2JIQ

A NEW CATALYTIC MECHANISM OF PERIPLASMIC NITRATE REDUCTASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 FROM CRYSTALLOGRAPHIC AND EPR DATA AND BASED ON DETAILED ANALYSIS OF THE SIXTH LIGAND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 2JIQ

Classification: OXIDOREDUCTASE

Total Structure Weight: 82741.09

Macromolecule Entities
Molecule Chains Length Organism Details
PERIPLASMIC NITRATE REDUCTASE A 723 Desulfovibrio desulfuricans EC#: 1.7.99.4 IUBMB
Gene Name(s): napA nap Ddes_0616
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9- TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN- 4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE (Synonym)
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MO
Query on MO

A MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO3
Query on NO3

A NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO2
Query on NO2

A NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

A UNKNOWN ATOM OR ION
X
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.155
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 105.21 α = 90.00
b = 105.21 β = 90.00
c = 130.68 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-06-28
  • Released Date: 2008-03-18
  • Deposition author(s): Najmudin, S., Gonzalez, P.J., Trincao, J., Coelho, C., Mukhopadhyay, A., Romao, C.C., Moura, I., Moura, J.J.G., Brondino, C.D., Romao, M.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor