Magnesium in PDB 4idq: Human Atlastin-1 1-446, N440T, GDPALF4-

The structure of Human Atlastin-1 1-446, N440T, GDPALF4-, PDB code: 4idq 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)	41.14 / 2.29
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	128.993, 267.084, 62.052, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.6

The structure of Human Atlastin-1 1-446, N440T, GDPALF4- also contains other interesting chemical elements:

Fluorine	(F)	16 atoms
Aluminium	(Al)	4 atoms

The binding sites of Magnesium atom in the Human Atlastin-1 1-446, N440T, GDPALF4- (pdb code 4idq). 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, GDPALF4-, PDB code: 4idq:
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, 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, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:16.0 occ:1.00 O2B A:GDP501 1.9 14.9 1.0 F4 A:ALF502 1.9 18.8 1.0 O A:HOH604 2.0 12.7 1.0 OG1 A:THR120 2.1 14.7 1.0 O A:HOH601 2.2 13.5 1.0 OG A:SER81 2.2 17.3 1.0 CB A:THR120 3.1 14.8 1.0 PB A:GDP501 3.1 13.3 1.0 CB A:SER81 3.2 16.4 1.0 O3B A:GDP501 3.3 16.6 1.0 AL A:ALF502 3.4 13.1 1.0 F1 A:ALF502 3.5 25.0 1.0 N A:SER81 3.8 15.6 1.0 OD2 A:ASP146 3.8 21.1 1.0 CA A:SER81 4.0 17.0 1.0 O1B A:GDP501 4.0 14.1 1.0 N A:THR120 4.1 16.7 1.0 CG2 A:THR120 4.1 14.9 1.0 F2 A:ALF502 4.1 18.6 1.0 CA A:THR120 4.2 18.9 1.0 O2A A:GDP501 4.2 17.0 1.0 O3A A:GDP501 4.2 31.8 1.0 OD1 A:ASP146 4.3 22.5 1.0 O A:HOH602 4.3 13.6 1.0 O A:THR147 4.4 20.5 1.0 O A:SER111 4.4 18.1 1.0 O1A A:GDP501 4.4 12.8 1.0 CG A:ASP146 4.5 20.5 1.0 PA A:GDP501 4.5 14.2 1.0 O A:HOH605 4.5 14.2 1.0 CB A:LYS80 4.8 12.6 1.0 NZ A:LYS80 4.8 12.6 1.0 C A:LYS80 4.8 19.5 1.0 NH2 A:ARG77 4.9 16.1 1.0

Magnesium binding site 2 out of 4 in the Human Atlastin-1 1-446, N440T, 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, N440T, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:24.6 occ:1.00 O B:HOH603 2.0 7.2 1.0 O2B B:GDP501 2.1 12.3 1.0 F4 B:ALF502 2.1 16.6 1.0 OG1 B:THR120 2.1 28.4 1.0 OG B:SER81 2.1 14.9 1.0 O B:HOH601 2.2 12.0 1.0 CB B:THR120 3.1 16.9 1.0 CB B:SER81 3.2 15.5 1.0 PB B:GDP501 3.3 13.2 1.0 O1B B:GDP501 3.3 19.3 1.0 F1 B:ALF502 3.5 10.6 1.0 AL B:ALF502 3.5 13.4 1.0 N B:SER81 3.7 19.5 1.0 OD2 B:ASP146 4.0 18.4 1.0 CA B:SER81 4.0 20.8 1.0 O1A B:GDP501 4.1 19.4 1.0 CG2 B:THR120 4.1 17.1 1.0 N B:THR120 4.1 17.3 1.0 O B:HOH612 4.1 24.4 1.0 OD1 B:ASP146 4.2 25.7 1.0 CA B:THR120 4.2 17.3 1.0 O B:SER111 4.3 22.4 1.0 O3B B:GDP501 4.3 16.3 1.0 O3A B:GDP501 4.3 20.5 1.0 F2 B:ALF502 4.4 26.7 1.0 O2A B:GDP501 4.4 16.3 1.0 O B:THR147 4.4 16.7 1.0 O B:HOH604 4.5 14.8 1.0 PA B:GDP501 4.5 18.3 1.0 CG B:ASP146 4.5 19.7 1.0 CB B:LYS80 4.8 16.0 1.0 C B:LYS80 4.8 20.1 1.0 NZ B:LYS80 4.9 13.5 1.0

