4HNO

High resolution crystal structure of DNA Apurinic/apyrimidinic (AP) endonuclease IV Nfo from Thermatoga maritima

Structural Biology Knowledgebase: 4HNO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.139
  • R-Value Work: 0.125

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HNO

Classification: HYDROLASE

Total Structure Weight: 33223.96

Macromolecule Entities
Molecule Chains Length Organism Details
Probable endonuclease 4 A 288 Thermotoga maritima EC#: 3.1.21.2 IUBMB
Gene Name(s): nfo TM_0362

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TRS
Query on TRS

A 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.139
  • R-Value Work: 0.125
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 123.37 α = 90.00
b = 123.37 β = 90.00
c = 35.40 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-20
  • Released Date: 2013-01-23
  • Deposition author(s): Shin, D.S., Hosfield, D.J., Arvai, A.S., Tsutakawa, S.E., Tainer, J.A.

Revision History

  • 2013-04-10
    Type: Citation | Details: Citation update
  • 2013-02-13
    Type: Citation | Details: Citation update