8XXK: Human 8-oxoguanine glycosylase K249H mutant

Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction intermediate derived from the crystal soaked into the solution at pH 4.0 under 298 K for 3 weeks. Determined by X-ray diffraction at 1.7 Å resolution. Released 23 Jul 2025.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,590
Mol. weight: 47.95 kDa
Ligands: A1LXK, MG
Released: 23 Jul 2025

Explore 8XXK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XXK contains 19 α-helices and 7 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	20-22	3
β-strand	24-27	4	1
α-helix	35-38	4
β-strand	47-51	5	1
β-strand	54-59	6	1
β-strand	62-68	7	1
β-strand	72-78	7	1
α-helix	87-89	3
α-helix	90-100	11
α-helix	106-116	11
α-helix	118-126	9
α-helix	137-147	11
α-helix	152-166	15
β-strand	169-173	5	2
β-strand	176-179	4	2
α-helix	180-183	4
α-helix	184-188	5
α-helix	192-198	7
α-helix	204-218	15
α-helix	223-230	8
α-helix	233-240	8
α-helix	248-257	10
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-324	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (5'-d(apgpcpgptpcpcpa)-3')	C	DNA	8	Homo sapiens
DNA (5'-d(gpgptpapgpapcpcptpgpgpapcpgp*c)-3')	D	DNA	16	Homo sapiens
N-glycosylase/DNA lyase	A	protein	336	Homo sapiens	O15527 (AlphaFold model)
DNA (5'-d(pgptpcptpapcp*c)-3')	G	DNA	7	Homo sapiens

Sequence of entity 1 (C), FASTA

>8XXK_1 DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*A)-3') (chains C)
AGCGTCCA

Sequence of entity 2 (D), FASTA

>8XXK_2 DNA (5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3') (chains D)
TGGTAGACCTGGACGC

Sequence of entity 3 (A), FASTA

>8XXK_3 N-glycosylase/DNA lyase (chains A)
GPGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQT
EEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQG
VRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAG
PEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTH
VADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGP
YAGWAQAVLFSADLRQSRHAQEPPAKRRKGSKGPEG

Sequence of entity 4 (G), FASTA

>8XXK_4 DNA (5'-D(P*GP*TP*CP*TP*AP*CP*C)-3') (chains G)
GTCTACC

Ligands and cofactors

ID	Name	Formula	Copies
A1LXK	[(2~{R},3~{S},5~{S})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-…	C10 H16 N5 O9 P	1
MG	Magnesium ion	Mg	2

Water and common crystallization additives (GOL, NA) are not listed.

Primary citation

Capturing a glycosylase reaction intermediate in DNA repair by freeze-trapping of a pH-responsive hOGG1 mutant. Unno, M., Morikawa, M., Sychrovsky, V. et al. Nucleic Acids Res (2025) 53. DOI 10.1093/nar/gkaf718 · PubMed

Other PDB entries of the same protein (UniProt O15527 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8XWC 1.45 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the substrate…
2XHI 1.55 Å, Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA…
5AN4 1.6 Å, Crystal structure of the human 8-oxoguanine glycosylase (OGG1) processed with the…
8XWU 1.68 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction…
8XXG 1.82 Å, Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction…
9NZ8 1.85 Å, Crystal structure of human OGG1 in a DNA-free state
1M3Q 1.9 Å, Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine
6RLW 2.0 Å, Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487
7AYY 2.0 Å, Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator…
9NZ9 2.0 Å, Crystal structure of product-bound human OGG1(WT)
1LWY 2.01 Å, hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine
2NOH 2.01 Å, Structure of catalytically inactive Q315A human 8-oxoguanine glycosylase complexed to…

Browse structure collections

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