Praseodymium in PDB 4afi: Complex Between VAMP7 Longin Domain and Fragment of Delta-Adaptin From AP3

The structure of Complex Between VAMP7 Longin Domain and Fragment of Delta-Adaptin From AP3, PDB code: 4afi was solved by H.M.Kent, P.R.Evans, J.P.Luzio, A.A.Peden, D.J.Owen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.01 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.555, 63.555, 217.915, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 25.3

The binding sites of Praseodymium atom in the Complex Between VAMP7 Longin Domain and Fragment of Delta-Adaptin From AP3 (pdb code 4afi). This binding sites where shown within 5.0 Angstroms radius around Praseodymium atom.
In total 2 binding sites of Praseodymium where determined in the Complex Between VAMP7 Longin Domain and Fragment of Delta-Adaptin From AP3, PDB code: 4afi:
Jump to Praseodymium binding site number: 1; 2;

Praseodymium binding site 1 out of 2 in the Complex Between VAMP7 Longin Domain and Fragment of Delta-Adaptin From AP3


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 1 of Complex Between VAMP7 Longin Domain and Fragment of Delta-Adaptin From AP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Pr1000 b:58.3 occ:1.00 OD1 A:ASP120 2.1 66.1 1.0 OD1 A:ASP121 2.1 66.2 1.0 OD2 A:ASP122 2.1 59.1 1.0 OD1 B:ASP45 2.3 71.0 1.0 OD2 B:ASP45 2.3 66.6 1.0 O A:HOH2002 2.5 31.8 1.0 CG B:ASP45 2.5 66.5 1.0 O A:HOH2001 2.8 20.7 1.0 CG A:ASP120 3.1 55.5 1.0 CG A:ASP121 3.1 66.2 1.0 OD2 A:ASP120 3.2 46.6 1.0 CG A:ASP122 3.2 66.8 1.0 OD2 A:ASP121 3.5 62.4 1.0 NZ A:LYS49 3.8 59.6 1.0 OD1 A:ASP122 3.9 64.4 1.0 OD1 A:ASN102 4.0 80.4 1.0 CB B:ASP45 4.0 65.8 1.0 N A:ASP121 4.1 66.0 1.0 O A:ASN102 4.3 66.0 1.0 N A:ASP122 4.3 63.4 1.0 CB A:ASP122 4.3 60.1 1.0 CB A:ASP121 4.4 63.3 1.0 CB A:ASP120 4.5 56.2 1.0 CB A:ASN102 4.6 74.6 1.0 CA A:ASP121 4.7 64.0 1.0 CG A:ASN102 4.7 82.6 1.0 C A:ASP121 4.9 61.9 1.0 C A:ASP120 4.9 63.6 1.0 CA A:ASP120 4.9 62.4 1.0 CA A:ASP122 5.0 63.1 1.0

Praseodymium binding site 2 out of 2 in the Complex Between VAMP7 Longin Domain and Fragment of Delta-Adaptin From AP3


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 2 of Complex Between VAMP7 Longin Domain and Fragment of Delta-Adaptin From AP3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Pr1000 b:83.8 occ:0.69 OD2 B:ASP122 2.1 83.8 1.0 OE2 B:GLU52 2.2 99.9 1.0 O B:HOH2002 2.5 65.1 1.0 OD1 B:ASP121 2.6 73.0 1.0 O B:HOH2001 2.6 53.1 1.0 OD2 B:ASP120 3.0 82.6 1.0 CD B:GLU52 3.2 0.6 1.0 CG B:ASP122 3.3 75.6 1.0 OD1 B:ASP120 3.5 69.8 1.0 CG B:ASP121 3.5 62.5 1.0 CG B:ASP120 3.6 71.8 1.0 OE1 B:GLU52 3.7 0.9 1.0 OD2 B:ASP121 3.7 55.1 1.0 OD1 B:ASP122 4.0 68.9 1.0 CB B:ASP122 4.4 70.2 1.0 CG B:GLU52 4.4 0.5 1.0 N B:ASP122 4.6 64.9 1.0 N B:ASP121 4.9 62.7 1.0 CB B:ASP121 4.9 59.2 1.0

H.M.Kent, P.R.Evans, I.B.Schaefer, S.R.Gray, C.M.Sanderson, J.P.Luzio, A.A.Peden, D.J.Owen. Structural Basis of the Intracellular Sorting of the Snare VAMP7 By the AP3 Adaptor Complex Dev.Cell V. 22 979 2012.
ISSN: ISSN 1534-5807
PubMed: 22521722
DOI: 10.1016/J.DEVCEL.2012.01.018