Atomistry » Sodium » PDB 2qd8-2r22 » 2qk9
Atomistry »
  Sodium »
    PDB 2qd8-2r22 »
      2qk9 »

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

Enzymatic activity of 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;

Protein crystallography data

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

Sodium Binding Sites:

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 2qk9

Go back to Sodium Binding Sites List in 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

Reference:

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
Page generated: Tue Dec 15 05:55:11 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy