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Yttrium in PDB 1nc2: Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota

Protein crystallography data

The structure of Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota, PDB code: 1nc2 was solved by T.M.Corneillie, A.J.Fisher, C.F.Meares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.20 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.335, 81.300, 160.923, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.7

Other elements in 1nc2:

The structure of Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota (pdb code 1nc2). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 2 binding sites of Yttrium where determined in the Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota, PDB code: 1nc2:
Jump to Yttrium binding site number: 1; 2;

Yttrium binding site 1 out of 2 in 1nc2

Go back to Yttrium Binding Sites List in 1nc2
Yttrium binding site 1 out of 2 in the Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y502

b:23.0
occ:1.00
O1 B:DOE500 2.3 26.4 1.0
O3 B:DOE500 2.4 20.0 1.0
O7 B:DOE500 2.4 23.9 1.0
O5 B:DOE500 2.5 20.3 1.0
N3 B:DOE500 2.6 16.7 1.0
N4 B:DOE500 2.7 24.6 1.0
N2 B:DOE500 2.8 19.8 1.0
N1 B:DOE500 2.8 25.7 1.0
O B:HOH506 2.8 9.5 1.0
C10 B:DOE500 3.2 26.6 1.0
C16 B:DOE500 3.3 22.9 1.0
C14 B:DOE500 3.3 15.7 1.0
C13 B:DOE500 3.4 18.6 1.0
C12 B:DOE500 3.4 18.6 1.0
C15 B:DOE500 3.5 22.9 1.0
C5 B:DOE500 3.5 18.3 1.0
C9 B:DOE500 3.5 25.6 1.0
C4 B:DOE500 3.5 19.2 1.0
C6 B:DOE500 3.5 22.7 1.0
C11 B:DOE500 3.5 18.0 1.0
C3 B:DOE500 3.6 20.5 1.0
C8 B:DOE500 3.6 23.1 1.0
C7 B:DOE500 3.6 22.9 1.0
C2 B:DOE500 3.6 23.3 1.0
C1 B:DOE500 3.6 26.3 1.0
NH1 B:ARG98 4.3 16.8 1.0
O2 B:DOE500 4.4 26.0 1.0
O8 B:DOE500 4.5 21.8 1.0
O6 B:DOE500 4.6 14.6 1.0
O4 B:DOE500 4.6 19.3 1.0
O B:HOH533 4.6 18.1 1.0
O B:HOH509 4.9 13.5 1.0

Yttrium binding site 2 out of 2 in 1nc2

Go back to Yttrium Binding Sites List in 1nc2
Yttrium binding site 2 out of 2 in the Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y- Dota within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Y503

b:21.8
occ:1.00
O1 D:DOE501 2.3 20.2 1.0
O7 D:DOE501 2.4 21.8 1.0
O3 D:DOE501 2.5 22.9 1.0
O5 D:DOE501 2.6 19.9 1.0
N4 D:DOE501 2.6 21.8 1.0
N3 D:DOE501 2.7 15.8 1.0
N1 D:DOE501 2.7 22.9 1.0
N2 D:DOE501 2.7 21.2 1.0
O D:HOH509 2.8 15.3 1.0
C10 D:DOE501 3.2 22.1 1.0
C16 D:DOE501 3.2 23.8 1.0
C12 D:DOE501 3.3 17.8 1.0
C11 D:DOE501 3.3 21.4 1.0
C15 D:DOE501 3.3 21.1 1.0
C14 D:DOE501 3.4 16.5 1.0
C9 D:DOE501 3.4 21.5 1.0
C13 D:DOE501 3.4 15.5 1.0
C8 D:DOE501 3.5 21.6 1.0
C7 D:DOE501 3.5 22.4 1.0
C4 D:DOE501 3.5 17.3 1.0
C6 D:DOE501 3.5 18.8 1.0
C3 D:DOE501 3.5 20.9 1.0
C5 D:DOE501 3.6 17.3 1.0
C1 D:DOE501 3.6 24.8 1.0
C2 D:DOE501 3.7 20.7 1.0
O2 D:DOE501 4.4 22.2 1.0
O8 D:DOE501 4.4 22.1 1.0
NH1 D:ARG98 4.5 10.1 1.0
O6 D:DOE501 4.5 18.2 1.0
O4 D:DOE501 4.5 20.3 1.0
O D:HOH507 4.7 12.6 1.0
O D:HOH504 5.0 13.1 1.0

Reference:

T.M.Corneillie, A.J.Fisher, C.F.Meares. Crystal Structures of Two Complexes of the Rare-Earth-Dota-Binding Antibody 2D12.5: Ligand Generality From A Chiral System. J.Am.Chem.Soc. V. 125 15039 2003.
ISSN: ISSN 0002-7863
PubMed: 14653738
DOI: 10.1021/JA037236Y
Page generated: Mon Jan 25 16:07:16 2021

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