RCSB PDB: Search

1AX6 \| pdb_00001ax6	Download File View File

SOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT OPPOSITE A-2 DELETION SITE IN THE NARI HOT SPOT SEQUENCE CONTEXT; NMR, 6 STRUCTURES

Mao, B., Gorin, A.A., Gu, Z., Hingerty, B.E., Broyde, S., Patel, D.J.

(1997) Biochemistry 36: 14479-14490

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(CTCGGC-[AF]G-CCATC)D(GATGGCCGAG) (nucleic acid)
Unique Ligands	AF

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1AX7 \| pdb_00001ax7	Download File View File

SOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT POSITIONED AT A TEMPLATE-PRIMER JUNCTION, NMR, 6 STRUCTURES

Mao, B., Gu, Z., Gorin, A.A., Hingerty, B.E., Broyde, S., Patel, D.J.

(1997) Biochemistry 36: 14491-14501

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(AAC-[AF]G-CTACCATCC)D(GGATGGTAG) (nucleic acid)
Unique Ligands	AF

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1AXL \| pdb_00001axl	Download File View File

SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES

Feng, B., Gorin, A.A., Kolbanovskiy, A., Hingerty, B.E., Geacintov, N.E., Broyde, S., Patel, D.J.

(1997) Biochemistry 36: 13780-13790

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG) (nucleic acid)
Unique Ligands	BAP

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1AXO \| pdb_00001axo	Download File View File

STRUCTURAL ALIGNMENT OF THE (+)-TRANS-ANTI-[BP]DG ADDUCT POSITIONED OPPOSITE DC AT A DNA TEMPLATE-PRIMER JUNCTION, NMR, 6 STRUCTURES

Feng, B., Gorin, A.A., Hingerty, B.E., Geacintov, N.E., Broyde, S., Patel, D.J.

(1997) Biochemistry 36: 13769-13779

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(AAC-[BP]G-CTACCATCC)D(GGATGGTAGC) (nucleic acid)
Unique Ligands	BAP

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1AXU \| pdb_00001axu	Download File View File

SOLUTION NMR STRUCTURE OF THE [AP]DG ADDUCT OPPOSITE DA IN A DNA DUPLEX, NMR, 9 STRUCTURES

Gu, Z., Gorin, A.A., Krishnasami, R., Hingerty, B.E., Basu, A.K., Broyde, S., Patel, D.J.

(1999) Biochemistry 38: 10843-10854

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(CCATC-[AP]G-CTACC)D(GGTAGAGATGG) (nucleic acid)
Unique Ligands	AP

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1AXV \| pdb_00001axv	Download File View File

SOLUTION NMR STRUCTURE OF THE [BP]DA ADDUCT OPPOSITE DT IN A DNA DUPLEX, 6 STRUCTURES

Mao, B., Gu, Z., Gorin, A.A., Chen, J., Hingerty, B.E., Amid, S., Broyde, S., Geacintov, N.E., Patel, D.J.

(1999) Biochemistry 38: 10831-10842

Released	1998-07-01
Method	SOLUTION NMR
Macromolecule	DNA DUPLEX D(CTCTC-[BP]A-CTTCC)D(GGAAGTGAGAG) (nucleic acid)
Unique Ligands	BAP

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1C0Y \| pdb_00001c0y	Download File View File

SOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT POSITIONED OPPOSITE DA AT A TEMPLATE-PRIMER JUNCTION

Gu, Z., Gorin, A., Hingerty, B.E., Broyde, S., Patel, D.J.

(1999) Biochemistry 38: 10855-10870

Released	1999-08-31
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(APAPCPGPCPTPAPCPCPAPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPTPGPGPTPAPGP*C)-3') (nucleic acid)
Unique Ligands	AF

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1FJ5 \| pdb_00001fj5	Download File View File

TAMOXIFEN-DNA ADDUCT

Shimotakahara, S., Gorin, A., Kolbanovskiy, A., Kettani, A., Hingerty, B.E., Amin, S., Broyde, S., Geacintov, N., Patel, D.J.

(2000) J Mol Biology 302: 377-393

Released	2000-09-11
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPCPAPTPCPGPCPTPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPAPGPCPGPAPTPGPG)-3') (nucleic acid)
Unique Ligands	TAX

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1HWV \| pdb_00001hwv	Download File View File

MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES DNA ADDUCT CONFORMATION: A LINK TO TUMORIGENIC ACTIVITY

Patel, D.J., Lin, C.H., Geacintov, N.E., Broyde, S., Huang, X., Kolbanovskii, A., Hingerty, B.E., Amin, S.

