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Yttrium in PDB 3dsz: Engineered Human Lipocalin 2 in Complex with Y-Dtpa

Protein crystallography data

The structure of Engineered Human Lipocalin 2 in Complex with Y-Dtpa, PDB code: 3dsz 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) 40.00 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.350, 82.350, 115.128, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 23

Yttrium Binding Sites:

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

Yttrium binding site 1 out of 2 in 3dsz

Go back to Yttrium Binding Sites List in 3dsz
Yttrium binding site 1 out of 2 in the Engineered Human Lipocalin 2 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 in Complex with Y-Dtpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y188

b:19.4
occ:1.00
O5 A:LIZ187 2.3 18.7 1.0
O3 A:LIZ187 2.4 11.3 1.0
O1 A:LIZ187 2.4 16.3 1.0
O7 A:LIZ187 2.4 18.8 1.0
O9 A:LIZ187 2.5 18.2 1.0
N2 A:LIZ187 2.5 15.7 1.0
N3 A:LIZ187 2.6 20.4 1.0
N1 A:LIZ187 2.7 17.0 1.0
O A:HOH189 2.9 32.9 1.0
C5 A:LIZ187 3.1 19.4 1.0
C7 A:LIZ187 3.2 21.8 1.0
C6 A:LIZ187 3.2 16.8 1.0
C1 A:LIZ187 3.2 17.9 1.0
C3 A:LIZ187 3.3 13.5 1.0
C8 A:LIZ187 3.3 20.1 1.0
C9 A:LIZ187 3.3 20.3 1.0
C10 A:LIZ187 3.3 19.4 1.0
C12 A:LIZ187 3.4 16.1 1.0
C11 A:LIZ187 3.4 14.1 1.0
C13 A:LIZ187 3.4 15.8 1.0
C2 A:LIZ187 3.4 17.1 1.0
C14 A:LIZ187 3.4 17.8 1.0
C4 A:LIZ187 3.5 12.4 1.0
NE2 A:GLN33 4.3 15.1 1.0
O8 A:LIZ187 4.3 21.8 1.0
O6 A:LIZ187 4.4 20.2 1.0
O2 A:LIZ187 4.4 21.8 1.0
O4 A:LIZ187 4.5 13.7 1.0
O10 A:LIZ187 4.6 20.6 1.0
O A:HOH193 4.7 18.4 1.0
O A:HOH190 4.8 40.9 1.0
C15 A:LIZ187 4.8 17.2 1.0
C18 A:LIZ187 4.8 18.6 1.0
C25 A:LIZ187 4.8 19.1 1.0

Yttrium binding site 2 out of 2 in 3dsz

Go back to Yttrium Binding Sites List in 3dsz
Yttrium binding site 2 out of 2 in the Engineered Human Lipocalin 2 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 in Complex with Y-Dtpa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y188

b:17.4
occ:1.00
O3 B:LIZ187 2.3 12.8 1.0
O1 B:LIZ187 2.4 14.3 1.0
O5 B:LIZ187 2.4 14.2 1.0
O7 B:LIZ187 2.5 18.9 1.0
N2 B:LIZ187 2.5 13.7 1.0
O9 B:LIZ187 2.5 18.6 1.0
N3 B:LIZ187 2.6 16.0 1.0
N1 B:LIZ187 2.6 16.5 1.0
O B:HOH223 2.7 14.4 1.0
C5 B:LIZ187 3.2 17.7 1.0
C7 B:LIZ187 3.2 18.9 1.0
C1 B:LIZ187 3.2 14.6 1.0
C6 B:LIZ187 3.2 14.5 1.0
C3 B:LIZ187 3.2 13.6 1.0
C11 B:LIZ187 3.3 15.0 1.0
C12 B:LIZ187 3.3 14.4 1.0
C8 B:LIZ187 3.3 16.4 1.0
C13 B:LIZ187 3.3 14.7 1.0
C9 B:LIZ187 3.4 15.6 1.0
C2 B:LIZ187 3.4 15.4 1.0
C10 B:LIZ187 3.4 15.3 1.0
C14 B:LIZ187 3.4 14.5 1.0
C4 B:LIZ187 3.5 12.4 1.0
O8 B:LIZ187 4.3 18.8 1.0
O2 B:LIZ187 4.4 15.9 1.0
O6 B:LIZ187 4.4 21.7 1.0
O4 B:LIZ187 4.4 15.2 1.0
NE2 B:GLN33 4.5 12.8 1.0
O10 B:LIZ187 4.6 19.5 1.0
O B:HOH231 4.6 20.3 1.0
O B:HOH296 4.7 51.6 1.0
C15 B:LIZ187 4.7 16.3 1.0
C25 B:LIZ187 4.8 19.8 1.0
C18 B:LIZ187 4.8 14.8 1.0
O B:HOH237 4.9 31.5 1.0
O B:HOH224 5.0 30.6 1.0

Reference:

H.J.Kim, A.Eichinger, A.Skerra. High-Affinity Recognition of Lanthanide(III) Chelate Complexes By A Reprogrammed Human Lipocalin 2 J.Am.Chem.Soc. V. 131 3565 2009.
ISSN: ISSN 0002-7863
PubMed: 19227970
DOI: 10.1021/JA806857R
Page generated: Wed Dec 16 02:40:53 2020

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