Magnesium in PDB 1e42: BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2

The structure of BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2, PDB code: 1e42 was solved by D.J.Owen, P.R.Evans, H.T.Mcmahon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.42 / 1.7
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.040, 124.590, 67.640, 90.00, 124.18, 90.00
R / Rfree (%)	19.6 / 24.6

The structure of BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2 also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium atom in the BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2 (pdb code 1e42). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2, PDB code: 1e42:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg960 b:42.1 occ:1.00 OD1 A:ASN872 2.1 29.7 1.0 O A:HOH2337 2.1 45.8 1.0 O A:HOH2198 2.1 42.4 1.0 O A:HOH2338 2.1 45.8 1.0 O A:HOH2332 2.1 37.2 1.0 O A:HOH2340 2.1 46.5 1.0 CG A:ASN872 3.1 33.2 1.0 O A:HOH2201 3.3 49.7 1.0 ND2 A:ASN872 3.6 32.9 1.0 O A:HOH2032 3.9 49.7 1.0 OH A:TYR874 4.1 34.7 1.0 O A:GLN869 4.4 28.0 1.0 CB A:ASN872 4.4 28.1 1.0 CA A:ASN872 4.6 27.5 1.0 N A:ASN872 4.7 25.3 1.0 CG A:GLU828 4.7 37.9 1.0 CA A:GLU828 4.9 28.5 1.0 CB A:GLU828 4.9 29.3 1.0

Magnesium binding site 2 out of 4 in the BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg960 b:35.4 occ:1.00 O B:HOH2357 2.1 39.5 1.0 OD1 B:ASN872 2.1 27.0 1.0 O B:HOH2225 2.1 40.3 1.0 O B:HOH2358 2.1 40.6 1.0 O B:HOH2361 2.1 39.0 1.0 O B:HOH2351 2.1 35.6 1.0 CG B:ASN872 3.2 28.4 1.0 ND2 B:ASN872 3.7 23.8 1.0 OH B:TYR874 3.9 34.1 1.0 O B:HOH2032 4.2 44.4 1.0 O B:GLN869 4.3 25.3 1.0 O B:HOH2355 4.3 44.8 1.0 CB B:ASN872 4.4 19.9 1.0 CA B:ASN872 4.6 20.4 1.0 N B:ASN872 4.6 18.8 1.0 OE1 B:GLN869 4.8 49.2 1.0 CG B:GLU828 4.9 36.2 1.0 CZ B:TYR874 5.0 29.1 1.0

Magnesium binding site 3 out of 4 in the BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg961 b:44.6 occ:1.00 O B:HOH2389 2.0 38.6 1.0 O B:HOH2332 2.1 43.0 1.0 O B:HOH2331 2.1 47.1 1.0 O B:HOH2330 2.1 43.4 1.0 O B:HOH2253 2.1 43.7 1.0 OE2 B:GLU849 2.2 31.7 1.0 CD B:GLU849 3.1 32.1 1.0 OE1 B:GLU849 3.3 31.3 1.0 NE2 B:GLN851 4.1 46.1 1.0 OE1 B:GLU902 4.2 32.3 1.0 OG B:SER915 4.2 28.3 1.0 O B:HOH2334 4.5 50.7 1.0 CG B:GLU849 4.5 28.8 1.0 O B:HOH2390 4.6 43.8 1.0 CB B:SER915 4.6 26.9 1.0 CZ2 B:TRP841 5.0 31.3 1.0 CD B:GLU902 5.0 30.5 1.0

Magnesium binding site 4 out of 4 in the BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of BETA2-Adaptin Appendage Domain, From Clathrin Adaptor AP2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg962 b:50.4 occ:1.00 O B:HOH2325 2.1 48.5 1.0 O B:HOH2317 2.1 43.8 1.0 O B:HOH2199 2.1 49.6 1.0 O B:HOH2316 2.1 53.2 1.0 O B:LYS842 2.1 33.9 1.0 O B:HOH2315 2.1 51.4 1.0 C B:LYS842 3.2 31.1 1.0 CA B:LYS842 3.8 31.5 1.0 O B:HOH2327 3.9 33.4 1.0 OD1 B:ASN846 4.2 40.9 1.0 CB B:LYS842 4.3 33.0 1.0 N B:ASP843 4.3 29.8 1.0 O B:ILE844 4.4 32.6 1.0 O B:ASP843 4.6 37.4 1.0 CA B:ASP843 4.6 30.9 1.0 C B:ASP843 4.7 33.8 1.0 CG B:ASN846 4.8 39.0 1.0 ND2 B:ASN846 4.9 43.4 1.0 O B:HOH2321 4.9 49.9 1.0

D.J.Owen, Y.Vallis, B.M.F.Pearse, H.T.Mcmahon, P.R.Evans. The Structure and Function of the BETA2-Adaptin Appendage Domain Embo J. V. 19 4216 2000.
ISSN: ISSN 0261-4189
PubMed: 10944104
DOI: 10.1093/EMBOJ/19.16.4216