9Z4Y | pdb_00009z4y

Human APE1 D210N with Mg and substrate tetrahydrofuran-containing DNA

PDB DOI: https://doi.org/10.2210/pdb9Z4Y/pdb

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-11-11 Released: 2026-09-23
Deposition Author(s): Tsutakawa, S.E., Tainer, J.A., Arvai, A.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Robert A. Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.231 (Depositor), 0.231 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Human APE1 D210N with Mg and substrate tetrahydrofuran-containing DNA

Tsutakawa, S.E., Tainer, J.A., Arvai, A.

To be published.

Macromolecule Content

Total Structure Weight: 76.65 kDa
Atom Count: 5,692
Modeled Residue Count: 593
Deposited Residue Count: 602
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair nuclease/redox regulator APEX1, mitochondrial	A, D	279	Homo sapiens	Mutation(s): 1 Gene Names: APEX1, APE, APE1, APEX, APX, HAP1, REF1 EC: 3.1.21 (UniProt), 3.1.11.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27695 (Homo sapiens) Explore P27695 Go to UniProtKB: P27695
PHAROS: P27695 GTEx: ENSG00000100823
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27695
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(GPCPTPAPCP(3DR)PGPAPTPCP*G)-3')	B, E	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (5'-D(CPGPAPTPCPGPGPTPAPGP*C)-3')	C, F	11	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth D] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D]	I [auth A], J [auth A], N [auth D], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth D] Focus chain O [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	G [auth A], H [auth A], K [auth B], L [auth D], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth D] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.231 (Depositor), 0.231 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.022	α = 90
b = 128.531	β = 96.413
c = 64.756	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-23

Deposition Author(s):

Tsutakawa, S.E.

Tainer, J.A.

Arvai, A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	p01 ca092584
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM046312
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 CA220430
Robert A. Welch Foundation	United States	G-0010