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Yttrium in PDB 4iaw: Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa

Protein crystallography data

The structure of Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa, PDB code: 4iaw was solved by A.Eichinger, A.Skerra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.36 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 113.260, 113.260, 119.980, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 27

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa (pdb code 4iaw). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 3 binding sites of Yttrium where determined in the Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa, PDB code: 4iaw:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 4iaw

Go back to Yttrium Binding Sites List in 4iaw
Yttrium binding site 1 out of 3 in the Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y202

b:15.0
occ:1.00
O4 A:LIZ201 2.3 14.6 1.0
O10 A:LIZ201 2.3 12.2 1.0
O6 A:LIZ201 2.3 15.1 1.0
O8 A:LIZ201 2.4 15.1 1.0
O2 A:LIZ201 2.5 15.9 1.0
O A:HOH377 2.6 11.0 1.0
N3 A:LIZ201 2.7 16.5 1.0
N1 A:LIZ201 2.7 15.8 1.0
N2 A:LIZ201 2.7 16.1 1.0
C5 A:LIZ201 3.1 16.1 1.0
C9 A:LIZ201 3.2 15.3 1.0
C7 A:LIZ201 3.2 14.3 1.0
C1 A:LIZ201 3.2 19.8 1.0
C3 A:LIZ201 3.3 17.8 1.0
C2 A:LIZ201 3.3 18.5 1.0
C6 A:LIZ201 3.3 15.1 1.0
C10 A:LIZ201 3.4 16.1 1.0
C8 A:LIZ201 3.4 12.9 1.0
C12 A:LIZ201 3.4 12.8 1.0
C11 A:LIZ201 3.4 17.5 1.0
C13 A:LIZ201 3.5 16.6 1.0
C4 A:LIZ201 3.5 15.6 1.0
C14 A:LIZ201 3.5 16.2 1.0
NE2 A:GLN33 4.2 11.3 1.0
O5 A:LIZ201 4.3 14.9 1.0
O7 A:LIZ201 4.3 9.6 1.0
O1 A:LIZ201 4.3 18.9 1.0
O9 A:LIZ201 4.4 12.5 1.0
O A:HOH312 4.4 17.0 1.0
O3 A:LIZ201 4.4 14.6 1.0
O A:HOH381 4.6 30.4 1.0
O A:HOH317 4.9 33.5 1.0
C18 A:LIZ201 4.9 17.7 1.0
C25 A:LIZ201 4.9 17.6 1.0
C15 A:LIZ201 5.0 15.8 1.0

Yttrium binding site 2 out of 3 in 4iaw

Go back to Yttrium Binding Sites List in 4iaw
Yttrium binding site 2 out of 3 in the Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y202

b:19.6
occ:1.00
O8 B:LIZ201 2.1 16.6 1.0
O6 B:LIZ201 2.2 21.3 1.0
O B:HOH341 2.4 15.2 1.0
O4 B:LIZ201 2.4 24.5 1.0
O2 B:LIZ201 2.4 9.7 1.0
O10 B:LIZ201 2.5 20.3 1.0
N2 B:LIZ201 2.5 18.4 1.0
N3 B:LIZ201 2.6 18.4 1.0
N1 B:LIZ201 2.8 18.7 1.0
C5 B:LIZ201 3.0 20.4 1.0
C7 B:LIZ201 3.0 19.0 1.0
C6 B:LIZ201 3.2 21.6 1.0
C1 B:LIZ201 3.2 17.4 1.0
C8 B:LIZ201 3.3 15.8 1.0
C9 B:LIZ201 3.3 21.4 1.0
C3 B:LIZ201 3.3 20.4 1.0
C10 B:LIZ201 3.3 20.4 1.0
C2 B:LIZ201 3.4 15.8 1.0
C13 B:LIZ201 3.4 16.4 1.0
C12 B:LIZ201 3.4 18.3 1.0
C14 B:LIZ201 3.5 15.8 1.0
C11 B:LIZ201 3.5 17.9 1.0
C4 B:LIZ201 3.6 17.1 1.0
O5 B:LIZ201 4.2 18.7 1.0
O B:HOH327 4.2 16.2 1.0
O7 B:LIZ201 4.2 16.9 1.0
O1 B:LIZ201 4.3 16.6 1.0
NE2 B:GLN33 4.4 18.5 1.0
O3 B:LIZ201 4.4 24.3 1.0
O9 B:LIZ201 4.5 22.1 1.0
C18 B:LIZ201 4.9 13.6 1.0
C15 B:LIZ201 4.9 13.5 1.0

Yttrium binding site 3 out of 3 in 4iaw

Go back to Yttrium Binding Sites List in 4iaw
Yttrium binding site 3 out of 3 in the Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Engineered Human Lipocalin 2 (C26) in Complex with Y-Dtpa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Y202

b:65.5
occ:1.00
O8 C:LIZ201 2.2 61.2 1.0
O10 C:LIZ201 2.3 63.1 1.0
O6 C:LIZ201 2.4 64.0 1.0
O2 C:LIZ201 2.4 76.6 1.0
N1 C:LIZ201 2.7 72.0 1.0
N2 C:LIZ201 2.7 67.9 1.0
O4 C:LIZ201 2.8 72.0 1.0
N3 C:LIZ201 2.8 65.5 1.0
C5 C:LIZ201 3.0 66.3 1.0
C1 C:LIZ201 3.1 75.5 1.0
C7 C:LIZ201 3.2 62.8 1.0
C9 C:LIZ201 3.2 64.5 1.0
C2 C:LIZ201 3.3 73.8 1.0
C6 C:LIZ201 3.3 67.3 1.0
C3 C:LIZ201 3.4 71.6 1.0
C10 C:LIZ201 3.4 65.2 1.0
C8 C:LIZ201 3.5 65.0 1.0
C11 C:LIZ201 3.5 72.5 1.0
C4 C:LIZ201 3.6 71.8 1.0
C13 C:LIZ201 3.6 66.7 1.0
C12 C:LIZ201 3.6 70.2 1.0
C14 C:LIZ201 3.6 66.6 1.0
O5 C:LIZ201 3.9 67.3 1.0
O1 C:LIZ201 4.3 76.3 1.0
O3 C:LIZ201 4.3 70.7 1.0
O7 C:LIZ201 4.3 60.0 1.0
O9 C:LIZ201 4.4 63.6 1.0
NE2 C:GLN33 4.4 69.3 1.0
C25 C:LIZ201 5.0 74.6 1.0

Reference:

E.Eggenstein, A.Eichinger, H.J.Kim, A.Skerra. Structure-Guided Engineering of Anticalins with Improved Binding Behavior and Biochemical Characteristics For Application in Radio-Immuno Imaging and/or Therapy J.Struct.Biol. V. 185 203 2014.
ISSN: ISSN 1047-8477
PubMed: 23542582
DOI: 10.1016/J.JSB.2013.03.009
Page generated: Wed Dec 16 02:41:13 2020

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