2025-01-08 : 18793 3D structures containing nucleic acids | RNAEQ v3.369all
NAKB entry image
Released2018-06-20Deposited: 2018-03-23
TitleTernary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dCTP analogue
AuthorsBatra VK, Wilson SH
MethodX-RAY DIFFRACTION2.02 Å Rwork: 0.1766 Rfree: 0.2286
P 1 21 1a=50.815 Å b=79.565 Å c=55.502 Å α=90° β=107.78° γ=90°
Software: HKL-2000, PDB_EXTRACT, PHENIX
Primary CitationMapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH Biochemistry (2018)
Entry ContentDeposited MW: 48.82 kDa
Analysis
Protein Annotations
Nonstandard Nucleotides
TypeDescription (hover for sequence)Chains(Auth)SourceMW(kDa)Links
DNACCGACGTCGCATCAGC (16-MER)THomo sapiens4.8
GCTGATGCGA (10-MER)PHomo sapiens3.1
GTCGG (5-MER)DHomo sapiens1.5
ProteinDNA polymerase betaAHomo sapiens38.3
Ligand2' deoxy 5' O [(R) {[(R) [dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine0.623
2' DEOXYCYTIDINE 5' MONOPHOSPHATE0.307
CHLORIDE ION0.035
MAGNESIUM ION0.024
SODIUM ION0.023
Assembly #Type, Components (Author Chain Ids)Oligomer | Point SymmetryActions
1author and software defined
DNA: CCGACGTCGCATCAGC (16-MER) (T)
DNA: GCTGATGCGA (10-MER) (P)
DNA: GTCGG (5-MER) (D)
Protein: DNA polymerase beta (A)
tetrameric(4) | C1View Assembly in 3D (Mol*)
View Nucleic Acid Parameters (DSSR)
Download Assembly mmCIF File (RCSB)