Magnesium in PDB 4akh: Dynein Motor Domain - Amppnp Complex

All present enzymatic activity of Dynein Motor Domain - Amppnp Complex:
2.5.1.18;

The structure of Dynein Motor Domain - Amppnp Complex, PDB code: 4akh was solved by H.Schmidt, E.S.Gleave, A.P.Carter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	175.560, 118.130, 201.020, 90.00, 90.29, 90.00
R / Rfree (%)	24.1 / 30.2

The binding sites of Magnesium atom in the Dynein Motor Domain - Amppnp Complex (pdb code 4akh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dynein Motor Domain - Amppnp Complex, PDB code: 4akh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dynein Motor Domain - Amppnp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dynein Motor Domain - Amppnp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5097 b:62.6 occ:1.00 O3G A:ATP5093 2.0 0.6 1.0 OG1 A:THR2081 2.3 91.9 1.0 O2A A:ATP5093 2.3 0.8 1.0 O1B A:ATP5093 2.5 88.8 1.0 OE2 A:GLU2195 2.7 0.2 1.0 PG A:ATP5093 3.2 0.5 1.0 OE2 A:GLU2511 3.2 0.7 1.0 O3B A:ATP5093 3.2 96.8 1.0 PB A:ATP5093 3.3 99.0 1.0 PA A:ATP5093 3.5 0.7 1.0 CB A:THR2081 3.6 88.3 1.0 O3A A:ATP5093 3.6 0.3 1.0 CD A:GLU2195 3.8 0.3 1.0 O2G A:ATP5093 3.9 0.6 1.0 OE1 A:GLU2511 3.9 0.9 1.0 OD2 A:ASP2155 4.0 0.6 1.0 CD A:GLU2511 4.0 0.4 1.0 NH2 A:ARG2552 4.2 0.9 1.0 OE1 A:GLU2195 4.2 0.1 1.0 O1A A:ATP5093 4.2 0.4 1.0 CG2 A:THR2081 4.4 84.4 1.0 O1G A:ATP5093 4.4 0.6 1.0 NH2 A:ARG2549 4.4 0.6 1.0 N A:THR2081 4.5 81.0 1.0 CA A:THR2081 4.6 83.5 1.0 O5' A:ATP5093 4.7 0.5 1.0 O2B A:ATP5093 4.8 0.6 1.0 NH1 A:ARG2507 4.9 0.7 1.0

Magnesium binding site 2 out of 2 in the Dynein Motor Domain - Amppnp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dynein Motor Domain - Amppnp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg5097 b:66.5 occ:1.00 O3G B:ATP5093 1.8 0.2 1.0 OG1 B:THR2081 1.9 0.1 1.0 O2A B:ATP5093 2.2 0.7 1.0 OE2 B:GLU2511 2.6 0.5 1.0 O1B B:ATP5093 2.7 99.9 1.0 CB B:THR2081 2.9 0.7 1.0 PG B:ATP5093 3.1 0.2 1.0 OE2 B:GLU2195 3.2 0.6 1.0 O3B B:ATP5093 3.2 0.7 1.0 PB B:ATP5093 3.4 0.1 1.0 PA B:ATP5093 3.5 0.9 1.0 CD B:GLU2511 3.5 0.7 1.0 CG2 B:THR2081 3.6 0.1 1.0 O3A B:ATP5093 3.7 1.0 1.0 OE1 B:GLU2511 3.7 0.0 1.0 NH2 B:ARG2552 4.0 0.4 1.0 O1G B:ATP5093 4.1 0.7 1.0 O2G B:ATP5093 4.1 0.1 1.0 CD B:GLU2195 4.2 0.7 1.0 OD1 B:ASP2155 4.2 0.1 1.0 CA B:THR2081 4.2 1.0 1.0 OE1 B:GLU2195 4.2 0.9 1.0 O1A B:ATP5093 4.4 0.2 1.0 N B:THR2081 4.4 0.1 1.0 O5' B:ATP5093 4.6 0.2 1.0 OD2 B:ASP2155 4.6 0.7 1.0 CG B:ASP2155 4.9 0.3 1.0 O2B B:ATP5093 4.9 0.9 1.0 CG B:GLU2511 4.9 0.1 1.0

H.Schmidt, E.S.Gleave, A.P.Carter. Insights Into Dynein Motor Domain Function From A 3.3 Angstrom Crystal Structure Nat.Struct.Mol.Biol. V. 19 492 2012.
ISSN: ISSN 1545-9993
PubMed: 22426545
DOI: 10.1038/NSMB.2272