Magnesium in PDB 4idp: Human Atlastin-1 1-446, N440T, Gppnhp

The structure of Human Atlastin-1 1-446, N440T, Gppnhp, PDB code: 4idp 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)	49.68 / 2.59
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	131.946, 268.121, 62.427, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.6

The binding sites of Magnesium atom in the Human Atlastin-1 1-446, N440T, Gppnhp (pdb code 4idp). 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 Atlastin-1 1-446, N440T, Gppnhp, PDB code: 4idp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Atlastin-1 1-446, N440T, 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, N440T, Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:35.2 occ:1.00 O A:HOH708 1.8 15.8 1.0 O2G A:GNP501 1.9 22.4 1.0 O A:HOH601 1.9 18.3 1.0 O2B A:GNP501 2.1 17.1 1.0 OG1 A:THR120 2.2 15.5 1.0 OG A:SER81 2.2 21.9 1.0 PG A:GNP501 3.2 19.1 1.0 CB A:THR120 3.2 18.7 1.0 CB A:SER81 3.2 21.6 1.0 PB A:GNP501 3.3 14.4 1.0 N3B A:GNP501 3.5 8.2 1.0 O A:HOH632 3.9 16.3 1.0 OD2 A:ASP146 3.9 24.6 1.0 N A:SER81 3.9 20.4 1.0 N A:THR120 3.9 14.1 1.0 O3G A:GNP501 4.0 15.4 1.0 CA A:SER81 4.1 20.7 1.0 O A:SER111 4.1 24.5 1.0 O1A A:GNP501 4.2 21.5 1.0 CA A:THR120 4.2 15.4 1.0 CG2 A:THR120 4.3 16.6 1.0 O1B A:GNP501 4.3 13.3 1.0 O3A A:GNP501 4.3 21.6 1.0 O1G A:GNP501 4.4 14.1 1.0 OD1 A:ASP146 4.5 24.6 1.0 CG A:ASP146 4.6 23.7 1.0 PA A:GNP501 4.6 18.6 1.0 O2A A:GNP501 4.6 14.6 1.0 O A:THR147 4.7 17.8 1.0 CB A:GLU119 4.8 32.2 1.0 CB A:LYS80 4.9 21.2 1.0 CG A:GLU119 4.9 38.4 1.0 C A:LYS80 5.0 18.9 1.0

Magnesium binding site 2 out of 4 in the Human Atlastin-1 1-446, N440T, 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, N440T, Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:44.1 occ:1.00 O2B B:GNP501 1.9 17.4 1.0 O2G B:GNP501 2.1 9.4 1.0 O B:HOH689 2.1 8.8 1.0 OG1 B:THR120 2.3 17.4 1.0 O B:HOH601 2.4 14.1 1.0 OG B:SER81 2.4 14.1 1.0 PB B:GNP501 3.1 20.1 1.0 PG B:GNP501 3.1 18.9 1.0 N3B B:GNP501 3.3 10.3 1.0 CB B:THR120 3.3 16.0 1.0 CB B:SER81 3.4 12.5 1.0 O3G B:GNP501 3.8 18.8 1.0 N B:SER81 3.8 13.1 1.0 OD2 B:ASP146 4.0 24.5 1.0 O1B B:GNP501 4.0 17.7 1.0 N B:THR120 4.1 17.6 1.0 OD1 B:ASP146 4.2 23.4 1.0 O3A B:GNP501 4.2 19.1 1.0 CA B:SER81 4.2 14.9 1.0 O1A B:GNP501 4.3 22.0 1.0 CG2 B:THR120 4.3 7.1 1.0 CA B:THR120 4.3 16.1 1.0 O B:THR147 4.4 20.3 1.0 O1G B:GNP501 4.4 16.7 1.0 NZ B:LYS80 4.5 13.2 1.0 CG B:ASP146 4.5 25.4 1.0 O B:HOH613 4.5 17.8 1.0 O B:SER111 4.5 34.2 1.0 PA B:GNP501 4.6 15.6 1.0 CB B:LYS80 4.6 13.4 1.0 CE B:LYS80 4.7 10.2 1.0 O2A B:GNP501 4.7 15.0 1.0 C B:LYS80 4.9 15.3 1.0

