2PFN: Na in the active site of DNA Polymerase lambda

Na in the active site of DNA Polymerase lambda. Determined by X-ray diffraction at 1.9 Å resolution. Released 15 May 2007.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,205
Mol. weight: 44.41 kDa
Ligands: DUP, MG
Released: 15 May 2007

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

Secondary structure: helices and β-sheets

2PFN contains 19 α-helices and 12 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: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	254-269	16
α-helix	273-287	15
α-helix	296-300	5
α-helix	307-317	11
α-helix	323-327	5
α-helix	331-339	9
α-helix	346-354	9
α-helix	360-366	7
α-helix	371-378	8
α-helix	380-384	5
β-strand	387-388	2	1
α-helix	389-406	18
β-strand	411-414	4	2
α-helix	416-419	4
β-strand	424-425	2	1
β-strand	428-433	6	2
α-helix	444-453	10
β-strand	457-462	6	2
β-strand	472-477	6	2
β-strand	487-493	7	2
α-helix	496-498	3
α-helix	499-507	9
α-helix	510-522	13
β-strand	525-527	3	3
β-strand	532-534	3	3
β-strand	538	1	4
β-strand	544	1	4
β-strand	549-551	3	3
α-helix	552	1
α-helix	556-562	7
α-helix	570-573	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Template	T	DNA	11
Primer	P	DNA	6
Downstream Primer	D	DNA	4
DNA polymerase lambda	A	protein	335	Homo sapiens	Q9UGP5 (AlphaFold model)

Sequence of entity 1 (T), FASTA

>2PFN_1 Template (chains T)
CGGCAGTACTG

Sequence of entity 2 (P), FASTA

>2PFN_2 Primer (chains P)
CAGTAC

Sequence of entity 3 (D), FASTA

>2PFN_3 Downstream Primer (chains D)
GCCG

Sequence of entity 4 (A), FASTA

>2PFN_4 DNA polymerase lambda (chains A)
MAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEAC
SIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSL
EDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRR
GKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLP
GPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNT
HGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW

Ligands and cofactors

ID	Name	Formula	Copies
DUP	2'-deoxyuridine 5'-alpha,beta-imido-triphosphate	C9 H16 N3 O13 P3	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Role of the catalytic metal during polymerization by DNA polymerase lambda. Garcia-Diaz, M., Bebenek, K., Krahn, J.M. et al. DNA Repair (Amst) (2007) 6:1333-1340. DOI 10.1016/j.dnarep.2007.03.005 · PubMed

Other PDB entries of the same protein (UniProt Q9UGP5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7M07 1.57 Å, Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M49 1.6 Å, DNA Polymerase Lambda, TTP:At Mn2+ Reaction State Ternary Complex, 5 min
9NPU 1.63 Å, Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M47 1.65 Å, DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 60 min
2BCQ 1.65 Å, DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp
7M09 1.65 Å, Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate…
7M4B 1.66 Å, DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 60 min
7M08 1.7 Å, Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB…
7M4L 1.7 Å, DNA Polymerase Lambda, TTPaS:At Mn2+ Product State Ternary Complex, 60 min
7M4K 1.72 Å, DNA Polymerase Lambda, TTPaS:At Ca2+ Ground State Ternary Complex
5IIJ 1.72 Å, Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a…
2BCR 1.75 Å, DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp

Browse structure collections

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