Magnesium in PDB 4idn: Human Atlastin-1 1-446, C-HIS6, Gppnhp

The structure of Human Atlastin-1 1-446, C-HIS6, Gppnhp, PDB code: 4idn was solved by L.J.Byrnes, A.Singh, K.Szeto, N.M.Benvin, J.P.O'donnell, W.R.Zipfel, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.688, 115.780, 181.127, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 21.8

The binding sites of Magnesium atom in the Human Atlastin-1 1-446, C-HIS6, Gppnhp (pdb code 4idn). 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 Atlastin-1 1-446, C-HIS6, Gppnhp, PDB code: 4idn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Atlastin-1 1-446, C-HIS6, Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Atlastin-1 1-446, C-HIS6, Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:19.5 occ:1.00 O1G A:GNP501 1.9 21.2 1.0 O A:HOH601 2.0 17.5 1.0 O1B A:GNP501 2.0 17.5 1.0 O A:HOH602 2.1 19.0 1.0 OG A:SER81 2.1 24.7 1.0 OG1 A:THR120 2.1 19.7 1.0 CB A:THR120 3.1 19.5 1.0 CB A:SER81 3.2 22.3 1.0 PG A:GNP501 3.2 26.5 1.0 PB A:GNP501 3.2 23.7 1.0 N3B A:GNP501 3.4 20.6 1.0 N A:THR120 3.8 27.5 1.0 N A:SER81 3.9 23.4 1.0 OD2 A:ASP146 4.0 25.8 1.0 O2A A:GNP501 4.0 21.7 1.0 CA A:THR120 4.1 23.0 1.0 O3G A:GNP501 4.1 28.6 1.0 O A:HOH606 4.1 36.4 1.0 CG2 A:THR120 4.1 18.9 1.0 CA A:SER81 4.2 21.8 1.0 O2B A:GNP501 4.2 22.3 1.0 OD1 A:ASP146 4.2 28.7 1.0 O A:SER111 4.3 29.6 1.0 O3A A:GNP501 4.3 24.1 1.0 O2G A:GNP501 4.3 28.3 1.0 CG A:ASP146 4.5 30.1 1.0 O A:THR147 4.5 23.1 1.0 PA A:GNP501 4.5 25.1 1.0 O1A A:GNP501 4.7 26.9 1.0 CB A:GLU119 4.8 33.1 1.0 CG A:GLU119 4.8 40.8 1.0 NZ A:LYS80 4.9 23.4 1.0 CB A:LYS80 4.9 17.5 1.0 C A:GLU119 5.0 29.5 1.0

Magnesium binding site 2 out of 2 in the Human Atlastin-1 1-446, C-HIS6, Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Atlastin-1 1-446, C-HIS6, Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:24.1 occ:1.00 O2G B:GNP501 2.0 30.1 1.0 OG1 B:THR120 2.0 29.8 1.0 OG B:SER81 2.0 26.5 1.0 O B:HOH775 2.1 25.8 1.0 O2B B:GNP501 2.1 26.7 1.0 O B:HOH606 2.2 27.9 1.0 CB B:THR120 3.1 29.1 1.0 CB B:SER81 3.2 25.3 1.0 PG B:GNP501 3.2 31.2 1.0 PB B:GNP501 3.3 29.7 1.0 N3B B:GNP501 3.4 24.4 1.0 N B:SER81 3.9 28.0 1.0 OD2 B:ASP146 3.9 34.4 1.0 N B:THR120 3.9 29.7 1.0 O B:HOH610 4.0 28.6 1.0 O3G B:GNP501 4.0 30.9 1.0 CA B:SER81 4.1 26.9 1.0 CA B:THR120 4.1 29.6 1.0 CG2 B:THR120 4.1 27.4 1.0 O1A B:GNP501 4.1 29.4 1.0 O B:SER111 4.3 29.6 1.0 OD1 B:ASP146 4.3 34.8 1.0 O1B B:GNP501 4.3 29.2 1.0 O3A B:GNP501 4.4 28.9 1.0 O1G B:GNP501 4.5 29.0 1.0 CG B:ASP146 4.5 33.6 1.0 PA B:GNP501 4.6 29.2 1.0 O B:THR147 4.6 25.3 1.0 O2A B:GNP501 4.7 30.9 1.0 CB B:GLU119 4.8 36.9 1.0 CB B:LYS80 4.9 19.9 1.0 NZ B:LYS80 4.9 23.1 1.0 CG B:GLU119 5.0 44.8 1.0 C B:LYS80 5.0 26.4 1.0

L.J.Byrnes, A.Singh, K.Szeto, N.M.Benvin, J.P.O'donnell, W.R.Zipfel, H.Sondermann. Structural Basis For Conformational Switching and Gtp Loading of the Large G Protein Atlastin. Embo J. V. 32 369 2013.
ISSN: ISSN 0261-4189
PubMed: 23334294
DOI: 10.1038/EMBOJ.2012.353