Iodine in PDB 3bsu: Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna

All present enzymatic activity of Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna:
3.1.26.4;

The structure of Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna, PDB code: 3bsu was solved by M.Nowotny, S.M.Cerritelli, R.Ghirlando, S.A.Gaidamakov, R.J.Crouch, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.492, 64.262, 140.322, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 29

The structure of Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iodine atom in the Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna (pdb code 3bsu). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna, PDB code: 3bsu:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:I9 b:25.9 occ:0.40 I5 E:5IU9 0.0 25.9 0.4 C5 E:5IU9 2.3 22.3 1.0 O E:HOH29 2.8 31.9 0.6 C6 E:5IU9 3.2 23.1 1.0 C4 E:5IU9 3.2 20.8 1.0 O4 E:5IU9 3.3 21.0 1.0 O E:HOH26 3.7 44.9 1.0 O E:HOH22 3.7 44.2 1.0 OP2 E:5IU9 3.8 24.7 1.0 C8 E:DG8 3.8 20.2 1.0 O E:HOH17 3.8 30.4 1.0 N7 E:DG8 3.8 20.6 1.0 O E:HOH27 3.9 41.8 1.0 N9 E:DG8 3.9 21.2 1.0 C5 E:DG8 4.0 18.6 1.0 C3' E:DG8 4.0 24.4 1.0 C2' E:DG8 4.1 23.2 1.0 C4 E:DG8 4.1 21.3 1.0 N3 E:5IU9 4.4 23.2 1.0 N1 E:5IU9 4.5 24.1 1.0 O5' E:5IU9 4.5 24.3 1.0 O E:HOH16 4.5 23.5 1.0 C1' E:DG8 4.6 23.3 1.0 P E:5IU9 4.6 23.9 1.0 C6 E:DG8 4.7 20.6 1.0 N3 E:DG8 4.8 20.2 1.0 O5' E:DG8 4.8 28.6 1.0 O3' E:DG8 4.8 22.0 1.0

Iodine binding site 2 out of 2 in the Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:I9 b:28.6 occ:0.40 I5 J:5IU9 0.0 28.6 0.4 C5 J:5IU9 2.2 27.4 1.0 O J:HOH29 2.7 19.5 0.6 C6 J:5IU9 3.1 28.0 1.0 C4 J:5IU9 3.2 27.5 1.0 O4 J:5IU9 3.4 26.1 1.0 N7 J:DG8 3.7 20.6 1.0 O J:HOH18 3.7 31.0 1.0 OP2 J:5IU9 3.7 29.2 1.0 C8 J:DG8 3.7 21.0 1.0 C5 J:DG8 3.9 19.3 1.0 O J:HOH16 3.9 34.6 1.0 N9 J:DG8 4.0 20.0 1.0 C3' J:DG8 4.0 23.9 1.0 C4 J:DG8 4.1 20.5 1.0 C2' J:DG8 4.3 23.8 1.0 N1 J:5IU9 4.4 30.4 1.0 N3 J:5IU9 4.4 27.9 1.0 O5' J:5IU9 4.4 31.4 1.0 P J:5IU9 4.6 28.9 1.0 C6 J:DG8 4.6 19.2 1.0 O5' J:DG8 4.7 28.5 1.0 C1' J:DG8 4.7 22.0 1.0 O J:HOH21 4.8 23.2 1.0 O3' J:DG8 4.8 23.9 1.0 O J:HOH23 4.9 42.5 1.0 N3 J:DG8 5.0 20.6 1.0 C2 J:5IU9 5.0 28.3 1.0

M.Nowotny, S.M.Cerritelli, R.Ghirlando, S.A.Gaidamakov, R.J.Crouch, W.Yang. Specific Recognition of Rna/Dna Hybrid and Enhancement of Human Rnase H1 Activity By Hbd. Embo J. V. 27 1172 2008.
ISSN: ISSN 0261-4189
PubMed: 18337749
DOI: 10.1038/EMBOJ.2008.44