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Magnesium in PDB 4akg: Dynein Motor Domain - Atp Complex

Enzymatic activity of Dynein Motor Domain - Atp Complex

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

Protein crystallography data

The structure of Dynein Motor Domain - Atp Complex, PDB code: 4akg 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 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 175.326, 117.918, 202.762, 90.00, 90.21, 90.00
R / Rfree (%) 23.9 / 30.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dynein Motor Domain - Atp Complex (pdb code 4akg). 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 - Atp Complex, PDB code: 4akg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4akg

Go back to Magnesium Binding Sites List in 4akg
Magnesium binding site 1 out of 2 in the Dynein Motor Domain - Atp 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 - Atp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5095

b:76.5
occ:1.00
OG1 A:THR2081 2.2 79.9 1.0
O2A A:ATP5093 2.2 0.0 1.0
O3G A:ATP5093 2.4 0.2 1.0
OE2 A:GLU2195 2.6 0.1 1.0
O1B A:ATP5093 3.0 79.9 1.0
OE2 A:GLU2511 3.0 89.9 1.0
CB A:THR2081 3.4 79.8 1.0
OE1 A:GLU2511 3.4 0.1 1.0
PA A:ATP5093 3.6 94.9 1.0
PG A:ATP5093 3.6 97.0 1.0
O3B A:ATP5093 3.6 89.8 1.0
CD A:GLU2511 3.6 0.2 1.0
CD A:GLU2195 3.7 0.2 1.0
OD1 A:ASP2155 3.7 0.2 1.0
PB A:ATP5093 3.8 89.7 1.0
NH2 A:ARG2552 3.9 0.2 1.0
CG2 A:THR2081 3.9 71.7 1.0
O3A A:ATP5093 4.0 90.5 1.0
OE1 A:GLU2195 4.2 0.8 1.0
O2G A:ATP5093 4.3 84.1 1.0
NH2 A:ARG2549 4.4 70.7 1.0
O1A A:ATP5093 4.4 0.7 1.0
OD2 A:ASP2155 4.5 0.8 1.0
CG A:ASP2155 4.6 0.1 1.0
CA A:THR2081 4.6 65.5 1.0
N A:THR2081 4.6 61.9 1.0
NH1 A:ARG2507 4.7 0.9 1.0
O5' A:ATP5093 4.7 84.7 1.0
O1G A:ATP5093 4.8 90.1 1.0
CG A:GLU2195 4.9 0.3 1.0

Magnesium binding site 2 out of 2 in 4akg

Go back to Magnesium Binding Sites List in 4akg
Magnesium binding site 2 out of 2 in the Dynein Motor Domain - Atp 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 - Atp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5095

b:86.6
occ:1.00
OG1 B:THR2081 2.2 0.8 1.0
O3G B:ATP5093 2.6 0.0 1.0
OE1 B:GLU2195 2.6 0.6 1.0
O2A B:ATP5093 2.7 0.3 1.0
O1B B:ATP5093 2.9 0.3 1.0
O2G B:ATP5093 3.0 93.2 1.0
PG B:ATP5093 3.2 0.3 1.0
CD B:GLU2195 3.5 0.3 1.0
OE2 B:GLU2511 3.5 0.5 1.0
OD1 B:ASP2155 3.6 0.4 1.0
CB B:THR2081 3.6 1.0 1.0
OD2 B:ASP2155 3.6 0.4 1.0
O3B B:ATP5093 3.6 0.3 1.0
OE2 B:GLU2195 3.8 0.9 1.0
PB B:ATP5093 3.8 0.2 1.0
NH2 B:ARG2549 3.8 0.6 1.0
OE1 B:GLU2511 4.0 0.0 1.0
CG B:ASP2155 4.0 0.1 1.0
PA B:ATP5093 4.0 0.9 1.0
CD B:GLU2511 4.2 0.6 1.0
CG2 B:THR2081 4.2 0.7 1.0
CE B:LYS2080 4.3 0.3 1.0
NH2 B:ARG2552 4.4 0.9 1.0
O3A B:ATP5093 4.4 0.9 1.0
NH1 B:ARG2507 4.5 87.5 1.0
NZ B:LYS2080 4.6 0.7 1.0
CA B:THR2081 4.6 0.6 1.0
N B:THR2081 4.6 0.2 1.0
O1G B:ATP5093 4.7 0.4 1.0
CG B:LYS2080 4.7 1.0 1.0
NH2 B:ARG2507 4.7 72.9 1.0
O1A B:ATP5093 4.7 0.2 1.0
CG B:GLU2195 4.7 0.1 1.0
CZ B:ARG2549 4.9 0.2 1.0
NE B:ARG2549 5.0 1.0 1.0

Reference:

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
Page generated: Mon Dec 14 09:08:06 2020

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