Magnesium binding site 3 out of 4 in the Human Atlastin-1 1-446, N440T, GDPALF4-


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, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:18.2 occ:1.00 O C:HOH603 1.9 8.1 1.0 O2B C:GDP501 2.0 12.4 1.0 F4 C:ALF502 2.0 19.6 1.0 OG C:SER81 2.1 15.0 1.0 OG1 C:THR120 2.2 22.2 1.0 O C:HOH601 2.2 8.0 1.0 CB C:SER81 3.1 14.1 1.0 CB C:THR120 3.1 13.8 1.0 PB C:GDP501 3.2 12.9 1.0 O1B C:GDP501 3.4 16.3 1.0 AL C:ALF502 3.5 13.5 1.0 F1 C:ALF502 3.6 12.6 1.0 N C:SER81 3.8 15.5 1.0 OD2 C:ASP146 3.9 20.2 1.0 CA C:SER81 4.0 18.4 1.0 N C:THR120 4.1 17.0 1.0 CG2 C:THR120 4.1 13.9 1.0 O1A C:GDP501 4.1 17.7 1.0 OD1 C:ASP146 4.2 22.2 1.0 CA C:THR120 4.2 17.7 1.0 O3B C:GDP501 4.2 15.2 1.0 O C:HOH616 4.3 22.8 1.0 O C:SER111 4.3 21.9 1.0 F2 C:ALF502 4.3 24.9 1.0 O3A C:GDP501 4.3 18.4 1.0 O C:THR147 4.3 14.1 1.0 CG C:ASP146 4.4 20.4 1.0 O2A C:GDP501 4.5 14.7 1.0 PA C:GDP501 4.5 16.6 1.0 O C:HOH604 4.6 11.1 1.0 CB C:LYS80 4.8 12.3 1.0 C C:LYS80 4.8 16.4 1.0 NZ C:LYS80 5.0 14.6 1.0

Magnesium binding site 4 out of 4 in the Human Atlastin-1 1-446, N440T, GDPALF4-


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, GDPALF4- within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:14.9 occ:1.00 F4 D:ALF502 2.0 22.1 1.0 O2B D:GDP501 2.0 7.9 1.0 OG D:SER81 2.1 15.0 1.0 O D:HOH601 2.1 11.7 1.0 OG1 D:THR120 2.1 14.6 1.0 O D:HOH602 2.2 6.9 1.0 CB D:THR120 3.1 13.8 1.0 CB D:SER81 3.2 12.6 1.0 PB D:GDP501 3.2 11.3 1.0 O3B D:GDP501 3.4 16.4 1.0 AL D:ALF502 3.5 16.2 1.0 F1 D:ALF502 3.5 20.8 1.0 OD2 D:ASP146 3.7 24.7 1.0 N D:SER81 3.9 12.4 1.0 N D:THR120 4.0 16.4 1.0 CA D:SER81 4.1 14.9 1.0 CG2 D:THR120 4.1 11.1 1.0 CA D:THR120 4.1 17.1 1.0 O D:HOH605 4.3 10.9 1.0 O1B D:GDP501 4.3 10.6 1.0 OD1 D:ASP146 4.3 22.9 1.0 F2 D:ALF502 4.3 15.1 1.0 O D:SER111 4.3 21.2 1.0 O3A D:GDP501 4.3 24.6 1.0 O2A D:GDP501 4.3 15.7 1.0 O D:THR147 4.3 15.5 1.0 CG D:ASP146 4.4 17.9 1.0 O D:HOH604 4.5 13.9 1.0 O1A D:GDP501 4.5 12.8 1.0 PA D:GDP501 4.6 11.4 1.0 O D:HOH749 4.6 51.1 1.0 CB D:LYS80 4.8 10.1 1.0 NZ D:LYS80 4.9 12.7 1.0 C D:LYS80 4.9 15.0 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