Chemical elements
  Yttrium
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    PDB 1dde-3uf3
      1dde
      1fs7
      1fs8
      1fs9
      1k7l
      1lva
      1mbu
      1mbx
      1nc2
      1py0
      1r6o
      1r6q
      1rvg
      1st0
      1st4
      1xkg
      1xvq
      2ahx
      2bec
      2c1c
      2e80
      2e81
      2r3c
      3bej
      3bfw
      3bnf
      3bng
      3bnh
      3bnj
      3bof
      3bol
      3dsz
      3h1w
      3io1
      3k38
      3k39
      3k3a
      3n9b
      3n9d
      3uf3

Yttrium in the structure of Crystal Structure of Thiol Peroxidase From Mycobacterium Tuberculosis (pdb 1xvq)






The binding sites of Yttrium atom in the structure of Crystal Structure of Thiol Peroxidase From Mycobacterium Tuberculosis (pdb code 1xvq). This binding sites where shown with 5.0 Angstroms radius around Yttrium atom.
The 1xvq structure was solved by B.S.RHO, J.D.PEDELACQ, L.W.HUNG, J.M.HOLTON, D.VIGIL, S.I.KIM, M.S.PARK, T.C.TERWILLIGER, TB STRUCTURAL GENOMICS CONSORTIUM (TBSGC), with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)26.9-1.8
Space groupH32
a (A)64.555
b (A)64.555
c (A)196.788
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)20.3
Rfree (%)22.5


Yttrium Binding Sites:

Yttrium binding site 1 out of 3 in 1xvq


Yttrium binding site 1 out of 3 in 1xvq
Click to enlarge
stereopicture of Yttrium binding site 1 out of 3 in 1xvq
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Yttrium in the PDB 1xvq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Glu16, A: Hoh548,

conact list:


AtomAtomDistance (A)
YOE1 A:Glu162.52
YCB A:Glu164.81
YOE2 A:Glu162.69
YCD A:Glu162.65
YCG A:Glu163.72
YO A:Hoh5484.81

interactive model:


Yttrium binding site 2 out of 3 in 1xvq


Yttrium binding site 2 out of 3 in 1xvq
Click to enlarge
stereopicture of Yttrium binding site 2 out of 3 in 1xvq
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Yttrium in the PDB 1xvq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Ser38, A: Asp40,

conact list:


AtomAtomDistance (A)
YOG A:Ser384.86
YCB A:Asp403.92
YOD2 A:Asp404.36
YOD1 A:Asp402.20
YCG A:Asp403.33

interactive model:


Yttrium binding site 3 out of 3 in 1xvq


Yttrium binding site 3 out of 3 in 1xvq
Click to enlarge
stereopicture of Yttrium binding site 3 out of 3 in 1xvq
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Yttrium in the PDB 1xvq. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Yttrium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asn9, A: Glu149, A: Hoh470,

conact list:


AtomAtomDistance (A)
YOD1 A:Asn94.36
YOE1 A:Glu1492.32
YOE2 A:Glu1493.44
YCD A:Glu1493.11
YCG A:Glu1494.32
YO A:Hoh4704.96

interactive model:




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