Nickel in PDB 4ew4: Mouse MBD4 Glycosylase Domain in Complex with Dna Containing A Ribose Sugar

The structure of Mouse MBD4 Glycosylase Domain in Complex with Dna Containing A Ribose Sugar, PDB code: 4ew4 was solved by H.Hashimoto, X.Zhang, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.40 / 2.79
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.120, 110.300, 119.710, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 27.7

The binding sites of Nickel atom in the Mouse MBD4 Glycosylase Domain in Complex with Dna Containing A Ribose Sugar (pdb code 4ew4). 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 Mouse MBD4 Glycosylase Domain in Complex with Dna Containing A Ribose Sugar, PDB code: 4ew4:

Nickel binding site 1 out of 1 in the Mouse MBD4 Glycosylase Domain in Complex with Dna Containing A Ribose Sugar


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Mouse MBD4 Glycosylase Domain in Complex with Dna Containing A Ribose Sugar within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni601 b:0.7 occ:1.00 O A:LEU508 2.0 88.5 1.0 OP1 C:DT20 2.0 0.9 1.0 O A:ILE511 2.0 0.5 1.0 O A:ILE506 2.1 0.2 1.0 C A:ILE511 2.9 70.8 1.0 C A:LEU508 3.1 98.4 1.0 N A:ILE511 3.2 75.1 1.0 C A:ILE506 3.3 97.9 1.0 P C:DT20 3.4 84.7 1.0 CA A:ILE511 3.5 70.2 1.0 N A:GLY510 3.8 92.8 1.0 CA A:HIS509 3.9 89.0 1.0 CB A:ILE511 3.9 70.8 1.0 N A:HIS509 3.9 98.2 1.0 N A:LEU508 4.0 95.5 1.0 N A:GLY512 4.0 77.2 1.0 C A:HIS509 4.1 87.9 1.0 C A:GLU507 4.1 0.5 1.0 OP2 C:DT20 4.1 77.1 1.0 O3' C:DC19 4.1 95.0 1.0 CA A:ILE506 4.1 93.7 1.0 CA A:LEU508 4.2 92.8 1.0 C A:GLY510 4.2 74.3 1.0 N A:GLU507 4.3 85.8 1.0 O A:GLU507 4.4 0.4 1.0 CG2 A:ILE506 4.5 71.3 1.0 CA A:GLU507 4.5 83.2 1.0 O5' C:DT20 4.5 70.0 1.0 CA A:GLY512 4.6 72.3 1.0 O A:PRO505 4.6 85.7 1.0 CA A:GLY510 4.6 84.5 1.0 CG2 A:ILE511 4.8 72.3 1.0 CB A:ILE506 4.9 72.8 1.0 O A:HIS509 5.0 91.3 1.0

H.Hashimoto, X.Zhang, X.Cheng. Excision of Thymine and 5-Hydroxymethyluracil By the MBD4 Dna Glycosylase Domain: Structural Basis and Implications For Active Dna Demethylation. Nucleic Acids Res. V. 40 8276 2012.
ISSN: ISSN 0305-1048
PubMed: 22740654
DOI: 10.1093/NAR/GKS628