Cobalt in PDB 7ygp: Dna Duplex Containing 5OHU-T Base Pairs

The structure of Dna Duplex Containing 5OHU-T Base Pairs, PDB code: 7ygp was solved by J.Kondo, H.Torigoe, F.Arakawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.79 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	36.672, 36.672, 54.99, 90, 90, 120
R / Rfree (%)	21.9 / 22.5

The binding sites of Cobalt atom in the Dna Duplex Containing 5OHU-T Base Pairs (pdb code 7ygp). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Dna Duplex Containing 5OHU-T Base Pairs, PDB code: 7ygp:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Dna Duplex Containing 5OHU-T Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Dna Duplex Containing 5OHU-T Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:108.2 occ:1.00 CO A:NCO101 0.0 108.2 1.0 N3 A:NCO101 2.0 72.5 1.0 N2 A:NCO101 2.0 67.3 1.0 N1 A:NCO101 2.0 75.9 1.0 N6 A:NCO101 2.0 86.7 1.0 N5 A:NCO101 2.0 96.8 1.0 N4 A:NCO101 2.0 76.3 1.0 N7 A:DG9 4.4 60.1 1.0 O6 A:DG9 4.5 61.9 1.0 N7 A:DG8 4.9 65.7 1.0

Cobalt binding site 2 out of 2 in the Dna Duplex Containing 5OHU-T Base Pairs


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Dna Duplex Containing 5OHU-T Base Pairs within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:99.7 occ:1.00 OP1 A:DC5 3.7 74.1 1.0 P A:DC5 4.8 70.5 1.0 OP2 A:DT6 4.9 52.1 1.0

H.Torigoe, J.Kondo, F.Arakawa. Specific Binding of Hg 2+ to Mismatched Base Pairs Involving 5-Hydroxyuracil in Duplex Dna. J.Inorg.Biochem. V. 241 12125 2023.
ISSN: ISSN 0162-0134
PubMed: 36716510
DOI: 10.1016/J.JINORGBIO.2023.112125