2VAN: DNA polymerse beta

Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by Structural and Kinetic Analyses. Determined by X-ray diffraction at 2.1 Å resolution. Released 15 Apr 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: RATTUS NORVEGICUS
Chains: 1
Atoms: 2,081
Mol. weight: 28.39 kDa
Released: 15 Apr 2008

Explore 2VAN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VAN contains 17 α-helices and 11 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: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	92-100	9
α-helix	108-115	8
α-helix	122-126	5
α-helix	129-131	3
α-helix	134-141	8
α-helix	145-147	3
β-strand	150-151	2	1
α-helix	152-169	18
β-strand	174-177	4	2
α-helix	179-182	4
β-strand	187-188	2	1
β-strand	191-196	6	2
α-helix	205-206	2
α-helix	208-220	13
β-strand	224-230	7	2
β-strand	234-239	6	2
α-helix	250-252	3
β-strand	253-259	7	2
α-helix	262-264	3
α-helix	265-273	9
α-helix	276-288	13
β-strand	291-293	3	3
β-strand	298-300	3	3
β-strand	301	1	4
β-strand	307	1	4
α-helix	310-312	3
α-helix	316-322	7
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerse beta	A	protein	245	RATTUS NORVEGICUS	P06766 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2VAN_1 DNA POLYMERSE BETA (chains A)
DDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRI
PREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPKL
LHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENDENEYPHRRIDIRLQPKDQYYCGVL
YFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEQDIFDYIQWRYREP
KDRSE

Primary citation

Mismatched Dntp Incorporation by DNA Polymerase Beta Does not Proceed Via Globally Different Conformational Pathways. Tang, K., Niebuhr, M., Tung, C. et al. Nucleic Acids Res (2008) 36:2948. DOI 10.1093/NAR/GKN138 · PubMed

Other PDB entries of the same protein (UniProt P06766 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UXO 2.1 Å, Crystal Structure of Rat DNA Polymerase Beta Mutator I260Q Apoenzyme
3V7J 2.25 Å, Co-crystal structure of Wild Type Rat polymerase beta: Enzyme-DNA binary complex
3V7K 2.27 Å, Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex
1BPB 2.3 Å, Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism
1RPL 2.3 Å, 2.3 Å crystal structure of the catalytic domain of DNA polymerase beta
1ZQW 2.3 Å, DNA polymerase beta (pol B) (E.C.2.7.7.7), 31-kd domain; soaked in the presence of cscl…
1ZQY 2.3 Å, DNA polymerase beta (pol B) (E.C.2.7.7.7), 31-kd domain; soaked in the presence of MGCL2…
3LQC 2.35 Å, X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain
1JN3 2.35 Å, Fidelity properties and structure of M282L mutator mutant of DNA polymerase: subtle…
3V72 2.49 Å, Crystal Structure of Rat DNA polymerase beta Mutator E295K: Enzyme-dsDNA
1ZQX 2.5 Å, DNA polymerase beta (pol B) (E.C.2.7.7.7), 31-kd domain; soaked in the presence of kcl…
3UXN 2.5 Å, Crystal Structure of Rat DNA Polymerase Beta, Wild Type Apoenzyme

Browse structure collections

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