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Magnesium 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:

Calcium (Ca) 8 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 3gn4

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:63.4
occ:1.00
 OD1 D:ASP24 2.5 74.1 1.0
O D:THR26 2.6 64.9 1.0
OD1 D:ASP22 2.7 79.5 1.0
OD2 D:ASP22 2.8 75.1 1.0
OD1 D:ASP20 3.0 68.1 1.0
OD2 D:ASP24 3.0 77.0 1.0
CG D:ASP24 3.1 80.0 1.0
CG D:ASP22 3.1 84.2 1.0
C D:THR26 3.4 58.9 1.0
CG2 D:THR26 3.4 57.8 1.0
CB D:THR26 3.6 62.3 1.0
CA D:THR26 3.9 65.8 1.0
CG D:ASP20 4.0 69.9 1.0
OE2 F:GLU45 4.2 57.8 1.0
N D:THR26 4.2 65.1 1.0
N D:ILE27 4.3 47.5 1.0
CB D:ASP24 4.5 68.6 1.0
CB D:ASP22 4.6 78.9 1.0
CA D:ILE27 4.6 48.8 1.0
OD2 D:ASP20 4.6 69.4 1.0
CD F:GLU45 4.9 50.5 1.0
N D:ASP24 5.0 67.2 1.0
OG1 D:THR26 5.0 56.4 1.0

Magnesium binding site 2 out of 8 in 3gn4

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:51.7
occ:1.00
 O D:HOH303 2.4 52.9 1.0
O D:HOH302 2.5 41.6 1.0
O D:THR62 2.5 51.0 1.0
OG1 D:THR62 2.7 52.7 1.0
O D:HOH301 2.8 50.3 1.0
C D:THR62 3.0 50.7 1.0
CB D:THR62 3.2 48.6 1.0
CA D:THR62 3.6 51.9 1.0
N D:ILE63 3.9 42.5 1.0
N D:THR62 4.0 46.9 1.0
OE1 D:GLU67 4.1 53.5 1.0
CA D:ILE63 4.3 46.6 1.0
CG2 D:THR62 4.7 44.2 1.0
OE2 D:GLU67 4.7 54.0 1.0
N D:ASP64 4.8 47.7 1.0
OD2 D:ASP64 4.8 67.0 1.0
C D:ILE63 4.8 51.1 1.0
CD D:GLU67 4.8 59.4 1.0
O D:VAL55 4.9 67.0 1.0

Magnesium binding site 3 out of 8 in 3gn4

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:57.8
occ:1.00
 O D:PHE99 2.5 47.6 1.0
OD1 D:ASP95 2.6 55.2 1.0
OD1 D:ASP93 2.7 45.2 1.0
OD1 D:ASN97 2.8 53.2 1.0
ND2 D:ASN97 2.9 53.1 1.0
CG D:ASN97 3.1 55.8 1.0
CG D:ASP95 3.1 60.7 1.0
OD2 D:ASP95 3.3 56.7 1.0
C D:PHE99 3.7 48.7 1.0
CG D:ASP93 4.0 44.5 1.0
N D:ASP95 4.0 48.2 1.0
N D:LYS94 4.2 43.5 1.0
CB D:ASP95 4.3 48.6 1.0
CA D:ILE100 4.4 38.8 1.0
CA D:ASP93 4.4 42.1 1.0
C D:ASP93 4.4 43.8 1.0
N D:ILE100 4.5 42.6 1.0
CB D:ASN97 4.5 50.0 1.0
CA D:ASP95 4.7 47.1 1.0
CA D:PHE99 4.7 47.5 1.0
N D:ASN97 4.8 54.6 1.0
CB D:ASP93 4.8 47.4 1.0
OD2 D:ASP93 4.8 41.9 1.0
N D:PHE99 4.8 44.2 1.0
CB D:LYS94 4.9 36.9 1.0
CA D:LYS94 4.9 44.2 1.0
CB D:PHE99 4.9 47.0 1.0
N D:GLY96 5.0 44.8 1.0
C D:LYS94 5.0 53.7 1.0

Magnesium binding site 4 out of 8 in 3gn4

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg204

b:50.1
occ:1.00
 O D:GLN135 2.5 48.9 1.0
O D:HOH304 2.6 46.4 1.0
OD1 D:ASP129 2.7 56.5 1.0
OD1 D:ASP131 2.7 70.0 1.0
OD2 D:ASP131 2.8 55.5 1.0
CG D:ASP131 3.0 69.4 1.0
CA D:ASP129 3.3 54.8 1.0
OD1 D:ASP133 3.3 58.0 1.0
CG D:ASP129 3.6 56.7 1.0
C D:GLN135 3.7 44.1 1.0
C D:ASP129 3.8 62.8 1.0
CB D:ASP129 3.8 52.3 1.0
O D:ALA128 3.8 58.4 1.0
N D:ILE130 4.1 62.9 1.0
CG D:ASP133 4.2 60.7 1.0
N D:ASP131 4.2 58.5 1.0
N D:ASP129 4.3 52.1 1.0
CA D:VAL136 4.4 46.8 1.0
CB D:ASP131 4.4 62.2 1.0
O D:ASP129 4.4 61.3 1.0
OD2 D:ASP133 4.4 57.2 1.0
N D:VAL136 4.5 43.6 1.0
C D:ALA128 4.5 58.0 1.0
N D:GLN135 4.6 48.1 1.0
CA D:GLN135 4.7 48.4 1.0
OD2 D:ASP129 4.8 54.6 1.0
CA D:ASP131 4.8 53.9 1.0
N D:GLY132 4.9 56.6 1.0
N D:ASN137 4.9 55.5 1.0

Magnesium binding site 5 out of 8 in 3gn4

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg201

b:55.6
occ:1.00
 OD1 H:ASP22 2.3 63.4 1.0
O H:THR26 2.4 55.3 1.0
OD1 H:ASP20 2.6 62.5 1.0
OD1 H:ASP24 2.9 63.3 1.0
CG H:ASP22 3.2 70.5 1.0
OD2 H:ASP22 3.4 76.2 1.0
C H:THR26 3.6 56.8 1.0
CG H:ASP24 3.6 68.1 1.0
OD2 H:ASP24 3.7 65.9 1.0
CG H:ASP20 3.8 59.1 1.0
OE1 B:GLN49 4.1 43.5 1.0
CA H:ASP20 4.3 61.2 1.0
CA H:THR26 4.4 55.1 1.0
N H:THR26 4.5 59.4 1.0
CB H:ASP22 4.5 66.9 1.0
CB H:THR26 4.5 54.5 1.0
N H:ASP22 4.5 61.2 1.0
N H:ILE27 4.6 50.4 1.0
CB H:ASP20 4.6 61.0 1.0
C H:ASP20 4.6 58.3 1.0
CA H:ILE27 4.7 48.2 1.0
OE2 B:GLU45 4.7 57.2 1.0
N H:LYS21 4.7 60.4 1.0
OD2 H:ASP20 4.7 55.0 1.0
N H:ASP24 4.8 57.6 1.0
CG2 H:THR26 4.9 53.2 1.0
N H:GLY23 5.0 59.6 1.0
CA H:ASP22 5.0 62.5 1.0

Magnesium binding site 6 out of 8 in 3gn4

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg202

b:48.2
occ:1.00
 OG1 H:THR62 2.3 54.9 1.0
O H:HOH306 2.3 47.5 1.0
O H:HOH305 2.4 49.2 1.0
O H:HOH303 2.4 48.9 1.0
O H:HOH304 2.4 52.3 1.0
O H:THR62 2.5 53.5 1.0
C H:THR62 3.1 52.1 1.0
CB H:THR62 3.1 48.7 1.0
CA H:THR62 3.4 53.5 1.0
N H:THR62 3.5 49.0 1.0
N H:ILE63 4.1 54.7 1.0
O H:VAL55 4.3 55.0 1.0
OD2 H:ASP58 4.4 46.4 1.0
OD1 H:ASP58 4.5 52.7 1.0
OE1 H:GLU67 4.5 54.2 1.0
OE2 H:GLU67 4.5 59.5 1.0
CG2 H:THR62 4.5 49.3 1.0
CB H:ASN60 4.5 46.8 1.0
OD1 H:ASP56 4.5 53.0 1.0
CA H:ILE63 4.7 50.8 1.0
CG1 H:VAL55 4.7 58.1 1.0
C H:GLY61 4.8 48.8 1.0
CG H:ASP58 4.9 52.6 1.0
CD H:GLU67 4.9 56.0 1.0

