Sodium in PDB 2qk9: Human Rnase H Catalytic Domain Mutant D210N in Complex with 18-Mer Rna/Dna Hybrid

All present enzymatic activity of Human Rnase H Catalytic Domain Mutant D210N in Complex with 18-Mer Rna/Dna Hybrid:
3.1.26.4;

The structure of Human Rnase H Catalytic Domain Mutant D210N in Complex with 18-Mer Rna/Dna Hybrid, PDB code: 2qk9 was solved by M.Nowotny, S.A.Gaidamakov, R.Ghirlando, S.M.Cerritelli, R.J.Crouch, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.55
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	158.578, 158.578, 142.055, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 21.6

The binding sites of Sodium atom in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 18-Mer Rna/Dna Hybrid (pdb code 2qk9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 18-Mer Rna/Dna Hybrid, PDB code: 2qk9:

Sodium binding site 1 out of 1 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 18-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 18-Mer Rna/Dna Hybrid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na9001 b:50.3 occ:1.00 OD2 A:ASP145 2.4 32.6 1.0 OP1 B:C10 2.5 34.5 1.0 OE2 A:GLU186 2.5 41.6 1.0 ND2 A:ASN210 2.6 34.3 1.0 O3' B:A9 2.9 32.2 1.0 O A:HOH9037 2.9 32.1 1.0 OE1 A:GLU186 2.9 42.7 1.0 CD A:GLU186 3.0 42.8 1.0 P B:C10 3.3 33.7 1.0 CG A:ASN210 3.4 35.0 1.0 CB A:ASN210 3.5 32.1 1.0 CG A:ASP145 3.6 33.6 1.0 C5' B:C10 3.9 30.3 1.0 O A:GLY146 3.9 35.6 1.0 O2' B:A9 4.1 27.3 1.0 O5' B:C10 4.1 32.1 1.0 O A:HOH9044 4.1 42.2 1.0 C3' B:A9 4.1 29.8 1.0 O A:HOH9002 4.2 50.5 1.0 O A:HOH9025 4.2 51.8 1.0 N A:GLY146 4.4 29.2 1.0 OD1 A:ASP145 4.4 35.0 1.0 CG A:GLU186 4.5 42.4 1.0 C4' B:A9 4.5 27.5 1.0 CB A:ASP145 4.5 30.4 1.0 OP2 B:C10 4.5 32.2 1.0 CA A:ASP145 4.6 27.9 1.0 OD1 A:ASN210 4.6 37.7 1.0 CA A:ASN210 4.7 32.4 1.0 C2' B:A9 4.7 28.7 1.0 N A:ASN210 4.7 30.8 1.0 C A:GLY146 4.9 34.2 1.0

M.Nowotny, S.A.Gaidamakov, R.Ghirlando, S.M.Cerritelli, R.J.Crouch, W.Yang. Structure of Human Rnase H1 Complexed with An Rna/Dna Hybrid: Insight Into Hiv Reverse Transcription Mol.Cell V. 28 264 2007.
ISSN: ISSN 1097-2765
PubMed: 17964265
DOI: 10.1016/J.MOLCEL.2007.08.015