Atomistry » Magnesium » PDB 3g8d-3gn6 » 3gn4
Atomistry »
  Magnesium »
    PDB 3g8d-3gn6 »
      3gn4 »

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

Go back to Magnesium Binding Sites List in 3gn4
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

Go back to Magnesium Binding Sites List in 3gn4
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

Go back to Magnesium Binding Sites List in 3gn4
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

Go back to Magnesium Binding Sites List in 3gn4
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

Go back to Magnesium Binding Sites List in 3gn4
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

Go back to Magnesium Binding Sites List in 3gn4
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

Go back to Magnesium Binding Sites List in 3gn4
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

Go back to Magnesium Binding Sites List in 3gn4
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy