Nickel in PDB 4xic: Antphd with 15BP Di-Thioate Modified Dna Duplex

The structure of Antphd with 15BP Di-Thioate Modified Dna Duplex, PDB code: 4xic was solved by M.A.White, L.Zandarashvili, J.Iwahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.44 / 2.69
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.539, 96.539, 89.546, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 27.2

The binding sites of Nickel atom in the Antphd with 15BP Di-Thioate Modified Dna Duplex (pdb code 4xic). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Antphd with 15BP Di-Thioate Modified Dna Duplex, PDB code: 4xic:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Antphd with 15BP Di-Thioate Modified Dna Duplex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Antphd with 15BP Di-Thioate Modified Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:65.0 occ:1.00 N7 B:DG1 2.4 41.2 1.0 O C:HOH202 2.5 41.8 1.0 C8 B:DG1 3.2 38.1 1.0 C5 B:DG1 3.5 29.9 1.0 O6 B:DG1 3.9 32.7 1.0 C6 B:DG1 4.1 31.2 1.0 N9 B:DG1 4.5 26.6 1.0 C4 B:DG1 4.6 26.6 1.0 O4 C:DT36 4.6 35.4 1.0 O5' B:DA0 4.8 32.3 1.0 N6 B:DA2 4.9 36.7 1.0 C2' B:DA0 5.0 39.6 1.0

Nickel binding site 2 out of 3 in the Antphd with 15BP Di-Thioate Modified Dna Duplex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Antphd with 15BP Di-Thioate Modified Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni102 b:56.8 occ:1.00 NE2 D:HIS21 2.2 56.3 1.0 CE1 D:HIS21 2.3 58.1 1.0 CD2 D:HIS21 3.5 50.7 1.0 ND1 D:HIS21 3.5 56.9 1.0 CG D:HIS21 4.1 48.9 1.0

Nickel binding site 3 out of 3 in the Antphd with 15BP Di-Thioate Modified Dna Duplex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Antphd with 15BP Di-Thioate Modified Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni101 b:0.5 occ:1.00 N7 E:DG1 3.1 76.5 1.0 O6 E:DG1 3.7 68.8 1.0 C5 E:DG1 4.0 76.8 1.0 C8 E:DG1 4.1 76.8 1.0 C6 E:DG1 4.2 68.8 1.0 C2 E:DA0 4.7 76.3 1.0 O4 F:DT36 4.9 94.3 1.0

L.Zandarashvili, D.Nguyen, K.M.Anderson, M.A.White, D.G.Gorenstein, J.Iwahara. Entropic Enhancement of Protein-Dna Affinity By Oxygen-to-Sulfur Substitution in Dna Phosphate. Biophys.J. V. 109 1026 2015.
ISSN: ESSN 1542-0086
PubMed: 26331260
DOI: 10.1016/J.BPJ.2015.07.032