Nickel in PDB 8dmu: Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose

The structure of Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose, PDB code: 8dmu was solved by Z.Zhang, C.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.25 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.048, 129.805, 199.433, 90, 90, 90
R / Rfree (%)	23.2 / 27.3

The structure of Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Nickel atom in the Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose (pdb code 8dmu). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose, PDB code: 8dmu:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni602 b:29.7 occ:1.00 O A:HOH865 1.8 21.4 1.0 NE2 C:HIS400 1.9 28.4 1.0 O C:HOH915 2.1 30.8 1.0 NE2 A:HIS400 2.3 29.9 1.0 O A:HOH810 2.3 29.5 1.0 O C:HOH743 2.4 28.8 1.0 CE1 C:HIS400 2.8 28.6 1.0 CD2 C:HIS400 3.0 29.4 1.0 CD2 A:HIS400 3.1 28.2 1.0 CE1 A:HIS400 3.3 29.5 1.0 ND1 C:HIS400 3.9 30.4 1.0 CG C:HIS400 4.1 29.4 1.0 O C:HOH827 4.1 33.2 1.0 CB C:ALA403 4.2 30.1 1.0 O A:HOH956 4.2 36.0 1.0 O C:HOH902 4.2 33.4 1.0 CB A:ALA403 4.3 29.4 1.0 CG A:HIS400 4.3 29.1 1.0 O A:HOH934 4.3 33.3 1.0 ND1 A:HIS400 4.4 29.9 1.0 O C:SER398 4.4 29.7 1.0 O A:HOH852 4.4 37.0 1.0 O A:SER398 4.4 25.1 1.0 O C:HOH707 4.5 35.5 1.0 CA C:ALA403 4.9 30.4 1.0 CA A:SER398 5.0 27.0 1.0 CA C:SER398 5.0 28.5 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Macrodomain CG3568 From Drosophila Melanogaster in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni602 b:24.0 occ:1.00 O B:HOH932 1.8 30.8 1.0 NE2 D:HIS400 1.9 22.5 1.0 O D:HOH919 2.0 27.6 1.0 O B:HOH826 2.2 26.6 1.0 NE2 B:HIS400 2.2 29.0 1.0 O D:HOH723 2.3 27.1 1.0 CE1 D:HIS400 2.8 30.2 1.0 CD2 D:HIS400 3.1 28.7 1.0 CD2 B:HIS400 3.2 27.0 1.0 CE1 B:HIS400 3.2 29.7 1.0 ND1 D:HIS400 4.0 25.1 1.0 O D:HOH787 4.0 38.6 1.0 O B:HOH903 4.1 31.9 1.0 O D:HOH779 4.1 30.2 1.0 O D:HOH905 4.1 29.0 1.0 CG D:HIS400 4.1 26.3 1.0 CB B:ALA403 4.2 31.1 1.0 CB D:ALA403 4.3 28.1 1.0 ND1 B:HIS400 4.3 27.6 1.0 CG B:HIS400 4.3 25.6 1.0 O B:HOH812 4.3 33.3 1.0 O D:SER398 4.4 28.1 1.0 O B:SER398 4.4 26.0 1.0 CA D:ALA403 4.9 29.1 1.0 CA B:ALA403 4.9 28.6 1.0

Z.Zhang, C.Das. Structure of Adp-Ribose-Bound Drosophila Macrodomain CG3568 To Be Published.