4MGT | pdb_00004mgt

ALKBH2 R110A cross-linked to undamaged dsDNA

• PDB DOI: https://doi.org/10.2210/pdb4MGT/pdb
• NAKB: 4MGT

• Classification: OXIDOREDUCTASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-08-28 Released: 2014-02-26 
• Deposition Author(s): Chen, B., Gan, J., Yang, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.276 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin

Chen, B., Gan, J., Yang, C.G.

(2014) Sci China Chem 57: 307-313

• DOI: https://doi.org/10.1007/s11426-013-5029-z

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.57 kDa 
• Atom Count: 2,160 
• Modeled Residue Count: 226 
• Deposited Residue Count: 232 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2	A	205	Homo sapiens	Mutation(s): 1  Gene Names: ALKBH2, ABH2 EC: 1.14.11.33
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NS38 (Homo sapiens) Explore Q6NS38  Go to UniProtKB:  Q6NS38
PHAROS:  Q6NS38 GTEx:  ENSG00000189046

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA1	B	14	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA2	C	13	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.276 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.099	α = 90
b = 129.099	β = 90
c = 84.466	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Chen, B., Gan, J., Yang, C.G.

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2014-05-28
  Changes: Non-polymer description
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary