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

The structure of Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8, PDB code: 5jlw 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)	19.30 / 2.09
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	61.266, 75.888, 93.696, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 24.2

The binding sites of Nickel atom in the Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8 (pdb code 5jlw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8, PDB code: 5jlw:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Antphd with 15BP Dna Duplex R-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 R-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni101 b:47.3 occ:0.97 O A:HOH206 1.8 37.3 1.0 NE2 A:HIS21 2.1 33.8 1.0 NE2 D:HIS21 2.2 33.0 1.0 CE1 D:HIS21 2.9 33.9 1.0 HE1 D:HIS21 3.0 40.6 1.0 CE1 A:HIS21 3.0 32.9 1.0 HE1 A:HIS21 3.1 39.5 1.0 CD2 A:HIS21 3.2 33.8 1.0 CD2 D:HIS21 3.3 31.3 1.0 HD2 A:HIS21 3.5 40.6 1.0 HD2 D:HIS21 3.6 37.6 1.0 ND1 D:HIS21 4.1 34.0 1.0 ND1 A:HIS21 4.2 33.5 1.0 CG A:HIS21 4.3 34.3 1.0 CG D:HIS21 4.3 31.7 1.0 HE1 A:PHE22 4.9 42.2 1.0 HD1 D:HIS21 4.9 40.8 1.0 HD1 A:HIS21 4.9 40.2 1.0

Nickel binding site 2 out of 6 in the Antphd with 15BP Dna Duplex R-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 R-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni101 b:77.2 occ:0.85 N7 B:DG1 2.5 45.8 1.0 O C:HOH122 3.0 65.6 1.0 H8 B:DG1 3.3 57.3 1.0 C8 B:DG1 3.3 47.8 1.0 C5 B:DG1 3.7 43.3 1.0 H62 B:DA2 4.0 44.4 1.0 O6 B:DG1 4.0 37.6 1.0 H2' B:DA0 4.1 63.5 1.0 O C:HOH112 4.2 51.3 1.0 C6 B:DG1 4.2 39.1 1.0 H61 B:DA2 4.5 44.4 1.0 N6 B:DA2 4.5 37.0 1.0 N9 B:DG1 4.6 48.8 1.0 N3 B:DA0 4.7 41.9 1.0 C4 B:DG1 4.8 44.0 1.0 H2 B:DA0 4.8 48.7 1.0 C2 B:DA0 4.8 40.6 1.0 HO5' B:DA0 4.9 68.8 1.0 H2'' B:DA0 5.0 63.5 1.0 C2' B:DA0 5.0 52.9 1.0

Nickel binding site 3 out of 6 in the Antphd with 15BP Dna Duplex R-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 R-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni102 b:74.7 occ:0.61 O B:HOH207 2.1 55.3 1.0 N7 B:DG12 2.7 45.8 1.0 H2'' B:DA11 3.3 79.5 1.0 O C:HOH102 3.5 39.9 1.0 C8 B:DG12 3.6 47.8 1.0 C5 B:DG12 3.7 43.6 1.0 H8 B:DA11 3.7 67.6 1.0 H8 B:DG12 3.7 57.3 1.0 O6 B:DG12 3.7 40.4 1.0 C8 B:DA11 3.8 56.3 1.0 C2' B:DA11 4.1 66.2 1.0 C6 B:DG12 4.1 41.2 1.0 H2' B:DA11 4.1 79.5 1.0 N9 B:DA11 4.2 57.2 1.0 N7 B:DA11 4.2 54.2 1.0 H62 B:DA13 4.3 50.0 1.0 C1' B:DA11 4.6 63.0 1.0 H1' B:DA11 4.7 75.6 1.0 H61 B:DA13 4.7 50.0 1.0 N6 B:DA13 4.7 41.7 1.0 C5 B:DA11 4.8 51.9 1.0 C4 B:DA11 4.8 52.9 1.0 N9 B:DG12 4.8 49.1 1.0 C4 B:DG12 4.9 45.7 1.0 O4 C:DT2 5.0 49.0 1.0

