Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61717.50 
• Atom Count: 4267 
• Residue Count: 543 
• Unique protein chains: 1

5KTQ

LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP

• DOI: 10.2210/pdb5KTQ/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli


• Deposited: 1998-09-22 Released: 1998-09-30 
• Deposition Author(s): Li, Y., Kong, Y., Korolev, S., Waksman, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.280 
• R-Value Work: 0.217 

Literature

Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.

Li, Y., Kong, Y., Korolev, S., Waksman, G.

(1998) Protein Sci. 7: 1116-1123

• PubMed: 9605316 
• DOI: 10.1002/pro.5560070505


• PubMed Abstract: 
  

The crystal structures of the Klenow fragment of the Thermus aquaticus DNA polymerase I (Klentaq1) complexed with four deoxyribonucleoside triphosphates (dNTP) have been determined to 2.5 A resolution. The dNTPs bind adjacent to the O helix of Klentaq1. The triphosphate moieties are at nearly identical positions in all four complexes and are anchored by three positively charged residues, Arg659, Lys663, and Arg587, and by two polar residues, His639 and Gln613. The configuration of the base moieties in the Klentaq1/dNTP complexes demonstrates variability suggesting that dNTP binding is primarily determined by recognition and binding of the phosphate moiety. However, when superimposed on the Taq polymerase/blunt end DNA complex structure (Eom et al., 1996), two of the dNTP/Klentaq1 structures demonstrate appropriate stacking of the nucleotide base with the 3' end of the DNA primer strand, suggesting that at least in these two binary complexes, the observed dNTP conformations are functionally relevant.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (DNA POLYMERASE I)	A	543	Thermus aquaticus	Mutation(s): 0  Gene Names: polA (pol1) EC: 2.7.7.7
Find proteins for P19821 (Thermus aquaticus) Go to UniProtKB:  P19821

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DCP	A	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.280 
• R-Value Work: 0.217 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 109.400	α = 90.00
b = 137.000	β = 90.00
c = 45.800	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-09-22 
• Released Date: 1998-09-30 
• Deposition Author(s): Li, Y., Kong, Y., Korolev, S., Waksman, G.

Revision History 

• Version 1.0: 1998-09-30
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance