Magnesium in PDB 6b9g: Human ATL1 Gtpase Domain Bound to Gdp

The structure of Human ATL1 Gtpase Domain Bound to Gdp, PDB code: 6b9g 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)	48.70 / 3.00
Space group	F 2 3 1
Cell size a, b, c (Å), α, β, γ (°)	308.032, 308.032, 308.032, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.5

The binding sites of Magnesium atom in the Human ATL1 Gtpase Domain Bound to Gdp (pdb code 6b9g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human ATL1 Gtpase Domain Bound to Gdp, PDB code: 6b9g:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human ATL1 Gtpase Domain 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 Gtpase Domain Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:83.6 occ:1.00 OD2 B:ASP146 2.6 76.1 1.0 CG B:ASP146 3.1 60.4 1.0 OD1 B:ASP146 3.1 71.6 1.0 OG B:SER81 3.3 76.8 1.0 OE1 B:GLN148 3.5 80.2 1.0 O3B B:GDP401 3.6 52.0 1.0 NE2 B:GLN124 3.8 56.9 1.0 O B:HOH513 3.9 43.9 1.0 O1B B:GDP401 4.0 65.5 1.0 CE B:LYS80 4.0 37.9 1.0 CD B:GLN148 4.2 79.8 1.0 NZ B:LYS80 4.4 43.6 1.0 PB B:GDP401 4.4 49.4 1.0 CB B:ASP146 4.4 42.6 1.0 CB B:SER81 4.6 51.5 1.0 CB B:LYS80 4.6 39.2 1.0 NE2 B:GLN148 4.7 93.8 1.0 N B:SER81 4.7 52.8 1.0 CB B:GLN148 5.0 51.5 1.0 CA B:SER81 5.0 54.3 1.0

Magnesium binding site 2 out of 4 in the Human ATL1 Gtpase Domain 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 Gtpase Domain Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:90.6 occ:1.00 OD2 C:ASP146 2.6 77.9 1.0 OD1 C:ASP146 3.1 74.5 1.0 CG C:ASP146 3.2 62.9 1.0 O1B C:GDP401 3.3 55.2 1.0 OE1 C:GLN148 3.3 77.0 1.0 OG C:SER81 3.4 80.2 1.0 CE C:LYS80 3.9 34.2 1.0 NE2 C:GLN124 4.1 61.0 1.0 CD C:GLN148 4.1 79.4 1.0 NZ C:LYS80 4.1 42.2 1.0 O C:HOH518 4.2 46.4 1.0 PB C:GDP401 4.4 49.9 1.0 CB C:LYS80 4.5 44.8 1.0 CB C:ASP146 4.5 45.6 1.0 O3B C:GDP401 4.6 46.5 1.0 O2B C:GDP401 4.6 51.1 1.0 NE2 C:GLN148 4.6 92.3 1.0 N C:SER81 4.6 48.4 1.0 CB C:SER81 4.7 53.6 1.0 CB C:GLN148 4.8 53.9 1.0 CA C:SER81 5.0 51.7 1.0

Magnesium binding site 3 out of 4 in the Human ATL1 Gtpase Domain Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human ATL1 Gtpase Domain Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:79.8 occ:1.00 O3B D:GDP401 2.9 54.8 1.0 OG D:SER81 3.0 70.6 1.0 OD2 D:ASP146 3.2 79.5 1.0 OE1 D:GLN148 3.3 70.4 1.0 OD1 D:ASP146 3.4 67.0 1.0 CG D:ASP146 3.6 63.6 1.0 O2B D:GDP401 3.8 66.5 1.0 NE2 D:GLN124 3.8 79.2 1.0 PB D:GDP401 4.0 54.2 1.0 CE D:LYS80 4.1 44.3 1.0 CD D:GLN148 4.2 69.3 1.0 NZ D:LYS80 4.3 48.0 1.0 CB D:SER81 4.3 38.3 1.0 N D:SER81 4.4 44.4 1.0 CB D:LYS80 4.6 44.1 1.0 NE2 D:GLN148 4.6 79.4 1.0 CA D:SER81 4.8 41.3 1.0 CB D:ASP146 4.9 51.6 1.0 CD D:GLN124 4.9 69.7 1.0 O3A D:GDP401 4.9 61.0 1.0

Magnesium binding site 4 out of 4 in the Human ATL1 Gtpase Domain Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human ATL1 Gtpase Domain Bound to Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:0.0 occ:1.00 O A:HOH503 2.3 63.8 1.0 O A:HOH517 2.6 61.4 1.0 O A:HOH501 3.0 66.8 1.0 O A:HOH510 3.1 59.8 1.0 OE1 A:GLN148 3.3 64.5 1.0 OG A:SER81 3.6 69.0 1.0 O2B A:GDP401 3.6 59.0 1.0 NE2 A:GLN124 3.7 86.8 1.0 NE2 A:GLN148 3.9 82.0 1.0 CD A:GLN148 3.9 71.6 1.0 OD2 A:ASP146 4.1 78.2 1.0 O A:HOH516 4.3 57.8 1.0 O3B A:GDP401 4.4 60.5 1.0 PB A:GDP401 4.6 56.6 1.0 CD A:GLN124 4.7 76.7 1.0 CG A:ASP146 4.7 63.4 1.0 OD1 A:ASP146 4.8 69.8 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