RCSB PDB: Search

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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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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1CR3 \| pdb_00001cr3	Download File View File

SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX

Suri, A.K., Mao, B., Amin, S., Geacintov, N.E., Patel, D.J.

(1999) J Mol Biology 292: 289-307

Released	2000-02-18
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPTPCPTPCPAPCPTPTPCPC)-3') (nucleic acid) DNA (5'-D(GPGPAPAPGPTPGPAPGPAPG)-3') (nucleic acid)
Unique Ligands	BC

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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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1XC9 \| pdb_00001xc9	Download File View File

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

Hsu, G.W., Huang, X., Luneva, N.P., Geacintov, N.E., Beese, L.S.

(2005) J Biological Chem 280: 3764-3770

Released	2004-12-14
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	DNA polymerase I (protein) DNA primer strand (nucleic acid) DNA template strand with benzo[a]pyrene adduct (nucleic acid)
Unique Ligands	BAP, MG, SO4
Unique branched monosaccharides	FRU, GLC

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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

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5WM1 \| pdb_00005wm1	Download File View File

Structure of the 10S (+)-trans-BP-dG modified Rev1 ternary complex

Rechkoblit, O., Kolbanovsky, A., Landes, H., Geacintov, N.E., Aggarwal, A.K.

(2017) Nat Commun 8: 965-965

Released	2017-10-25
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	DNA repair protein REV1 (protein) DNA (5'-D(GPGPGPGPTPGPTPGPGPTPAP(DDG))-3') (nucleic acid) DNA (5'-D(PAPTPCPGPCPTPAPCPCPAPCPAPCPCPCPC)-3') (nucleic acid)
Unique Ligands	BAP, DCP, EDO, GOL, MG, PEG

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5WM8 \| pdb_00005wm8	Download File View File

Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex

Rechkoblit, O., Kolbanovsky, A., Landes, H., Geacintov, N.E., Aggarwal, A.K.

(2017) Nat Commun 8: 965-965

Released	2017-10-25
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	DNA repair protein REV1 (protein) DNA (5'-D(GPGPGPGPTPGPTPGPGPTPAP(DDG))-3') (nucleic acid) DNA (5'-D(PAPTPCPGPCPTPAPCPCPAPCPAPCPCPCPC)-3') (nucleic acid)
Unique Ligands	BAP, DCP, EDO, GOL, MG, PEG

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5WMB \| pdb_00005wmb	Download File View File

Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex (the BP residue is disordered)

Rechkoblit, O., Kolbanovsky, A., Landes, H., Geacintov, N.E., Aggarwal, A.K.

(2017) Nat Commun 8: 965-965

Released	2017-10-25
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharomyces cerevisiae S288C synthetic construct
Macromolecule	DNA repair protein REV1 (protein) DNA (5'-D(GPGPGPGPTPGPTPGPGPTPAP(DDG))-3') (nucleic acid) DNA (5'-D(PAPTPCPGPCPTPAPCPCPAPCPAPCPCP*C)-3') (nucleic acid)
Unique Ligands	DCP, EDO, GOL, MG, PEG

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

1AXV | pdb_00001axv

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

1CR3 | pdb_00001cr3

SOLUTION CONFORMATION OF THE (+)TRANS-ANTI-BENZO[G]CHRYSENE-DA ADDUCT OPPOSITE DT IN A DNA DUPLEX

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

1XC9 | pdb_00001xc9

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

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

5WM1 | pdb_00005wm1

Structure of the 10S (+)-trans-BP-dG modified Rev1 ternary complex

5WM8 | pdb_00005wm8

Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex

5WMB | pdb_00005wmb

Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex (the BP residue is disordered)

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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

1AXL | pdb_00001axl

1AXO | pdb_00001axo

1AXV | pdb_00001axv

1CR3 | pdb_00001cr3

1HWV | pdb_00001hwv

1HX4 | pdb_00001hx4

1XC9 | pdb_00001xc9

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

5WM1 | pdb_00005wm1

5WM8 | pdb_00005wm8

5WMB | pdb_00005wmb