 1.0
OD1 F:ASP93 2.9 57.7 1.0
CG F:ASP95 3.1 69.4 1.0
CD F:GLU104 3.1 58.7 1.0
CG F:ASN97 3.1 63.7 1.0
ND2 F:ASN97 3.1 61.8 1.0
OE2 F:GLU104 3.6 68.4 1.0
C F:PHE99 3.8 60.7 1.0
CG F:GLU104 3.9 55.2 1.0
CG F:ASP93 4.2 58.3 1.0
CB F:ASN97 4.3 55.9 1.0
CB F:ASP95 4.5 69.7 1.0
N F:PHE99 4.5 53.5 1.0
CA F:PHE99 4.6 58.1 1.0
N F:SER101 4.7 56.3 1.0
CB F:PHE99 4.7 57.5 1.0
N F:ILE100 4.7 56.2 1.0
N F:ASN97 4.7 65.9 1.0
OE1 F:GLN135 4.7 72.0 1.0
CA F:ILE100 4.8 52.3 1.0
OG F:SER101 4.8 64.2 1.0
CA F:ASP93 4.9 57.4 1.0
CB F:SER101 4.9 60.2 1.0
CB F:GLU104 5.0 50.9 1.0
CB F:ASP93 5.0 54.0 1.0

Calcium binding site 8 out of 8 in 3gn4

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Calcium binding site 8 out of 8 in the Myosin Lever Arm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca204

b:90.7
occ:1.00
 OE2 F:GLU140 2.6 60.5 1.0
OD2 F:ASP133 2.6 76.3 1.0
O F:GLN135 2.7 68.7 1.0
OD1 F:ASP131 2.8 60.7 1.0
OD1 F:ASP133 2.8 62.2 1.0
OD2 F:ASP131 3.1 59.8 1.0
CG F:ASP133 3.1 68.8 1.0
CD F:GLU140 3.1 62.7 1.0
OD1 F:ASP129 3.3 62.0 1.0
N F:ASN137 3.3 50.1 1.0
CG F:ASP131 3.3 68.8 1.0
C F:GLN135 3.5 65.4 1.0
OE1 F:GLU140 3.6 57.9 1.0
CA F:VAL136 3.8 56.1 1.0
CB F:ASN137 3.9 50.9 1.0
CG F:ASN137 3.9 58.1 1.0
OD1 F:ASN137 3.9 64.3 1.0
CG F:GLU140 3.9 62.2 1.0
C F:VAL136 4.0 51.4 1.0
N F:VAL136 4.0 56.0 1.0
CA F:ASN137 4.2 51.3 1.0
CG F:ASP129 4.5 62.1 1.0
CA F:GLN135 4.5 61.8 1.0
ND2 F:ASN137 4.5 58.5 1.0
CD2 F:PHE99 4.5 64.2 1.0
CB F:ASP133 4.6 61.8 1.0
CE2 F:PHE99 4.7 68.0 1.0
CB F:GLN135 4.7 63.6 1.0
N F:GLN135 4.7 64.2 1.0
CB F:ASP131 4.8 59.2 1.0

Reference:

M.Mukherjea, P.Llinas, H.Kim, M.Travaglia, D.Safer, J.Menetrey, C.Franzini-Armstrong, P.R.Selvin, A.Houdusse, H.L.Sweeney. Myosin VI Dimerization Triggers An Unfolding of A Three-Helix Bundle in Order to Extend Its Reach Mol.Cell V. 35 305 2009.
ISSN: ISSN 1097-2765
PubMed: 19664948
DOI: 10.1016/J.MOLCEL.2009.07.010
Page generated: Sat Jul 13 10:42:54 2024

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