Magnesium in PDB 6b9d: Human ATL1 Mutant - R77A Bound to Gdp

The structure of Human ATL1 Mutant - R77A Bound to Gdp, PDB code: 6b9d was solved by J.P.O'donnell, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.18 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.058, 68.429, 75.883, 117.00, 89.81, 99.04
R / Rfree (%)	20.5 / 23.9

The binding sites of Magnesium atom in the Human ATL1 Mutant - R77A Bound to Gdp (pdb code 6b9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human ATL1 Mutant - R77A Bound to Gdp, PDB code: 6b9d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human ATL1 Mutant - R77A Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human ATL1 Mutant - R77A Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:55.3 occ:1.00 OD2 A:ASP146 2.9 43.0 1.0 OD1 A:ASP146 3.0 43.9 1.0 NE2 A:GLN148 3.0 58.5 1.0 O3B A:GDP501 3.1 39.9 1.0 CG A:ASP146 3.3 37.0 1.0 CD A:GLN148 3.3 56.3 1.0 OG A:SER81 3.4 55.7 1.0 CE A:LYS80 3.6 46.2 1.0 NZ A:LYS80 3.6 45.0 1.0 OE1 A:GLN148 3.7 45.3 1.0 CB A:GLN148 3.7 51.2 1.0 CG A:GLN148 3.9 59.3 1.0 PB A:GDP501 4.0 32.3 1.0 O1B A:GDP501 4.0 29.9 1.0 CB A:LYS80 4.2 33.5 1.0 CA A:GLN148 4.3 44.1 1.0 O2B A:GDP501 4.4 33.7 1.0 N A:SER81 4.4 30.4 1.0 CB A:ASP146 4.6 33.6 1.0 CB A:SER81 4.7 43.3 1.0 CD A:LYS80 4.8 41.7 1.0 N A:GLN148 4.8 37.8 1.0 CG A:LYS80 4.9 32.7 1.0 CA A:SER81 5.0 37.3 1.0

Magnesium binding site 2 out of 2 in the Human ATL1 Mutant - R77A Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human ATL1 Mutant - R77A Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:59.5 occ:1.00 OD1 B:ASP146 2.7 41.6 1.0 OD2 B:ASP146 2.9 45.9 1.0 O2B B:GDP501 3.1 48.4 1.0 CG B:ASP146 3.1 39.6 1.0 NE2 B:GLN148 3.3 51.9 1.0 CE B:LYS80 3.4 41.3 1.0 NZ B:LYS80 3.5 41.3 1.0 CD B:GLN148 3.6 53.4 1.0 CB B:LYS80 3.8 32.5 1.0 OE1 B:GLN148 3.8 50.8 1.0 PB B:GDP501 3.9 33.8 1.0 O1B B:GDP501 4.0 26.6 1.0 O3B B:GDP501 4.1 29.9 1.0 CB B:GLN148 4.1 43.0 1.0 N B:SER81 4.2 38.1 1.0 CG B:GLN148 4.3 52.8 1.0 CD B:LYS80 4.5 38.4 1.0 CA B:GLN148 4.5 40.3 1.0 CB B:ASP146 4.6 30.0 1.0 CG B:LYS80 4.6 35.7 1.0 CB B:SER81 4.6 49.9 1.0 C B:LYS80 4.7 29.8 1.0 CA B:LYS80 4.8 29.4 1.0 CA B:SER81 4.8 47.6 1.0 N B:GLN148 4.9 37.1 1.0 O B:THR147 5.0 31.3 1.0

J.P.O'donnell, L.J.Byrnes, R.B.Cooley, H.Sondermann. A Hereditary Spastic Paraplegia-Associated Atlastin Variant Exhibits Defective Allosteric Coupling in the Catalytic Core. J. Biol. Chem. V. 293 687 2018.
ISSN: ESSN 1083-351X
PubMed: 29180453
DOI: 10.1074/JBC.RA117.000380