Gadolinium in PDB 1nc4: Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd- Dota

The structure of Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd- Dota, PDB code: 1nc4 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)	29.39 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.569, 82.239, 160.934, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.8

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

Chlorine

(Cl)

2 atoms

The binding sites of Gadolinium atom in the Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd- Dota (pdb code 1nc4). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 2 binding sites of Gadolinium where determined in the Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd- Dota, PDB code: 1nc4:
Jump to Gadolinium binding site number: 1; 2;

Gadolinium binding site 1 out of 2 in the Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd- Dota


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd- Dota within 5.0Å range: probe atom residue distance (Å) B Occ B:Gd502 b:19.9 occ:1.00 O3 B:DOF500 2.4 16.9 1.0 O1 B:DOF500 2.4 24.4 1.0 O7 B:DOF500 2.6 17.7 1.0 N4 B:DOF500 2.7 22.2 1.0 N3 B:DOF500 2.7 25.3 1.0 N2 B:DOF500 2.7 25.1 1.0 N1 B:DOF500 2.8 27.7 1.0 O5 B:DOF500 2.8 23.8 1.0 O B:HOH513 2.8 13.9 1.0 C12 B:DOF500 3.3 22.1 1.0 C13 B:DOF500 3.3 23.1 1.0 C10 B:DOF500 3.3 24.6 1.0 C16 B:DOF500 3.3 19.6 1.0 C15 B:DOF500 3.4 18.3 1.0 C11 B:DOF500 3.4 21.8 1.0 C14 B:DOF500 3.5 24.9 1.0 C9 B:DOF500 3.5 24.9 1.0 C7 B:DOF500 3.5 20.1 1.0 C8 B:DOF500 3.5 22.8 1.0 C6 B:DOF500 3.6 21.3 1.0 C4 B:DOF500 3.6 23.8 1.0 C2 B:DOF500 3.6 28.1 1.0 C5 B:DOF500 3.6 25.0 1.0 C3 B:DOF500 3.6 24.1 1.0 C1 B:DOF500 3.7 30.1 1.0 NH1 B:ARG98 4.4 12.1 1.0 O4 B:DOF500 4.4 27.5 1.0 O2 B:DOF500 4.5 24.9 1.0 O B:HOH548 4.5 15.0 1.0 O8 B:DOF500 4.5 19.9 1.0 O6 B:DOF500 4.7 26.5 1.0 O B:HOH512 4.9 20.7 1.0

Gadolinium binding site 2 out of 2 in the Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd- Dota


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd- Dota within 5.0Å range: probe atom residue distance (Å) B Occ D:Gd503 b:18.6 occ:1.00 O3 D:DOF501 2.3 20.4 1.0 O1 D:DOF501 2.5 14.4 1.0 O5 D:DOF501 2.6 13.7 1.0 N3 D:DOF501 2.6 17.6 1.0 N4 D:DOF501 2.7 18.7 1.0 N2 D:DOF501 2.7 21.8 1.0 N1 D:DOF501 2.7 24.2 1.0 O D:HOH505 2.9 20.3 1.0 O7 D:DOF501 3.0 31.7 1.0 C12 D:DOF501 3.1 21.0 1.0 C11 D:DOF501 3.3 19.0 1.0 C13 D:DOF501 3.3 15.5 1.0 C10 D:DOF501 3.3 18.6 1.0 C14 D:DOF501 3.3 13.3 1.0 C16 D:DOF501 3.4 24.4 1.0 C15 D:DOF501 3.4 21.1 1.0 C6 D:DOF501 3.5 18.5 1.0 C9 D:DOF501 3.5 18.7 1.0 C8 D:DOF501 3.5 20.1 1.0 C5 D:DOF501 3.5 16.4 1.0 C7 D:DOF501 3.5 21.5 1.0 C3 D:DOF501 3.5 20.1 1.0 C4 D:DOF501 3.5 19.4 1.0 C2 D:DOF501 3.6 22.3 1.0 C1 D:DOF501 3.6 24.1 1.0 O8 D:DOF501 4.3 22.5 1.0 O4 D:DOF501 4.3 25.6 1.0 NH1 D:ARG98 4.4 12.2 1.0 O2 D:DOF501 4.5 17.8 1.0 O6 D:DOF501 4.5 13.4 1.0 O D:HOH509 4.7 19.0 1.0

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