Nickel in PDB 4xid: Antphd with 15BP Dna Duplex

The structure of Antphd with 15BP Dna Duplex, PDB code: 4xid 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)	37.60 / 2.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.443, 96.443, 90.142, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.4

The binding sites of Nickel atom in the Antphd with 15BP Dna Duplex (pdb code 4xid). 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 Dna Duplex, PDB code: 4xid:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Antphd with 15BP 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 Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:85.3 occ:1.00 N7 B:DG1 2.2 65.4 1.0 O C:HOH202 2.2 61.9 1.0 C8 B:DG1 3.2 69.0 1.0 C5 B:DG1 3.2 55.3 1.0 O6 B:DG1 3.4 66.7 1.0 C6 B:DG1 3.7 55.9 1.0 N9 B:DG1 4.4 52.4 1.0 C4 B:DG1 4.4 53.2 1.0 O5' B:DA0 4.6 63.7 1.0 N6 B:DA2 4.7 58.3 1.0 O4 C:DT37 4.7 74.3 1.0 C2' B:DA0 4.8 48.4 1.0 N3 B:DA0 4.9 55.3 1.0

Nickel binding site 2 out of 3 in the Antphd with 15BP 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 Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni101 b:90.4 occ:1.00 NE2 D:HIS21 2.3 78.2 1.0 O D:HOH201 2.3 55.4 1.0 CE1 D:HIS21 2.8 80.5 1.0 CD2 D:HIS21 3.5 69.3 1.0 ND1 D:HIS21 4.0 78.4 1.0 CG D:HIS21 4.3 69.5 1.0

Nickel binding site 3 out of 3 in the Antphd with 15BP 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 Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni102 b:0.9 occ:1.00 O6 E:DG1 2.7 0.7 1.0 N7 E:DG1 3.1 0.1 1.0 C6 E:DG1 3.5 0.5 1.0 C5 E:DG1 3.6 0.3 1.0 C8 E:DG1 4.3 0.5 1.0 C2 E:DA0 4.6 0.7 1.0 N1 E:DG1 4.8 0.5 1.0 C4 E:DG1 5.0 1.0 1.0 N3 E:DA0 5.0 0.6 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