Magnesium in PDB 4ido: Human Atlastin-1 1-446, C-HIS6, GDPALF4-

The structure of Human Atlastin-1 1-446, C-HIS6, GDPALF4-, PDB code: 4ido 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)	43.74 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.610, 116.430, 185.400, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.9

The structure of Human Atlastin-1 1-446, C-HIS6, GDPALF4- also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Human Atlastin-1 1-446, C-HIS6, GDPALF4- (pdb code 4ido). 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, GDPALF4-, PDB code: 4ido:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Atlastin-1 1-446, C-HIS6, GDPALF4-


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, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:14.1 occ:1.00 O1B A:GDP501 1.9 11.2 1.0 F3 A:ALF502 2.0 17.6 1.0 O A:HOH601 2.0 14.9 1.0 O A:HOH920 2.1 10.3 1.0 OG A:SER81 2.2 13.0 1.0 OG1 A:THR120 2.3 18.2 1.0 CB A:SER81 3.1 12.2 1.0 PB A:GDP501 3.2 14.6 1.0 CB A:THR120 3.2 18.5 1.0 O3B A:GDP501 3.5 20.1 1.0 AL A:ALF502 3.5 20.3 1.0 F1 A:ALF502 3.7 22.9 1.0 N A:SER81 3.8 22.1 1.0 OD2 A:ASP146 4.0 19.2 1.0 CA A:SER81 4.0 19.5 1.0 O2A A:GDP501 4.1 14.2 1.0 N A:THR120 4.1 13.1 1.0 O2B A:GDP501 4.2 17.1 1.0 F2 A:ALF502 4.2 14.8 1.0 CG2 A:THR120 4.2 15.1 1.0 OD1 A:ASP146 4.2 16.3 1.0 O3A A:GDP501 4.3 13.9 1.0 CA A:THR120 4.3 20.9 1.0 O A:HOH770 4.3 19.5 1.0 O A:SER111 4.4 21.3 1.0 O A:THR147 4.4 15.5 1.0 O1A A:GDP501 4.5 15.3 1.0 CG A:ASP146 4.5 21.6 1.0 PA A:GDP501 4.5 15.0 1.0 CB A:LYS80 4.8 9.5 1.0 C A:LYS80 4.8 23.0 1.0 O A:HOH697 4.9 12.8 1.0 NZ A:LYS80 4.9 8.8 1.0

Magnesium binding site 2 out of 2 in the Human Atlastin-1 1-446, C-HIS6, GDPALF4-


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, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:17.5 occ:1.00 O B:HOH938 2.0 15.5 1.0 O2B B:GDP501 2.0 13.8 1.0 F2 B:ALF502 2.1 22.8 1.0 OG B:SER81 2.1 13.8 1.0 OG1 B:THR120 2.2 17.8 1.0 O B:HOH601 2.2 18.9 1.0 CB B:THR120 3.1 21.3 1.0 CB B:SER81 3.2 18.8 1.0 PB B:GDP501 3.3 16.4 1.0 AL B:ALF502 3.6 17.7 1.0 O3B B:GDP501 3.6 10.6 1.0 F4 B:ALF502 3.7 21.4 1.0 N B:SER81 3.7 24.0 1.0 OD2 B:ASP146 3.8 24.2 1.0 CA B:SER81 4.0 25.3 1.0 CG2 B:THR120 4.0 18.6 1.0 OD1 B:ASP146 4.1 20.7 1.0 O B:HOH610 4.2 16.1 1.0 N B:THR120 4.2 15.2 1.0 O1A B:GDP501 4.2 25.6 1.0 O1B B:GDP501 4.2 27.4 1.0 O B:THR147 4.3 17.1 1.0 F3 B:ALF502 4.3 21.2 1.0 CA B:THR120 4.3 19.1 1.0 CG B:ASP146 4.3 21.9 1.0 O B:SER111 4.4 17.9 1.0 O2A B:GDP501 4.5 15.3 1.0 O3A B:GDP501 4.5 19.4 1.0 PA B:GDP501 4.6 18.8 1.0 CB B:LYS80 4.7 20.1 1.0 O B:HOH789 4.7 12.2 1.0 C B:LYS80 4.8 21.3 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