2HZV

NikR-operator DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.303
  • R-Value Work: 0.261

Literature

Macromolecules
Sequence Display for 2HZV

Classification: METAL BINDING PROTEIN / DNA

Total Structure Weight: 159482.33


Macromolecule Entities
Molecule Chains Length Organism Details
Nickel-responsive regulator A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 133 Escherichia coli Mutation: M1M, M105M
Gene Name(s): nikR yhhG b3481 JW3446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3' I, K 30 synthetic
5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3' J, L 30 synthetic

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

A, C, D, E, F, G, H NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B, C, E, F, G, H POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D, E, F, G, H L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.303
  • R-Value Work: 0.261
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 197.20 α = 90.00
b = 76.13 β = 110.27
c = 132.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-08-09
  • Released Date: 2006-08-22
  • Deposition author(s): Schreiter, E.R., Drennan, C.L.

Revision History

  • 2008-05-01
    Type: Version format compliance
  • 2011-07-13
    Type: Version format compliance