Magnesium binding site 3 out of 4 in the Human Atlastin-1 1-446, N440T, Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Atlastin-1 1-446, N440T, Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:36.0 occ:1.00 O C:HOH692 1.9 21.7 1.0 O2G C:GNP501 2.0 13.9 1.0 O2B C:GNP501 2.1 19.1 1.0 OG C:SER81 2.3 16.0 1.0 OG1 C:THR120 2.4 20.1 1.0 O C:HOH601 2.4 8.1 1.0 PG C:GNP501 3.1 18.5 1.0 CB C:THR120 3.2 14.1 1.0 PB C:GNP501 3.2 18.3 1.0 CB C:SER81 3.4 11.7 1.0 N3B C:GNP501 3.4 15.2 1.0 OD2 C:ASP146 3.7 23.4 1.0 O3G C:GNP501 3.7 21.8 1.0 N C:SER81 3.8 19.7 1.0 OD1 C:ASP146 4.1 22.9 1.0 O1B C:GNP501 4.1 16.1 1.0 CG2 C:THR120 4.1 10.7 1.0 CA C:SER81 4.1 16.2 1.0 N C:THR120 4.1 17.9 1.0 O C:THR147 4.2 22.2 1.0 CG C:ASP146 4.3 21.8 1.0 CA C:THR120 4.3 14.8 1.0 O3A C:GNP501 4.4 21.2 1.0 O C:HOH614 4.5 16.6 1.0 O1A C:GNP501 4.5 19.2 1.0 O1G C:GNP501 4.5 13.9 1.0 CB C:LYS80 4.6 13.9 1.0 O C:SER111 4.6 21.7 1.0 NZ C:LYS80 4.6 14.0 1.0 CE C:LYS80 4.7 12.8 1.0 PA C:GNP501 4.8 20.1 1.0 O2A C:GNP501 4.8 21.0 1.0 C C:LYS80 4.9 16.4 1.0

Magnesium binding site 4 out of 4 in the Human Atlastin-1 1-446, N440T, Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Atlastin-1 1-446, N440T, Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:31.6 occ:1.00 O D:HOH695 1.9 18.2 1.0 O2G D:GNP501 2.0 24.7 1.0 O D:HOH601 2.1 20.9 1.0 O2B D:GNP501 2.1 23.9 1.0 OG D:SER81 2.2 18.3 1.0 OG1 D:THR120 2.2 17.8 1.0 CB D:THR120 3.1 17.0 1.0 CB D:SER81 3.2 14.9 1.0 PG D:GNP501 3.3 21.9 1.0 PB D:GNP501 3.4 19.3 1.0 OD2 D:ASP146 3.6 25.5 1.0 N3B D:GNP501 3.6 20.8 1.0 N D:SER81 3.8 18.1 1.0 O D:HOH613 4.0 14.3 1.0 N D:THR120 4.0 17.5 1.0 O3G D:GNP501 4.1 13.9 1.0 CG2 D:THR120 4.1 11.9 1.0 CA D:SER81 4.1 14.1 1.0 OD1 D:ASP146 4.1 25.2 1.0 CA D:THR120 4.2 19.2 1.0 O D:SER111 4.2 26.1 1.0 CG D:ASP146 4.3 24.3 1.0 O1B D:GNP501 4.3 17.2 1.0 O1A D:GNP501 4.3 19.6 1.0 O3A D:GNP501 4.5 23.2 1.0 O D:THR147 4.5 26.2 1.0 O1G D:GNP501 4.5 20.4 1.0 PA D:GNP501 4.7 18.0 1.0 O2A D:GNP501 4.7 19.2 1.0 CB D:LYS80 4.7 8.9 1.0 C D:LYS80 4.9 17.3 1.0 NZ D:LYS80 5.0 13.4 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