Iodine in PDB 6ukf: Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution

The structure of Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution, PDB code: 6ukf was solved by J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.39 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.018, 37.317, 69.027, 90.00, 109.77, 90.00
R / Rfree (%)	15.5 / 16.6

The structure of Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iodine atom in the Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution (pdb code 6ukf). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution, PDB code: 6ukf:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:I3 b:26.0 occ:1.00 I5 B:5IU3 0.0 26.0 1.0 C5 B:5IU3 2.0 17.5 1.0 C4 B:5IU3 2.9 14.7 1.0 C6 B:5IU3 3.0 15.2 1.0 H6 B:5IU3 3.0 18.3 1.0 O4 B:5IU3 3.1 16.8 1.0 H2' B:DG2 3.4 25.1 1.0 H2'' B:DG2 3.5 25.1 1.0 O X:HOH865 3.6 19.5 1.0 H8 B:DG2 3.7 26.2 1.0 O B:HOH209 3.8 23.4 1.0 C8 B:DG2 3.8 21.9 1.0 H73 B:DT4 3.8 20.0 1.0 C2' B:DG2 3.9 20.9 1.0 N9 B:DG2 4.1 20.5 1.0 N7 B:DG2 4.2 20.4 1.0 N1 B:5IU3 4.2 14.3 1.0 N3 B:5IU3 4.2 14.0 1.0 O X:HOH966 4.3 36.8 1.0 C1' B:DG2 4.5 21.0 1.0 C4 B:DG2 4.7 19.7 1.0 O4 B:DT4 4.7 16.2 1.0 C5 B:DG2 4.7 18.8 1.0 C7 B:DT4 4.7 16.7 1.0 H1' B:DG2 4.8 25.2 1.0 C2 B:5IU3 4.8 14.3 1.0 HN3 B:5IU3 4.9 16.8 1.0 H71 B:DT4 4.9 20.0 1.0

Iodine binding site 2 out of 2 in the Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hhai Endonuclease in Complex with Dna at 1 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:I10 b:40.6 occ:1.00 I5 B:5IU10 0.0 40.6 1.0 C5 B:5IU10 2.0 38.6 1.0 C4 B:5IU10 2.9 36.3 1.0 C6 B:5IU10 2.9 39.5 1.0 H2' B:DT9 2.9 36.7 1.0 H6 B:5IU10 3.0 47.4 1.0 O4 B:5IU10 3.1 33.8 1.0 O B:HOH219 3.2 39.9 1.0 C6 B:DT9 3.7 20.3 1.0 H6 B:DT9 3.7 24.3 1.0 OP2 B:5IU10 3.8 31.5 1.0 C2' B:DT9 3.9 30.6 1.0 C5 B:DT9 3.9 19.0 1.0 H71 B:DT9 4.1 26.1 1.0 H3' B:DT9 4.1 38.0 1.0 H73 B:DT9 4.1 26.1 1.0 N1 B:DT9 4.2 22.6 1.0 N3 B:5IU10 4.2 34.5 1.0 N1 B:5IU10 4.2 38.4 1.0 C7 B:DT9 4.3 21.8 1.0 O B:HOH201 4.4 39.1 1.0 H2'' B:DT9 4.4 36.7 1.0 C4 B:DT9 4.6 17.9 1.0 C3' B:DT9 4.6 31.7 1.0 C1' B:DT9 4.7 27.7 1.0 C2 B:DT9 4.7 21.1 1.0 C2 B:5IU10 4.8 36.9 1.0 N3 B:DT9 4.8 17.9 1.0 HN3 B:5IU10 4.9 41.5 1.0 O6 B:DG11 4.9 50.4 1.0 H42 A:DC3 4.9 44.2 1.0

J.R.Horton, J.Yang, X.Zhang, T.Petronzio, A.Fomenkov, G.G.Wilson, R.J.Roberts, X.Cheng. Structure of Hhai Endonuclease with Cognate Dna at An Atomic Resolution of 1.0 Angstrom Nucleic Acids Res. 2019.
ISSN: ESSN 1362-4962