Magnesium 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:

Iodine

(I)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hybrid-Binding Domain of Human Rnase H1 in Complex with 12- Mer Rna/Dna, PDB code: 3bsu:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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 A:Mg501 b:51.5 occ:1.00 OE1 A:GLU45 2.0 37.4 1.0 CD A:GLU45 2.9 36.1 1.0 CG A:GLU45 3.6 35.6 1.0 CD1 A:PHE40 3.8 31.2 1.0 N A:LEU41 3.8 27.2 1.0 OE2 A:GLU45 3.8 41.5 1.0 CA A:PHE40 4.1 32.4 1.0 CB A:GLU45 4.2 31.9 1.0 CB A:PHE40 4.3 32.3 1.0 CG A:PHE40 4.5 31.6 1.0 C A:PHE40 4.5 29.0 1.0 CG A:LEU41 4.6 25.4 1.0 CB A:LEU41 4.6 25.4 1.0 CE1 A:PHE40 4.7 30.9 1.0 CA A:LEU41 4.8 24.6 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 C:Mg502 b:51.8 occ:1.00 OE2 C:GLU45 2.1 46.3 1.0 N C:LEU41 3.0 35.0 1.0 CA C:PHE40 3.3 35.6 1.0 CD C:GLU45 3.3 44.5 1.0 CB C:PHE40 3.4 37.6 1.0 C C:PHE40 3.6 35.3 1.0 CD1 C:PHE40 3.7 38.2 1.0 CG C:GLU45 3.8 42.2 1.0 CG C:PHE40 4.0 37.7 1.0 CA C:LEU41 4.1 34.4 1.0 CB C:LEU41 4.2 34.6 1.0 OE1 C:GLU45 4.3 45.6 1.0 CB C:GLU45 4.3 36.0 1.0 CG C:LEU41 4.3 36.6 1.0 O C:VAL39 4.5 36.3 1.0 N C:THR42 4.6 31.2 1.0 N C:PHE40 4.6 36.0 1.0 C C:LEU41 4.8 32.4 1.0 O C:PHE40 4.8 34.6 1.0 CE1 C:PHE40 4.9 36.7 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