Magnesium in PDB 4dcn: Crystal Structure Analysis of the ARFAPTIN2 Bar Domain in Complex with ARL1

The structure of Crystal Structure Analysis of the ARFAPTIN2 Bar Domain in Complex with ARL1, PDB code: 4dcn was solved by K.Nakamura, Y.Xie, M.Kawasaki, R.Kato, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.764, 111.125, 119.809, 90.00, 90.00, 90.00
R / Rfree (%)	26.4 / 33.3

The binding sites of Magnesium atom in the Crystal Structure Analysis of the ARFAPTIN2 Bar Domain in Complex with ARL1 (pdb code 4dcn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure Analysis of the ARFAPTIN2 Bar Domain in Complex with ARL1, PDB code: 4dcn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure Analysis of the ARFAPTIN2 Bar Domain in Complex with ARL1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of the ARFAPTIN2 Bar Domain in Complex with ARL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:23.8 occ:1.00 O2G A:GNP202 1.8 61.4 1.0 O A:HOH301 1.9 24.9 1.0 O2B A:GNP202 2.1 64.0 1.0 OG1 A:THR48 2.2 56.6 1.0 O A:HOH302 2.4 17.2 1.0 OG1 A:THR31 2.4 55.7 1.0 PG A:GNP202 3.1 61.3 1.0 N3B A:GNP202 3.2 62.5 1.0 PB A:GNP202 3.3 63.7 1.0 N A:THR48 3.3 57.4 1.0 CB A:THR48 3.3 56.8 1.0 CB A:THR31 3.6 56.0 1.0 O A:ILE46 3.6 59.1 1.0 O2A A:GNP202 3.8 66.0 1.0 CA A:THR48 3.8 56.8 1.0 O1G A:GNP202 4.0 60.8 1.0 O3G A:GNP202 4.2 61.3 1.0 C A:PRO47 4.2 57.9 1.0 O3A A:GNP202 4.2 65.0 1.0 CA A:PRO47 4.3 58.4 1.0 O1B A:GNP202 4.3 63.3 1.0 CG2 A:THR31 4.4 55.9 1.0 OD2 A:ASP67 4.4 55.5 1.0 PA A:GNP202 4.4 66.1 1.0 N A:THR31 4.5 56.1 1.0 CG2 A:THR48 4.6 56.3 1.0 CA A:THR31 4.6 56.1 1.0 C A:ILE46 4.7 59.3 1.0 O1A A:GNP202 4.8 66.1 1.0 OD1 A:ASP67 4.9 56.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure Analysis of the ARFAPTIN2 Bar Domain in Complex with ARL1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of the ARFAPTIN2 Bar Domain in Complex with ARL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:16.2 occ:1.00 O2G B:GNP202 1.7 22.6 1.0 O2B B:GNP202 1.9 25.2 1.0 O B:HOH301 1.9 26.0 1.0 OG1 B:THR31 1.9 28.9 1.0 O B:HOH302 2.0 34.5 1.0 OG1 B:THR48 2.1 25.9 1.0 PG B:GNP202 3.0 23.2 1.0 PB B:GNP202 3.1 24.5 1.0 CB B:THR48 3.2 26.1 1.0 CB B:THR31 3.3 28.4 1.0 N3B B:GNP202 3.4 23.5 1.0 N B:THR31 3.8 28.6 1.0 N B:THR48 3.8 25.9 1.0 O2A B:GNP202 3.9 23.1 1.0 O1G B:GNP202 4.0 22.3 1.0 CA B:THR48 4.1 26.0 1.0 CA B:THR31 4.1 28.6 1.0 O3A B:GNP202 4.1 23.8 1.0 O3G B:GNP202 4.1 23.1 1.0 O1B B:GNP202 4.1 23.8 1.0 OD2 B:ASP67 4.2 31.3 1.0 CG2 B:THR31 4.2 28.3 1.0 OD1 B:ASP67 4.3 32.2 1.0 CG2 B:THR48 4.3 25.8 1.0 PA B:GNP202 4.3 22.8 1.0 O B:ILE46 4.3 26.6 1.0 O1A B:GNP202 4.4 21.8 1.0 CB B:LYS30 4.6 28.7 1.0 CG B:ASP67 4.7 30.9 1.0 C B:PRO47 4.7 26.0 1.0 C B:LYS30 4.9 28.6 1.0 CA B:PRO47 4.9 26.0 1.0 CE B:LYS30 4.9 29.2 1.0

K.Nakamura, Z.Man, Y.Xie, A.Hanai, H.Makyio, M.Kawasaki, R.Kato, H.-W.Shin, K.Nakayama, S.Wakatsuki. Structural Basis For Membrane Binding Specificity of the Bin/Amphiphysin/Rvs (Bar) Domain of Arfaptin-2 Determined By ARL1 Gtpase J.Biol.Chem. V. 287 25478 2012.
ISSN: ISSN 0021-9258
PubMed: 22679020
DOI: 10.1074/JBC.M112.365783