Magnesium in PDB 4py5: Thermovibrio Ammonificans Rnase H3 in Complex with 19-Mer Rna/Dna

The structure of Thermovibrio Ammonificans Rnase H3 in Complex with 19-Mer Rna/Dna, PDB code: 4py5 was solved by M.Figiel, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.09 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.449, 67.661, 107.514, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.3

The binding sites of Magnesium atom in the Thermovibrio Ammonificans Rnase H3 in Complex with 19-Mer Rna/Dna (pdb code 4py5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Thermovibrio Ammonificans Rnase H3 in Complex with 19-Mer Rna/Dna, PDB code: 4py5:

Magnesium binding site 1 out of 1 in the Thermovibrio Ammonificans Rnase H3 in Complex with 19-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 Thermovibrio Ammonificans Rnase H3 in Complex with 19-Mer Rna/Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:25.2 occ:1.00 OD1 A:ASN78 2.1 22.7 1.0 O A:HOH425 2.3 25.4 1.0 OP2 B:A8 2.4 17.4 1.0 O A:GLU79 2.5 8.8 1.0 O A:HOH406 2.6 11.7 1.0 OP1 B:G7 2.9 19.1 1.0 CG A:ASN78 3.2 16.0 1.0 O A:HOH538 3.6 22.9 1.0 C5' B:G7 3.6 15.9 1.0 C A:GLU79 3.6 10.6 1.0 P B:A8 3.6 15.2 1.0 ND2 A:ASN78 3.7 20.6 1.0 O5' B:G7 3.9 16.7 1.0 CB A:SER215 3.9 9.0 1.0 P B:G7 4.1 18.5 1.0 N A:GLU79 4.1 13.2 1.0 O3' B:G7 4.2 14.3 1.0 OP1 B:A8 4.3 11.5 1.0 CA A:SER215 4.4 7.6 1.0 N A:ALA80 4.5 11.2 1.0 CB A:ASN78 4.5 12.0 1.0 OG A:SER112 4.5 13.0 1.0 CA A:GLU79 4.5 10.7 1.0 C4' B:G7 4.6 14.4 1.0 CA A:ALA80 4.6 10.3 1.0 O A:HOH426 4.8 26.6 1.0 C3' B:G7 4.8 14.9 1.0 OD1 A:ASP111 4.8 23.9 1.0 O5' B:A8 4.8 11.6 1.0 CB A:ALA80 4.9 7.0 1.0 O A:SER215 4.9 10.4 1.0 C A:ASN78 5.0 13.6 1.0

M.Figiel, M.Nowotny. Crystal Structure of Rnase H3-Substrate Complex Reveals Parallel Evolution of Rna/Dna Hybrid Recognition. Nucleic Acids Res. V. 42 9285 2014.
ISSN: ISSN 0305-1048
PubMed: 25016521
DOI: 10.1093/NAR/GKU615