Nickel binding site 4 out of 6 in the Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni103 b:0.8 occ:1.00 N3 B:DA3 3.1 38.5 1.0 O2 C:DT13 3.2 44.0 1.0 H1' B:DA3 3.2 51.2 1.0 H5' B:DA4 3.2 57.8 1.0 O4' B:DA4 3.5 40.5 1.0 H2 B:DA3 3.6 45.9 1.0 H2 B:DA2 3.7 44.1 1.0 H4' B:DA4 3.7 51.1 1.0 O C:HOH113 3.9 53.7 1.0 C2 B:DA3 3.9 38.2 1.0 H5' C:DC14 3.9 68.0 1.0 H1' C:DT13 3.9 59.8 1.0 C4' B:DA4 3.9 42.6 1.0 C5' B:DA4 4.0 48.1 1.0 C1' B:DA3 4.1 42.7 1.0 C4 B:DA3 4.2 38.8 1.0 O4' C:DC14 4.2 56.6 1.0 H4' C:DC14 4.2 69.0 1.0 O4' B:DA3 4.3 43.9 1.0 C2 C:DT13 4.4 44.0 1.0 C2 B:DA2 4.4 36.8 1.0 H5'' B:DA4 4.5 57.8 1.0 N9 B:DA3 4.6 39.7 1.0 C4' C:DC14 4.6 57.5 1.0 C1' B:DA4 4.6 39.9 1.0 C5' C:DC14 4.6 56.7 1.0 H1' B:DA4 4.6 47.9 1.0 C1' C:DT13 4.8 49.8 1.0 N3 B:DA2 4.9 38.2 1.0 H4' B:DA3 4.9 56.3 1.0 O B:HOH212 5.0 38.3 1.0 H5'' C:DC14 5.0 68.0 1.0

Nickel binding site 5 out of 6 in the Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni101 b:59.0 occ:1.00 O E:HOH218 2.2 45.9 1.0 O E:HOH205 2.2 32.2 1.0 N7 E:DG2 2.3 29.4 1.0 C8 E:DG2 3.3 29.8 1.0 C5 E:DG2 3.4 29.9 1.0 H8 E:DG2 3.4 35.8 1.0 O6 E:DG2 3.6 30.8 1.0 C6 E:DG2 3.9 29.3 1.0 H2' E:DA1 3.9 46.2 1.0 H62 E:DA3 3.9 41.6 1.0 O F:HOH220 4.2 63.3 1.0 N6 E:DA3 4.5 34.6 1.0 H61 E:DA3 4.5 41.6 1.0 N9 E:DG2 4.5 32.5 1.0 C4 E:DG2 4.5 31.0 1.0 O E:HOH216 4.6 39.4 1.0 C2' E:DA1 4.7 38.5 1.0 HO5' E:DA1 4.7 46.7 1.0 O5' E:DA1 4.7 38.9 1.0 H2'' E:DA1 4.8 46.2 1.0 H3' E:DA1 4.9 47.9 1.0 N3 E:DA1 4.9 34.0 1.0

Nickel binding site 6 out of 6 in the Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Antphd with 15BP Dna Duplex R-Monothioated at Cytidine-8 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni102 b:83.6 occ:0.78 N7 E:DG13 3.1 51.1 1.0 H2'' E:DA12 3.3 81.5 1.0 H62 E:DA14 3.7 57.6 1.0 H8 E:DA12 3.8 67.5 1.0 C8 E:DA12 3.9 56.2 1.0 H8 E:DG13 3.9 66.2 1.0 C8 E:DG13 3.9 55.2 1.0 O E:HOH213 4.1 48.4 1.0 C2' E:DA12 4.1 67.9 1.0 C5 E:DG13 4.1 48.7 1.0 O6 E:DG13 4.2 47.0 1.0 H2' E:DA12 4.3 81.5 1.0 N6 E:DA14 4.3 48.0 1.0 N9 E:DA12 4.3 58.2 1.0 N7 E:DA12 4.4 54.0 1.0 H61 E:DA14 4.4 57.6 1.0 C6 E:DG13 4.6 47.4 1.0 C1' E:DA12 4.6 63.7 1.0 H1' E:DA12 4.7 76.5 1.0 O E:HOH226 4.7 60.0 1.0 C4 E:DA12 4.9 54.8 1.0 C5 E:DA12 4.9 52.7 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