› 4b21

X-ray diffraction
1.45Å resolution

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

Released:
DOI: 10.2210/pdb4b21/pdb
PDB entry 4b21 coloured by chain, front view.
PDB entry 4b21 coloured by chain, side view.
PDB entry 4b21 coloured by chain, top view.
Source organisms:
Primary publication:
Sculpting of DNA at abasic sites by DNA glycosylase homolog mag2.
Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrøm RJ, McMurray CT, Alseth I, Tainer JA, Bjørås M
Structure 21 154-166 (2013)
PMID: 23245849

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117228 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Alkylbase DNA glycosidase-like protein mag2 Chain: A
Molecule details ›
Chain: A
Length: 232 amino acids
Theoretical weight: 26.36 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O94468 (Residues: 1-213; Coverage: 100%)
Gene names: SPBC23G7.11, mag2
Sequence domains: HhH-GPD superfamily base excision DNA repair protein
Structure domains:
5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3' Chain: X
Molecule details ›
Chain: X
Length: 11 nucleotides
Theoretical weight: 3.23 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3' Chain: Y
Molecule details ›
Chain: Y
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand BGC 1 x BGC
Ligand PO4 3 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: I222
Unit cell:
a: 68.926Å b: 84.746Å c: 126.713Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.207 0.221
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

2 review citations

Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair.
Lafrance-Vanasse et al. (2015)
1 more

2 mentions without citation

Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
Opron et al. (2016)
1 more