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

Protein crystallography data

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

Praseodymium Binding Sites:

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 4afi

Go back to Praseodymium Binding Sites List in 4afi
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 4afi

Go back to Praseodymium Binding Sites List in 4afi
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

Reference:

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
Page generated: Wed Dec 16 02:03:00 2020

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