Atomistry » Calcium » PDB 2bir-2bw1 » 2bkh
Atomistry »
  Calcium »
    PDB 2bir-2bw1 »
      2bkh »

Calcium in PDB 2bkh: Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure

Protein crystallography data

The structure of Myosin VI Nucleotide-Free (MDINSERT2) Crystal Structure, PDB code: 2bkh was solved by J.Menetrey, A.Bahloul, C.Yengo, A.Wells, C.Morris, H.L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.4
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.570, 104.437, 90.284, 90.00, 91.26, 90.00
R / Rfree (%) 20.6 / 25.4

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 2bkh

Go back to Calcium Binding Sites List in 2bkh
Calcium binding site 1 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) 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) Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1148

b:65.9
occ:1.00
O B:THR26 2.1 69.3 1.0
OD1 B:ASP20 2.3 61.5 1.0
OD2 B:ASP22 2.4 65.0 1.0
OD2 B:ASP24 2.6 66.2 1.0
OE2 B:GLU31 2.7 78.6 1.0
CG B:ASP24 3.2 66.5 1.0
OE1 B:GLU31 3.2 78.0 1.0
OD1 B:ASP24 3.3 67.3 1.0
C B:THR26 3.3 69.6 1.0
CG B:ASP22 3.3 65.3 1.0
CD B:GLU31 3.3 78.1 1.0
OD1 B:ASP22 3.4 66.6 1.0
CG B:ASP20 3.5 62.2 1.0
N B:THR26 4.1 68.3 1.0
CA B:THR26 4.2 69.0 1.0
OD2 B:ASP20 4.2 60.8 1.0
N B:ILE27 4.3 70.3 1.0
CG2 B:THR26 4.3 68.8 1.0
N B:ASP24 4.3 65.8 1.0
CB B:ASP20 4.3 62.4 1.0
CA B:ILE27 4.4 70.9 1.0
CB B:ASP24 4.4 66.4 1.0
CA B:ASP20 4.4 62.5 1.0
CB B:THR26 4.7 69.0 1.0
N B:THR28 4.7 72.5 1.0
CA B:ASP24 4.7 66.2 1.0
CB B:ASP22 4.8 65.2 1.0
C B:ASP20 4.8 63.2 1.0
CG B:GLU31 4.8 77.7 1.0
N B:GLY23 4.9 65.4 1.0
CG2 B:THR28 4.9 73.2 1.0
N B:GLY25 5.0 66.8 1.0
C B:ASP24 5.0 66.3 1.0
N B:ASP22 5.0 64.9 1.0
C B:ILE27 5.0 71.5 1.0
N B:LYS21 5.0 64.1 1.0

Calcium binding site 2 out of 4 in 2bkh

Go back to Calcium Binding Sites List in 2bkh
Calcium binding site 2 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) 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) Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1149

b:71.5
occ:1.00
O B:THR62 2.1 69.8 1.0
OE1 B:GLU67 2.3 62.6 1.0
OD2 B:ASP56 2.3 75.7 1.0
OD1 B:ASN60 2.3 72.5 1.0
OD1 B:ASP58 2.7 77.0 1.0
OE2 B:GLU67 2.8 65.4 1.0
CD B:GLU67 2.9 64.5 1.0
C B:THR62 3.3 70.2 1.0
OD2 B:ASP58 3.4 77.2 1.0
CG B:ASP56 3.4 75.6 1.0
CG B:ASP58 3.4 76.2 1.0
CG B:ASN60 3.5 72.6 1.0
OD2 B:ASP64 3.9 70.9 1.0
OD1 B:ASP56 4.1 75.0 1.0
ND2 B:ASN60 4.1 72.8 1.0
N B:ILE63 4.1 69.9 1.0
N B:THR62 4.2 70.8 1.0
CA B:ILE63 4.2 69.6 1.0
CA B:THR62 4.2 70.3 1.0
N B:ASP64 4.3 68.9 1.0
CA B:ASP56 4.4 76.2 1.0
CG B:GLU67 4.4 66.0 1.0
CG2 B:THR62 4.4 70.2 1.0
N B:ASN60 4.4 73.1 1.0
CB B:ASP56 4.4 76.1 1.0
CB B:ASN60 4.7 72.8 1.0
CG B:ASP64 4.7 69.8 1.0
N B:GLY59 4.7 74.3 1.0
C B:ASP56 4.8 76.3 1.0
C B:ILE63 4.8 69.3 1.0
CB B:THR62 4.8 70.2 1.0
N B:ASP58 4.8 75.9 1.0
CB B:ASP58 4.8 75.8 1.0
N B:ALA57 4.9 76.2 1.0
CA B:ASN60 4.9 72.8 1.0

