2G8I

B. halodurans RNase H catalytic domain D192N mutant in complex with Mn2+ and RNA/DNA hybrid (non-P nick at the active site)

Structural Biology Knowledgebase: 2G8I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2G8I

Classification: HYDROLASE / RNA / DNA

Total Structure Weight: 20402.46


Macromolecule Entities
Molecule Chains Length Organism Details
Ribonuclease H A 142 Bacillus halodurans EC#: 3.1.26.4 IUBMB
Fragment: Bh-RNase HC
Mutation: D192N
Gene Name(s): rnhA BH0863
Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*UP*CP*GP*AP*CP*A)-3' B 6 synthetic
5'-D(*AP*TP*GP*TP*CP*G)-3' C 6 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MPD
Query on MPD

A (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.173
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.12 α = 90.00
b = 37.08 β = 96.53
c = 61.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-02
  • Released Date: 2006-04-25
  • Deposition author(s): Nowotny, M., Yang, W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4