(2001) J Mol Biology 306: 1059-1080

Released	2001-03-21
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPAPTPCPGPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPCPGPAPTPGPG)-3' (nucleic acid)
Unique Ligands	BPI

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1HX4 \| pdb_00001hx4	Download File View File

MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES DNA ADDUCT CONFORMATION: A LINK TO TUMORIGENIC ACTIVITY

Patel, D.J., Lin, C.H., Geacintov, N.E., Broyde, S., Huang, X., Kolbanovskii, A., Hingerty, B.E., Amin, S.

(2001) J Mol Biology 306: 1059-1080

Released	2001-03-21
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPAPTPCPGPCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPCPGPAPTPGPG)-3' (nucleic acid)
Unique Ligands	BPJ

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1PYJ \| pdb_00001pyj	Download File View File

Solution Structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11mer DNA duplex

Peterson, L.A., Vu, C., Hingerty, B.E., Broyde, S., Cosman, M.

(2003) Biochemistry 42: 13134-13144

Released	2004-04-20
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPAPTPAPTPGPGPCPCPC)-3' (nucleic acid) 5'-DGPGPGPCPCPAPTPAPTPGPG)-3' (nucleic acid)

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1Y9H \| pdb_00001y9h	Download File View File

Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement

Zhang, N., Lin, C., Huang, X., Kolbanovskiy, A., Hingerty, B.E., Amin, S., Broyde, S., Geacintov, N.E., Patel, D.J.

(2005) J Mol Biology 346: 951-965

Released	2005-03-22
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPAPTP(5CM)P(BPG)PCPTPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPAPGPCPGPAPTPGPG)-3' (nucleic acid)
Unique Ligands	BAP

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2ASD \| pdb_00002asd	Download File View File

oxoG-modified Insertion Ternary Complex

Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., Patel, D.J.

(2006) PLoS Biol 4: 1-18

Released	2006-01-10
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (protein) 5'-D(CPTAPAPCP(8OG)PCPTPAPCPCPAPTPCPCPAPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPTPGPGPAPTPGPGPTPAP(DDG))-3' (nucleic acid)
Unique Ligands	CA, DCP

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2ASJ \| pdb_00002asj	Download File View File

oxoG-modified Preinsertion Binary Complex

Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., Patel, D.J.

(2006) PLoS Biol 4: 1-18

Released	2006-01-10
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (protein) 5'-D(CPTPAPAPCP(8OG)CPTPAPCPCPAPTPCPCPAPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPTPGPGPAPTPGPGPTPAP(DDG))-3' (nucleic acid)
Unique Ligands	CA

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2ASL \| pdb_00002asl	Download File View File

oxoG-modified Postinsertion Binary Complex

Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., Patel, D.J.

(2006) PLoS Biol 4: 1-18

Released	2006-01-10
Method	X-RAY DIFFRACTION 2.65 Å
Organisms	Saccharolobus solfataricus
Macromolecule	DNA polymerase IV (protein) 5'-D(CPTAPAPCP(8OG)PCPTPAPCPCPAPTPCPCPAPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPTPGPGPAPTPGPGPTPAPGP*(DOC))-3' (nucleic acid)
Unique Ligands	CA

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2ATL \| pdb_00002atl	Download File View File

Unmodified Insertion Ternary Complex

Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., Patel, D.J.

(2006) PLoS Biol 4: 1-18

Released	2006-01-10
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Dpo4 polymerase IV (protein) 5'-D(CPTAPAPCPGPCPTPAPCPCPAPTPCPCPAPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPTPGPGPAPTPGPGPTPAP(DDG))-3' (nucleic acid)
Unique Ligands	CA, DCP

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2AU0 \| pdb_00002au0	Download File View File

Unmodified preinsertion binary complex

Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N.E., Patel, D.J.

(2006) PLoS Biol 4: 1-18

Released	2006-01-10
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Saccharolobus solfataricus
Macromolecule	Dpo4 polymerase IV (protein) 5'-D(CPTPAPAPCPGCPTPAPCPCPAPTPCPCPAPAPCPC)-3' (nucleic acid) 5'-D(GPGPTPTPGPGPAPTPGPGPTPAP(DDG))-3' (nucleic acid)
Unique Ligands	CA

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2LZK \| pdb_00002lzk	Download File View File

NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing

Tang, Y., Liu, Z., Ding, S., Lin, C.H., Cai, Y., Rodriguez, F.A., Sayer, J.M., Jerina, D.M., Amin, S., Broyde, S., Geacintov, N.E.

(2012) Biochemistry 51: 9751-9762

Released	2012-11-21
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPCPAPTPCPGPCPTPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPAPGPCPGPAPTPGPG)-3') (nucleic acid)
Unique Ligands	14L

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2MIV \| pdb_00002miv	Download File View File

NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations

Rodriguez, F.A., Liu, Z., Lin, C.H., Ding, S., Cai, Y., Kolbanovskiy, A., Kolbanovskiy, M., Amin, S., Broyde, S., Geacintov, N.E.

