1FN7 | pdb_00001fn7

COUPLING OF DAMAGE RECOGNITION AND CATALYSIS BY A HUMAN BASE-EXCISION DNA REPAIR PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb1FN7/pdb
• NAKB: 1FN7

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-08-21 Released: 2001-04-21 
• Deposition Author(s): Norman, D.P.G., Bruner, S.D., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.270 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Coupling of substrate recognition and catalysis by a human base-excision DNA repair protein.

Norman, D.P., Bruner, S.D., Verdine, G.L.

(2001) J Am Chem Soc 123: 359-360

• PubMed: 11456534 
• DOI: https://doi.org/10.1021/ja003144m
• Primary Citation Related Structures: 
  1FN7

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Organizational Affiliation: 
• Department of Chemistry and Chemical Biology Harvard University, 12 Oxford Street Cambridge, Massachusetts 02138, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.72 kDa 
• Atom Count: 3,170 
• Modeled Residue Count: 344 
• Deposited Residue Count: 347 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
8-OXOGUANINE DNA GLYCOSYLASE 1	C [auth A]	317	Homo sapiens	Mutation(s): 0  EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O15527 (Homo sapiens) Explore O15527  Go to UniProtKB:  O15527
PHAROS:  O15527 GTEx:  ENSG00000114026

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')	A [auth C]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')	B [auth D]	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.270 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.113	α = 90
b = 92.113	β = 90
c = 211.014	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-21 
Deposition Author(s): Norman, D.P.G., Bruner, S.D., Verdine, G.L.

Revision History  

• Version 1.0: 2001-04-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations