1N39: N-glycosylase/DNA lyase

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. Determined by X-ray diffraction at 2.2 Å resolution. Released 4 Mar 2003.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,192
Mol. weight: 44.73 kDa
Ligands: CA
Released: 4 Mar 2003

Explore 1N39 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N39 contains 20 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: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	24-27	4	1
α-helix	35-38	4
β-strand	48-51	4	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	90-99	10
α-helix	106-116	11
α-helix	118-124	7
α-helix	137-147	11
α-helix	152-166	15
α-helix	168	1
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	204-217	14
α-helix	222-226	5
α-helix	227-230	4
α-helix	233-240	8
α-helix	248-257	10
α-helix	269-279	11
α-helix	293-307	15
α-helix	311-323	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA complement strand	B	DNA	15
DNA inhibitor strand	C	DNA	15
N-glycosylase/DNA lyase	A	protein	317	Homo sapiens	O15527 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>1N39_1 DNA complement strand (chains B)
GGTAGACCTGGACGC

Sequence of entity 2 (C), FASTA

>1N39_2 DNA inhibitor strand (chains C)
GCGTCCANGTCTACC

Sequence of entity 3 (A), FASTA

>1N39_3 N-glycosylase/DNA lyase (chains A)
GSEGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQ
TEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQ
GVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALA
GPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGT
KVADCICLMALDKPQAVPVEVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWG
PYAGWAQAVLFSADLRQ

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Structural and biochemical exploration of a critical amino acid in human 8-oxoguanine glycosylase. Norman, D.P., Chung, S.J., Verdine, G.L. Biochemistry (2003) 42:1564-1572. DOI 10.1021/bi026823d · 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…
8XXK 1.7 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

Browse structure collections

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