1LV5

Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP

Structural Biology Knowledgebase: 1LV5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.218

Literature

Macromolecules
Sequence Display for 1LV5

Classification: TRANSFERASE / DNA

Total Structure Weight: 148221.41


Macromolecule Entities
Molecule Chains Length Organism Details
DNA POLYMERASE I A, B 580 Geobacillus stearothermophilus EC#: 2.7.7.7 IUBMB
Fragment: BACILLUS FRAGMENT (ANALOGOUS TO THE E. COLI KLENOW FRAGMENT)
Gene Name(s): polA pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' C, E 10 synthetic PRIMER STRAND
5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3' D, F 14 synthetic Template Strand

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DCP
Query on DCP

A, B 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.218
  • Space Group: P 31
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.68 α = 90.00
b = 91.68 β = 90.00
c = 190.12 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-24
  • Released Date: 2003-03-25
  • Deposition author(s): Johnson, S.J., Taylor, J.S., Beese, L.S.

Revision History

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