Calcium binding site 3 out of 4 in 2bkh

Go back to Calcium Binding Sites List in 2bkh
Calcium binding site 3 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) 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) Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1150

b:91.5
occ:1.00
O B:PHE99 2.4 68.1 1.0
OD1 B:ASP93 2.4 80.5 1.0
OD1 B:ASP95 2.6 81.8 1.0
OE2 B:GLU104 2.6 82.6 1.0
OE1 B:GLU104 2.7 82.1 1.0
OD1 B:ASN97 2.9 71.7 1.0
CD B:GLU104 3.0 81.7 1.0
CG B:ASP93 3.4 81.7 1.0
CG B:ASN97 3.5 71.8 1.0
C B:PHE99 3.6 68.2 1.0
ND2 B:ASN97 3.7 70.7 1.0
CG B:ASP95 3.8 80.6 1.0
N B:GLY96 4.0 77.0 1.0
N B:ASN97 4.0 73.3 1.0
OD2 B:ASP93 4.1 82.9 1.0
CA B:ASP93 4.1 81.4 1.0
N B:PHE99 4.3 67.5 1.0
OD2 B:ASP95 4.4 81.4 1.0
CB B:ASP93 4.4 81.5 1.0
N B:ASP95 4.4 80.0 1.0
CA B:PHE99 4.5 67.0 1.0
N B:ILE100 4.5 69.3 1.0
C B:ASP93 4.5 81.3 1.0
CG B:GLU104 4.5 80.6 1.0
N B:LYS94 4.5 81.1 1.0
CA B:ILE100 4.6 70.4 1.0
CA B:GLY96 4.6 75.9 1.0
CB B:ASN97 4.7 72.3 1.0
C B:ASP95 4.8 78.5 1.0
C B:GLY96 4.8 74.7 1.0
CA B:ASN97 4.8 72.3 1.0
CB B:ASP95 4.9 79.7 1.0
CA B:ASP95 4.9 79.5 1.0

Calcium binding site 4 out of 4 in 2bkh

Go back to Calcium Binding Sites List in 2bkh
Calcium binding site 4 out of 4 in the Myosin VI Nucleotide-Free (MDINSERT2) 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) Crystal Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1151

b:90.5
occ:1.00
OD2 B:ASP129 2.2 84.9 1.0
O B:GLN135 2.6 84.9 1.0
OE1 B:GLU140 2.6 84.2 1.0
OD2 B:ASP133 2.8 86.7 1.0
OD2 B:ASP131 3.2 84.8 1.0
CG B:ASP129 3.3 85.3 1.0
OD1 B:ASP131 3.4 83.9 1.0
CD B:GLU140 3.6 84.6 1.0
CG B:ASP131 3.6 84.8 1.0
CG B:ASP133 3.6 85.9 1.0
C B:GLN135 3.6 84.8 1.0
OE2 B:GLU140 3.8 83.3 1.0
OD1 B:ASP133 3.8 86.1 1.0
N B:ASN137 3.9 85.0 1.0
ND2 B:ASN137 4.0 85.1 1.0
OD1 B:ASP129 4.0 84.3 1.0
CA B:VAL136 4.1 84.6 1.0
CG B:ASN137 4.2 85.4 1.0
N B:VAL136 4.3 84.6 1.0
CB B:ASP129 4.3 85.4 1.0
CE2 B:PHE99 4.4 58.4 1.0
CA B:ASP129 4.5 85.5 1.0
C B:VAL136 4.5 84.7 1.0
CB B:ASN137 4.6 85.3 1.0
OD1 B:ASN137 4.6 84.7 1.0
N B:GLN135 4.7 84.8 1.0
CA B:GLN135 4.7 84.7 1.0
N B:ASP131 4.8 85.2 1.0
CD2 B:PHE99 4.8 60.0 1.0
CB B:ASP133 4.9 85.5 1.0
N B:ASP133 4.9 85.3 1.0
N B:ILE130 4.9 85.3 1.0
C B:ASP129 4.9 85.4 1.0
CB B:ASP131 4.9 84.8 1.0
CA B:ASN137 4.9 85.3 1.0
CG B:GLU140 5.0 84.7 1.0

Reference:

J.Menetrey, A.Bahloul, A.Wells, C.Yengo, C.Morris, H.L.Sweeney, A.Houdusse. The Structure of the Myosin VI Motor Reveals the Mechanism of Directionality Reversal Nature V. 435 779 2005.
ISSN: ISSN 0028-0836
PubMed: 15944696
DOI: 10.1038/NATURE03592
Page generated: Sat Dec 12 03:32:29 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy