RCSB PDB: Search

2HKB \| pdb_00002hkb	Download File View File

NMR Structure of the B-DNA Dodecamer CTCGGCGCCATC

Wang, F., DeMuro, N.E., Elmquist, C.E., Stover, J.S., Rizzo, C.J., Stone, M.P.

(2006) J Am Chem Soc 128: 10085-10095

Released	2006-10-03
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	5'-D(CPTPCPGPGPCPGPCPCPAPTPC)-3' (nucleic acid) 5'-D(GPAPTPGPGPCPGPCPCPGPAPG)-3' (nucleic acid)

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2HKC \| pdb_00002hkc	Download File View File

NMR Structure of the IQ-modified Dodecamer CTCGGC[IQ]GCCATC

Wang, F., DeMuro, N.E., Elmquist, C.E., Stover, J.S., Rizzo, C.J., Stone, M.P.

(2006) J Am Chem Soc 128: 10085-10095

Released	2006-10-03
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	5'-D(CPTPCPGPGPCPGPCPCPAPTPC)-3' (nucleic acid) 5'-D(GPAPTPGPGPCPGPCPCPGPAPG)-3' (nucleic acid)
Unique Ligands	GIQ

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2HLI \| pdb_00002hli	Download File View File

Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence

Cho, Y.-J., Wang, H., Kozekov, I.D., Kurtz, A.J., Jacob, J., Voehler, M., Smith, J., Harris, T.M., Rizzo, C.J., Stone, M.P.

(2006) Chem Res Toxicol 19: 1019-1029

Released	2006-09-19
Method	SOLUTION NMR
Macromolecule	DNA dodecamer (nucleic acid) DNA dodecamer with S-crotonaldehyde adduct (nucleic acid)

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2HMD \| pdb_00002hmd	Download File View File

Stereochemistry Modulates Stability of Reduced Inter-Strand Cross-Links Arising From R- and S-alpha-methyl-gamma-OH-1,N2-propano-2'-Deoxyguanine in the 5'-CpG-3' DNA Sequence

Cho, Y.-J., Kozekov, I.D., Harris, T.M., Rizzo, C.J., Stone, M.P.

(2007) Biochemistry 46: 2608-2621

Released	2007-03-13
Method	SOLUTION NMR
Macromolecule	DNA dodecamer with interstrand cross-link (nucleic acid)

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2HMR \| pdb_00002hmr	Download File View File

Solution structure of reduced interstrand cross-link arising from S-alpha-methyl-gamma-OH-1,N2-propano-2'-deoxyguanosine in the 5'-CpG-3' DNA sequence

Cho, Y.-J., Kozekov, I.D., Harris, T.M., Rizzo, C.J., Stone, M.P.

(2007) Biochemistry 46: 2608-2621

Released	2007-03-13
Method	SOLUTION NMR
Macromolecule	DNA dodecamer with interstrand cross-link (nucleic acid)

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2K8T \| pdb_00002k8t	Download File View File

Solution NMR structure of trans-4-hydroxynonenal derived dG adduct of (6R,8S,11R)-configuration opposite dC

Huang, H., Wang, H., Qi, N., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

(2008) Biochemistry 47: 11457-11472

Released	2008-11-04
Method	SOLUTION NMR
Macromolecule	5'-D(DGPDCPDTPDAPDGPDCPDGPDAPDGPDTPDCPDC)-3' (nucleic acid) 5'-D(DGPDGPDAPDCPDTPDCPDGPDCPDTPDAPDGPDC)-3' (nucleic acid)
Unique Ligands	HNB

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2K8U \| pdb_00002k8u	Download File View File

Solution NMR structure of trans-4-hydroxynonenal derived dG adduct of (6S,8R,11S)-configuration matched with dC

Huang, H., Wang, H., Qi, N., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

(2008) Biochemistry 47: 11457-11472

Released	2008-11-04
Method	SOLUTION NMR
Macromolecule	5'-D(DGPDCPDTPDAPDGPDCPDGPDAPDGPDTPDCPDC)-3' (nucleic acid) 5'-D(DGPDGPDAPDCPDTPDCPDGPDCPDTPDAPDGPDC)-3' (nucleic acid)
Unique Ligands	HNB

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2KAR \| pdb_00002kar	Download File View File

HNE-dG adduct mismatched with dA in acidic solution

Huang, H., Wang, H., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

(2009) Chem Res Toxicol 22: 187-200

Released	2009-05-26
Method	SOLUTION NMR
Macromolecule	5'-D(DGPDCPDTPDAPDGPDCPDGPDAPDGPDTPDCPDC)-3' (nucleic acid) 5'-D(DGPDGPDAPDCPDTPDAPDGPDCPDTPDAPDGPDC)-3' (nucleic acid)
Unique Ligands	HND

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2KAS \| pdb_00002kas	Download File View File

HNE-dG adduct mismatched with dA in basic solution

Huang, H., Wang, H., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

(2009) Chem Res Toxicol 22: 187-200

Released	2009-05-26
Method	SOLUTION NMR
Macromolecule	5'-D(DGPDCPDTPDAPDGPDCPDGPDAPDGPDTPDCPDC)-3' (nucleic acid) 5'-D(DGPDGPDAPDCPDTPDAPDGPDCPDTPDAPDGPDC)-3' (nucleic acid)
Unique Ligands	HND

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2KTP \| pdb_00002ktp	Download File View File

Structure of the 1,N2-ethenodeoxyguanosine lesion opposite a one-base deletion in duplex DNA

Shanmugam, G., Kozekov, I.D., Guengerich, P.F., Rizzo, C.J., Stone, M.P.

(2010) Biochemistry 49: 2615-2626

Released	2010-03-23
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPGPCPAPTP(GNE)PGPAPAPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPTPTPCPAPTPGPCP*G)-3') (nucleic acid)

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2KV6 \| pdb_00002kv6	Download File View File

Tetrapeptide KWKK conjugated to oligonucleotide duplex by a trimethylene tether

Huang, H., Kozekov, I.D., Kozekova, A., Rizzo, C.J., McCullough, A., LLoyd, R.S., Stone, M.P.

(2010) Biochemistry 49: 6155-6164

Released	2010-07-21
Method	SOLUTION NMR
Macromolecule	KWKK Tetrapeptide (protein) 5'-D(GPCPTPAPGPCPGPAPGPTPCPC)-3' (nucleic acid) 5'-D(GPGPAPCPTPCPGPCPTPAPGPC)-3' (nucleic acid)

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2LBI \| pdb_00002lbi	Download File View File

N2-dG:N2-dG interstrand cross-link induced by trans-4-hydroxynonenal

Huang, H., Kozekov, I.D., Wang, H., Kozekova, A., Rizzo, C.J., Stone, M.P.

(2011) J Am Chem Soc 133: 16101-16110

Released	2012-04-04
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(GPCPTPAPGPCPGPAPGPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPCPTPCPGPCPTPAPGPC)-3') (nucleic acid)
Unique Ligands	HND

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2LG2 \| pdb_00002lg2	Download File View File

Structure of the duplex containing HNE derived (6S,8R,11S) N2-dG cyclic hemiacetal when placed opposite dT

Huang, H., Wang, H., Kozekova, A., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

To be published

Released	2012-08-01
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(GPCPTPAPGPCPGPAPGPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPCPTPTPGPCPTPAPGPC)-3') (nucleic acid)
Unique Ligands	2LE

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2LG3 \| pdb_00002lg3	Download File View File

Structure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT

Huang, H., Wang, H., Kozekova, A., Lloyd, R.S., Rizzo, C.J., Stone, M.P.

To be published

Released	2012-08-01
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(GPCPTPAPGPCPGPAPGPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPCPTPTPGPCPTPAPGPC)-3') (nucleic acid)
Unique Ligands	HND

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2MAV \| pdb_00002mav	Download File View File

NMR Structure of N2-IQ-dG at the G3 position in the NarI recognition sequence

Stavros, K.M., Hawkins, E.K., Rizzo, C.J., Stone, M.P.

(2014) Nucleic Acids Res 42: 3450-3463

Released	2014-05-14
Method	SOLUTION NMR
Macromolecule	DNA_(5'-D(CPTPCPGPGPCPGPCPCPAPTPC)-3') (nucleic acid) DNA_(5'-D(GPAPTPGPGPCPGPCPCPGPAPG)-3') (nucleic acid)

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2V4Q \| pdb_00002v4q	Download File View File

Post-insertion complex of the Y-family DNA polymerase Dpo4 with M1dG containing template DNA

Eoff, R.L., Stafford, J.B., Szekely, J., Rizzo, C.J., Egli, M., Guengerich, F.P., Marnett, L.J.

(2009) Biochemistry 48: 7079

Released	2009-06-16
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPCPC)-3' (nucleic acid) 5'-D(TPCPAPC M1GPGPAPAPTPCPCP TPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DGT

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2V4R \| pdb_00002v4r	Download File View File

Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine

Eoff, R.L., Stafford, J.B., Szekely, J., Rizzo, C.J., Egli, M., Guengerich, F.P., Marnett, L.J.

(2009) Biochemistry 48: 7079

Released	2009-06-16
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharolobus solfataricus P2 synthetic construct
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPC)-3' (nucleic acid) 5'-D(TPCPAPCPM1GPGPAPAPTPCPCP TPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	CA, DGT

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2W9A \| pdb_00002w9a	Download File View File

Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dGTP

Eoff, R.L., Zhang, H., Kosekov, I.D., Rizzo, C.J., Egli, M., Guengerich, F.P.

(2009) J Biological Chem 284: 17687

Released	2009-05-12
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPCPDOC)-3' (nucleic acid) 5'-D(TPCPAPCPO2GPGPAPAPTPCP CPTPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	DGT, MG

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2W9B \| pdb_00002w9b	Download File View File

Binary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA

Eoff, R.L., Zhang, H., Kosekov, I.D., Rizzo, C.J., Egli, M., Guengerich, F.P.

(2009) J Biological Chem 284: 17687

Released	2009-05-12
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPCPDOCP)-3' (nucleic acid) 5'-D(TPCPAPTPM2GPGPAPAPTPCPCP TPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	MG

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2W9C \| pdb_00002w9c	Download File View File

Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dTTP

Eoff, R.L., Zhang, H., Kosekov, I.D., Rizzo, C.J., Egli, M., Guengerich, F.P.

(2009) J Biological Chem 284: 17687

Released	2009-05-12
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA POLYMERASE IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAP TPTPDOCP)-3' (nucleic acid) 5'-D(TPCPAPCPO2GPGPAPAPTPCPCP TPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	MG, TTP

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2Z2G \| pdb_00002z2g	Download File View File

NMR Structure of the IQ-modified Dodecamer CTC[IQ]GGCGCCATC

Wang, F., Elmquist, C.E., Stover, J.S., Rizzo, C.J., Stone, M.P.

(2007) Biochemistry 46: 8498-8516

Released	2007-10-02
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	DNA (5'-D(DCPDTPDCPDGPDGPDCPDGPDCPDCPDAPDTPDC)-3') (nucleic acid) DNA (5'-D(DGPDAPDTPDGPDGPDCPDGPDCPDCPDGPDAPDG)-3') (nucleic acid)
Unique Ligands	GIQ

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2Z2H \| pdb_00002z2h	Download File View File

NMR Structure of the IQ-modified Dodecamer CTCG[IQ]GCGCCATC

Wang, F., Elmquist, C.E., Stover, J.S., Rizzo, C.J., Stone, M.P.

(2007) Biochemistry 46: 8498-8516

Released	2007-10-02
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	DNA (5'-D(DCPDTPDCPDGPDGPDCPDGPDCPDCPDAPDTPDC)-3') (nucleic acid) DNA (5'-D(DGPDAPDTPDGPDGPDCPDGPDCPDCPDGPDAPDG)-3') (nucleic acid)
Unique Ligands	GIQ

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3T5H \| pdb_00003t5h	Download File View File

Ternary complex of HNE Adduct modified DNA (5'-CXG-3' vs 13-mer) with Dpo4 and incoming dDGT

Banerjee, S., Christov, P.P., Kozekova, A., Rizzo, C.J., Stone, M.P.

(2012) Chem Res Toxicol 25: 422-435

Released	2012-02-15
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) DNA (5'-D(CPAPCP(HN1)PGPAPAPTPCPCPTPTPCPCPCPCPC)-3') (nucleic acid) DNA (5'-D(GPGPGPGPGPAPAPGPGPAPTPTPC)-3') (nucleic acid)
Unique Ligands	CA, DGT

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3T5J \| pdb_00003t5j	Download File View File

Ternary complex of HNE Adduct modified DNA (5'-TXG-3' vs 13-mer) with Dpo4 and incoming dDTP

Banerjee, S., Christov, P.P., Kozekova, A., Rizzo, C.J., Stone, M.P.

(2012) Chem Res Toxicol 25: 422-435

Released	2012-02-15
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) DNA (5'-D(CPAPTP(HN1)PGPAPAPTPCPCPTPTPCPCPCPCPC)-3') (nucleic acid) DNA (5'-D(GPGPGPGPGPAPAPGPGPAPTPTPC)-3') (nucleic acid)
Unique Ligands	CA, DTP

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3T5K \| pdb_00003t5k	Download File View File

Ternary complex of HNE Adduct modified DNA (5'-TXG-3' vs 14-mer) with Dpo4 and incoming dDTP

Banerjee, S., Christov, P.P., Kozekova, A., Rizzo, C.J., Stone, M.P.

(2012) Chem Res Toxicol 25: 422-435

Released	2012-02-15
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) DNA (5'-D(CPAPTP(HN0)PGPAPAPTPCPCPTPTPCPCPCPCPC)-3') (nucleic acid) DNA (5'-D(GPGPGPGPGPAPAPGPGPAPTPTPCP*C)-3') (nucleic acid)
Unique Ligands	CA, DTP

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2HKB | pdb_00002hkb

2HKC | pdb_00002hkc

2HLI | pdb_00002hli

2HMD | pdb_00002hmd

2HMR | pdb_00002hmr

2K8T | pdb_00002k8t

2K8U | pdb_00002k8u

2KAR | pdb_00002kar

2KAS | pdb_00002kas

2KTP | pdb_00002ktp

2KV6 | pdb_00002kv6

2LBI | pdb_00002lbi

2LG2 | pdb_00002lg2

2LG3 | pdb_00002lg3

2MAV | pdb_00002mav

2V4Q | pdb_00002v4q

2V4R | pdb_00002v4r

2W9A | pdb_00002w9a

2W9B | pdb_00002w9b

2W9C | pdb_00002w9c

2Z2G | pdb_00002z2g

2Z2H | pdb_00002z2h

3T5H | pdb_00003t5h

3T5J | pdb_00003t5j

3T5K | pdb_00003t5k