1HUZ: DNA polymerase

Crystal structure of DNA polymerase complexed with DNA and cr-pcp. Determined by X-ray diffraction at 2.6 Å resolution. Released 23 Apr 2001.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Rattus norvegicus
Chains: 6
Atoms: 5,994
Mol. weight: 88.81 kDa
Ligands: MDN, CR
Released: 23 Apr 2001

Explore 1HUZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1HUZ contains 41 α-helices and 18 β-strands across 2 chains. 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: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-28	16
α-helix	33-46	14
α-helix	56-59	4
α-helix	67-79	13
α-helix	83-90	8
α-helix	92-100	9
α-helix	108-116	9
α-helix	122-125	4
α-helix	134-141	8
α-helix	143-147	5
α-helix	149	1
β-strand	150-151	2	1
α-helix	152-169	18
β-strand	174-177	4	2
β-strand	187-188	2	1
β-strand	191-196	6	2
α-helix	209-220	12
β-strand	224-230	7	2
β-strand	234-239	6	2
α-helix	249-252	4
β-strand	253-259	7	2
α-helix	262-264	3
α-helix	265-271	7
α-helix	276-289	14
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

Chain B: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	13-24	12
α-helix	25-29	5
α-helix	33-47	15
α-helix	56-60	5
α-helix	67-79	13
α-helix	83-90	8
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	143-147	5
α-helix	152-169	18
β-strand	174-177	4	5
α-helix	179-182	4
β-strand	191-196	6	5
α-helix	209-220	12
β-strand	224-230	7	5
β-strand	234-239	6	5
β-strand	253-259	7	5
α-helix	262-264	3
α-helix	265-273	9
α-helix	276-289	14
β-strand	291-293	3	6
β-strand	298-300	3	6
α-helix	310-312	3
α-helix	316-322	7
α-helix	330-332	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-d(apaptpapgpgpcpgptpcp*g)-3'	C, T	DNA	11
5'-d(pcpgpapcpgpcpcpt)-3'	D, P	DNA	8
DNA polymerase beta	A, B	protein	335	Rattus norvegicus	P06766 (AlphaFold model)

Sequence of entity 1 (C, T), FASTA

>1HUZ_1 5'-D(*AP*AP*TP*AP*GP*GP*CP*GP*TP*CP*G)-3' (chains C, T)
AATAGGCGTCG

Sequence of entity 2 (D, P), FASTA

>1HUZ_2 5'-D(P*CP*GP*AP*CP*GP*CP*CP*T)-3' (chains D, P)
CGACGCCT

Sequence of entity 3 (A, B), FASTA

>1HUZ_3 DNA POLYMERASE BETA (chains A, B)
MSKRKAPQETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAK
KLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIK
TLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGS
FRRGAESSGDMDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQ
LPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRP
LGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSE

Ligands and cofactors

ID	Name	Formula	Copies
MDN	Methylenediphosphonic acid	C H6 O6 P2	2
CR	Chromium ion	Cr	2

Primary citation

Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes. Arndt, J.W., Gong, W., Zhong, X. et al. Biochemistry (2001) 40:5368-5375. DOI 10.1021/bi002176j · PubMed

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

2VAN 2.1 Å, Nucleotidyl Transfer Mechanism of Mismatched dNTP Incorporation by DNA Polymerase b by…
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…

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