(2014) Biochemistry 53: 1827-1841

Released	2014-04-02
Method	SOLUTION NMR
Macromolecule	DNA_(5'-D(CPCPAPTPCPGPCPTPAPCPC)-3') (nucleic acid) DNA_(5'-D(GPGPTPAPGPGPAPTPGP*G)-3') (nucleic acid)
Unique Ligands	2QL

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2MIW \| pdb_00002miw	Download File View File

Nuclear magnetic resonance studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations

Rodriguez, F.A., Liu, Z., Lin, C.H., Ding, S., Cai, Y., Kolbanovskiy, A., Kolbanovskiy, M., Amin, S., Broyde, S., Geacintov, N.E.

(2014) Biochemistry 53: 1827-1841

Released	2014-04-02
Method	SOLUTION NMR
Macromolecule	DNA_(5'-D(CPCPAPTPCPGPCPTPAPCPC)-3') (nucleic acid) DNA_(5'-D(GPGPTPAPGPCPGPAPTPGPG)-3') (nucleic acid)
Unique Ligands	2QL

1AX6 | pdb_00001ax6

SOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT OPPOSITE A-2 DELETION SITE IN THE NARI HOT SPOT SEQUENCE CONTEXT; NMR, 6 STRUCTURES

1AX7 | pdb_00001ax7

SOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT POSITIONED AT A TEMPLATE-PRIMER JUNCTION, NMR, 6 STRUCTURES

1AXL | pdb_00001axl

SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES

1AXO | pdb_00001axo

STRUCTURAL ALIGNMENT OF THE (+)-TRANS-ANTI-[BP]DG ADDUCT POSITIONED OPPOSITE DC AT A DNA TEMPLATE-PRIMER JUNCTION, NMR, 6 STRUCTURES

1AXU | pdb_00001axu

SOLUTION NMR STRUCTURE OF THE [AP]DG ADDUCT OPPOSITE DA IN A DNA DUPLEX, NMR, 9 STRUCTURES

1AXV | pdb_00001axv

SOLUTION NMR STRUCTURE OF THE [BP]DA ADDUCT OPPOSITE DT IN A DNA DUPLEX, 6 STRUCTURES

1C0Y | pdb_00001c0y

SOLUTION STRUCTURE OF THE [AF]-C8-DG ADDUCT POSITIONED OPPOSITE DA AT A TEMPLATE-PRIMER JUNCTION

1FJ5 | pdb_00001fj5

TAMOXIFEN-DNA ADDUCT

1HWV | pdb_00001hwv

MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES DNA ADDUCT CONFORMATION: A LINK TO TUMORIGENIC ACTIVITY

1HX4 | pdb_00001hx4

MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES DNA ADDUCT CONFORMATION: A LINK TO TUMORIGENIC ACTIVITY

1PYJ | pdb_00001pyj

Solution Structure of an O6-[4-oxo-4-(3-pyridyl)butyl]guanine adduct in an 11mer DNA duplex

1Y9H | pdb_00001y9h

Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of a benzo[a]pyrene diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement

2ASD | pdb_00002asd

oxoG-modified Insertion Ternary Complex

2ASJ | pdb_00002asj

oxoG-modified Preinsertion Binary Complex

2ASL | pdb_00002asl

oxoG-modified Postinsertion Binary Complex

2ATL | pdb_00002atl

Unmodified Insertion Ternary Complex

2AU0 | pdb_00002au0

Unmodified preinsertion binary complex

2LZK | pdb_00002lzk

NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing

2MIV | pdb_00002miv

NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations

2MIW | pdb_00002miw

Nuclear magnetic resonance studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations

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Experimental Method

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Refinement Resolution (Å)

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Enzyme Classification Name

Symmetry Type

SCOP Classification

1AX6 | pdb_00001ax6

1AX7 | pdb_00001ax7

1AXL | pdb_00001axl

1AXO | pdb_00001axo

1AXU | pdb_00001axu

1AXV | pdb_00001axv

1C0Y | pdb_00001c0y

1FJ5 | pdb_00001fj5

1HWV | pdb_00001hwv

1HX4 | pdb_00001hx4

1PYJ | pdb_00001pyj

1Y9H | pdb_00001y9h

2ASD | pdb_00002asd

2ASJ | pdb_00002asj

2ASL | pdb_00002asl

2ATL | pdb_00002atl

2AU0 | pdb_00002au0

2LZK | pdb_00002lzk

2MIV | pdb_00002miv

2MIW | pdb_00002miw