Nickel in PDB 2w94: Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution

The structure of Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution, PDB code: 2w94 was solved by K.Saboia Aragao, A.Imberty, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.60 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.530, 274.371, 85.928, 90.00, 90.00, 90.00
R / Rfree (%)	16.474 / 20.593

The structure of Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Nickel atom in the Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution (pdb code 2w94). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution, PDB code: 2w94:

Nickel binding site 1 out of 1 in the Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Native Structure of the Discoidin I From Dictyostelium Discoideum at 1.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1258 b:23.6 occ:1.00 ND1 B:HIS16 2.3 23.7 1.0 ND1 C:HIS16 2.3 22.3 1.0 ND1 A:HIS16 2.5 24.7 1.0 O C:HOH2035 3.1 34.2 1.0 CG B:HIS16 3.2 23.5 1.0 CG C:HIS16 3.3 22.2 1.0 CE1 B:HIS16 3.3 28.2 1.0 CE1 C:HIS16 3.3 25.4 1.0 CG A:HIS16 3.4 20.4 1.0 CB B:HIS16 3.4 17.2 1.0 CB A:HIS16 3.5 15.2 1.0 CB C:HIS16 3.5 16.2 1.0 CE1 A:HIS16 3.5 23.1 1.0 CA B:HIS16 3.7 17.1 1.0 CA A:HIS16 3.7 14.8 1.0 CA C:HIS16 3.8 15.5 1.0 O A:HOH2017 4.0 35.5 1.0 CD2 B:HIS16 4.4 26.3 1.0 NE2 B:HIS16 4.4 29.8 1.0 CD2 C:HIS16 4.5 25.6 1.0 NE2 C:HIS16 4.5 27.4 1.0 N B:HIS16 4.5 17.1 1.0 N A:HIS16 4.5 15.5 1.0 O A:CYS15 4.6 17.9 1.0 CD2 A:HIS16 4.6 22.6 1.0 O C:CYS15 4.6 17.1 1.0 O A:HOH2027 4.6 26.9 1.0 N C:HIS16 4.6 15.3 1.0 O B:CYS15 4.6 18.5 1.0 NE2 A:HIS16 4.6 24.6 1.0 O C:HOH2024 4.7 32.2 1.0 O B:HOH2024 4.7 35.1 1.0 C B:HIS16 4.9 16.7 1.0 C A:HIS16 4.9 15.0 1.0 N A:LEU17 4.9 13.8 1.0 C A:CYS15 4.9 17.0 1.0 C B:CYS15 4.9 17.9 1.0 C C:CYS15 5.0 17.5 1.0 N B:LEU17 5.0 15.1 1.0

S.Mathieu, K.Saboia Aragao, A.Imberty, A.Varrot. Discoidin I From Dictyostelium Discoideum and Interactions with Oligosaccharides: Specificity, Affinity, Crystal Structures and Comparison with Discoidin II. J.Mol.Biol. V. 400 540 2010.
ISSN: ISSN 0022-2836
PubMed: 20580724
DOI: 10.1016/J.JMB.2010.05.042