Magnesium binding site 7 out of 8 in 3gn4

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg203

b:52.8
occ:1.00
 O H:PHE99 2.2 58.6 1.0
OD1 H:ASP93 2.2 53.1 1.0
OD1 H:ASP95 2.6 61.9 1.0
OD1 H:ASN97 2.9 55.9 1.0
CG H:ASP95 3.0 63.5 1.0
OD2 H:ASP95 3.0 61.8 1.0
C H:PHE99 3.4 55.1 1.0
CG H:ASP93 3.4 54.4 1.0
CG H:ASN97 3.7 58.9 1.0
N H:ASP95 3.8 51.3 1.0
ND2 H:ASN97 4.0 52.3 1.0
N H:LYS94 4.2 51.8 1.0
N H:PHE99 4.2 54.0 1.0
CA H:PHE99 4.2 53.3 1.0
OD2 H:ASP93 4.2 56.4 1.0
CA H:ASP93 4.2 45.8 1.0
CB H:ASP95 4.2 56.8 1.0
C H:ASP93 4.3 48.1 1.0
N H:ILE100 4.4 50.2 1.0
CB H:ASP93 4.4 49.4 1.0
CA H:ASP95 4.4 52.9 1.0
CB H:PHE99 4.5 54.7 1.0
N H:ASN97 4.5 56.0 1.0
CA H:ILE100 4.5 42.2 1.0
N H:GLY96 4.6 53.9 1.0
C H:ASP95 4.6 55.8 1.0
CB H:ASN97 4.8 58.4 1.0
C H:LYS94 4.8 56.8 1.0
O H:ASP93 4.9 45.0 1.0
CA H:LYS94 4.9 50.6 1.0

Magnesium binding site 8 out of 8 in 3gn4

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Myosin Lever Arm within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg204

b:55.5
occ:1.00
 OD2 H:ASP133 2.1 65.2 1.0
OD1 H:ASP131 2.3 73.1 1.0
OD1 H:ASP129 2.4 63.9 1.0
OD1 H:ASP133 2.4 76.9 1.0
O H:HOH302 2.5 51.2 1.0
CG H:ASP133 2.6 72.7 1.0
O H:GLN135 2.7 63.0 1.0
CG H:ASP131 3.1 76.6 1.0
OD2 H:ASP131 3.3 75.8 1.0
CG H:ASP129 3.6 65.2 1.0
C H:GLN135 3.7 58.5 1.0
CA H:ASP129 3.9 61.8 1.0
CB H:ASP133 4.1 69.0 1.0
N H:GLN135 4.2 52.8 1.0
N H:ASP133 4.3 66.4 1.0
CB H:GLN135 4.3 53.4 1.0
CA H:GLN135 4.3 48.9 1.0
CB H:ASP129 4.3 62.0 1.0
C H:ASP129 4.4 60.8 1.0
O H:ALA128 4.5 60.6 1.0
N H:ASP131 4.5 65.6 1.0
CB H:ASP131 4.6 73.3 1.0
OD2 H:ASP129 4.6 62.2 1.0
N H:VAL136 4.6 55.9 1.0
CA H:ASP133 4.7 64.4 1.0
N H:ILE130 4.7 61.5 1.0
CA H:VAL136 4.8 55.5 1.0
N H:GLY132 4.8 66.1 1.0
N H:GLY134 4.9 66.3 1.0
CA H:ASP131 4.9 68.1 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: Wed Aug 14 14:50:11 2024

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