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  Praseodymium
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    PDB 1k0z-4flb
      1k0z
      2f1r
      2if5
      2isn
      2vsy
      2vxb
      2vxc
      2wvi
      2znr
      3fou
      3mvc
      4afi
      4flb

Praseodymium in the structure of Complex Between VAMP7 Longin Domain and Fragment of Delta- Adaptin From AP3 (pdb 4afi)






The binding sites of Praseodymium atom in the structure of Complex Between VAMP7 Longin Domain and Fragment of Delta- Adaptin From AP3 (pdb code 4afi). This binding sites where shown with 5.0 Angstroms radius around Praseodymium atom.
The 4afi structure was solved by H.M.KENT, P.R.EVANS, J.P.LUZIO, A.A.PEDEN, D.J.OWEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)61.0-2.8
Space groupP43212
a (A)63.555
b (A)63.555
c (A)217.915
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)23.057
Rfree (%)25.266


Praseodymium Binding Sites:

Praseodymium binding site 1 out of 2 in 4afi


Praseodymium binding site 1 out of 2 in 4afi
Click to enlarge
stereopicture of Praseodymium binding site 1 out of 2 in 4afi
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Praseodymium in the PDB 4afi. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Praseodymium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Lys49, A: Asn102, A: Asp120, A: Asp121, A: Asp122, B: Asp45, A: Hoh2001, A: Hoh2002,

conact list:


AtomAtomDistance (A)
PrNZ A:Lys493.76
PrO A:Asn1024.30
PrCB A:Asn1024.58
PrOD1 A:Asn1023.97
PrCG A:Asn1024.72
PrCB A:Asp1204.50
PrOD2 A:Asp1203.23
PrC A:Asp1204.90
PrOD1 A:Asp1202.10
PrCG A:Asp1203.05
PrCA A:Asp1204.94
PrN A:Asp1214.12
PrCB A:Asp1214.43
PrOD2 A:Asp1213.52
PrC A:Asp1214.87
PrOD1 A:Asp1212.12
PrCG A:Asp1213.12
PrCA A:Asp1214.67
PrN A:Asp1224.30
PrCB A:Asp1224.34
PrOD2 A:Asp1222.12
PrOD1 A:Asp1223.87
PrCG A:Asp1223.24
PrCA A:Asp1224.96
PrCB B:Asp454.00
PrOD2 B:Asp452.29
PrOD1 B:Asp452.28
PrCG B:Asp452.54
PrO A:Hoh20012.77
PrO A:Hoh20022.53

interactive model:


Praseodymium binding site 2 out of 2 in 4afi


Praseodymium binding site 2 out of 2 in 4afi
Click to enlarge
stereopicture of Praseodymium binding site 2 out of 2 in 4afi
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Praseodymium in the PDB 4afi. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Praseodymium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Glu52, B: Asp120, B: Asp121, B: Asp122, B: Hoh2001, B: Hoh2002,

conact list:


AtomAtomDistance (A)
PrOE1 B:Glu523.66
PrOE2 B:Glu522.18
PrCD B:Glu523.22
PrCG B:Glu524.44
PrOD2 B:Asp1202.95
PrOD1 B:Asp1203.48
PrCG B:Asp1203.62
PrN B:Asp1214.89
PrCB B:Asp1214.90
PrOD2 B:Asp1213.72
PrOD1 B:Asp1212.57
PrCG B:Asp1213.52
PrN B:Asp1224.65
PrCB B:Asp1224.36
PrOD2 B:Asp1222.08
PrOD1 B:Asp1223.99
PrCG B:Asp1223.29
PrO B:Hoh20012.62
PrO B:Hoh20022.50

interactive model:




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