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Magnesium in PDB 4dbr: Myosin VI D179Y (Md) Pre-Powerstroke State

Protein crystallography data

The structure of Myosin VI D179Y (Md) Pre-Powerstroke State, PDB code: 4dbr was solved by O.Pylypenko, H.L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.36 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.940, 93.530, 102.430, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.6

Other elements in 4dbr:

The structure of Myosin VI D179Y (Md) Pre-Powerstroke State also contains other interesting chemical elements:

Vanadium (V) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Myosin VI D179Y (Md) Pre-Powerstroke State (pdb code 4dbr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Myosin VI D179Y (Md) Pre-Powerstroke State, PDB code: 4dbr:

Magnesium binding site 1 out of 1 in 4dbr

Go back to Magnesium Binding Sites List in 4dbr
Magnesium binding site 1 out of 1 in the Myosin VI D179Y (Md) Pre-Powerstroke State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Myosin VI D179Y (Md) Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg810

b:14.1
occ:1.00
O2 A:VO4811 2.1 10.3 1.0
O A:HOH1626 2.2 7.9 1.0
O A:HOH1627 2.2 9.9 1.0
O1B A:ADP809 2.2 7.7 1.0
OG1 A:THR158 2.3 9.4 1.0
OG A:SER204 2.3 8.0 1.0
CB A:THR158 3.1 9.9 1.0
CB A:SER204 3.3 8.7 1.0
PB A:ADP809 3.3 8.1 1.0
V A:VO4811 3.5 9.8 1.0
O2B A:ADP809 3.5 10.0 1.0
N A:SER204 3.7 7.2 1.0
N A:THR158 4.0 9.1 1.0
CA A:SER204 4.1 7.9 1.0
O2A A:ADP809 4.1 8.9 1.0
OD1 A:ASP456 4.1 12.4 1.0
CA A:THR158 4.1 7.5 1.0
CG2 A:THR158 4.2 8.6 1.0
O3A A:ADP809 4.2 9.9 1.0
OD2 A:ASP456 4.3 13.5 1.0
O3B A:ADP809 4.4 9.7 1.0
O4 A:VO4811 4.4 10.2 1.0
PA A:ADP809 4.5 8.3 1.0
O A:HOH1001 4.5 16.1 1.0
O1 A:VO4811 4.5 7.8 1.0
O1A A:ADP809 4.6 8.7 1.0
O A:ASN202 4.6 7.7 1.0
CG A:ASP456 4.6 13.6 1.0
ND2 A:ASN200 4.6 7.8 1.0
O A:ILE457 4.7 8.9 1.0
C A:SER203 4.8 11.1 1.0
ND2 A:ASN194 4.8 8.9 1.0
O3 A:VO4811 4.9 9.8 1.0

Reference:

L.Song, O.Pylypenko, Z.Yang, A.Houdusse, L.H.Sweeney. Mutations in Myosin VI That Cause A Loss of Coordination Between Heads Provide Insights Into the Structural Changes Underlying Force Generation and the Importance of Gating To Be Published.
Page generated: Mon Dec 14 12:06:49 2020

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