Nickel in PDB 5jlx: Antphd with 15BP Dna Duplex S-Monothioated at Cytidine-8

The structure of Antphd with 15BP Dna Duplex S-Monothioated at Cytidine-8, PDB code: 5jlx was solved by M.A.White, L.Zandarashvili, J.Iwahara, D.Nguyen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.67 / 2.75
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.864, 75.581, 91.876, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.6

The binding sites of Nickel atom in the Antphd with 15BP Dna Duplex S-Monothioated at Cytidine-8 (pdb code 5jlx). 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 S-Monothioated at Cytidine-8, PDB code: 5jlx:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Antphd with 15BP Dna Duplex S-Monothioated at Cytidine-8


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 S-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:42.3 occ:1.00 O A:HOH203 1.9 50.5 1.0 NE2 A:HIS21 2.2 40.5 1.0 NE2 D:HIS21 2.2 35.3 1.0 O D:HOH103 2.2 65.8 1.0 CE1 D:HIS21 2.8 37.4 1.0 CE1 A:HIS21 3.0 42.4 1.0 CD2 A:HIS21 3.3 44.9 1.0 CD2 D:HIS21 3.4 39.9 1.0 ND1 D:HIS21 4.0 46.4 1.0 ND1 A:HIS21 4.2 37.1 1.0 CG A:HIS21 4.4 33.2 1.0 CG D:HIS21 4.4 31.9 1.0

Nickel binding site 2 out of 3 in the Antphd with 15BP Dna Duplex S-Monothioated at Cytidine-8


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 S-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:1.0 occ:1.00 N7 B:DG1 2.6 67.5 1.0 C8 B:DG1 3.4 68.5 1.0 C5 B:DG1 3.8 68.7 1.0 O6 B:DG1 4.1 56.5 1.0 C6 B:DG1 4.3 67.3 1.0 N3 B:DA0 4.5 63.2 1.0 C2 B:DA0 4.5 56.9 1.0 N9 B:DG1 4.7 67.6 1.0 N6 B:DA2 4.8 67.0 1.0 O5' B:DA0 4.8 77.3 1.0 C4 B:DG1 4.9 64.8 1.0

Nickel binding site 3 out of 3 in the Antphd with 15BP Dna Duplex S-Monothioated at Cytidine-8


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 S-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni101 b:68.5 occ:1.00 O E:HOH203 1.9 54.4 1.0 N7 E:DG2 2.5 38.0 1.0 C8 E:DG2 3.4 48.8 1.0 C5 E:DG2 3.5 34.9 1.0 O6 E:DG2 3.7 54.4 1.0 C6 E:DG2 4.0 40.3 1.0 N6 E:DA3 4.6 43.1 1.0 N9 E:DG2 4.6 47.0 1.0 O5' E:DA1 4.6 38.7 1.0 C4 E:DG2 4.7 41.7 1.0 O E:HOH202 4.7 44.4 1.0

D.Nguyen, L.Zandarashvili, M.A.White, J.Iwahara. Stereospecific Effects of Oxygen-to-Sulfur Substitution in Dna Phosphate on Ion Pair Dynamics and Protein-Dna Affinity. Chembiochem V. 17 1636 2016.
ISSN: ESSN 1439-7633
PubMed: 27271797
DOI: 10.1002/CBIC.201600265