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235,458 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Jerina, D.M."

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Search Summary

This query matches 11 Structures.

Refinements

Structure Determination Methodology

experimental (11)

Scientific Name of Source Organism

	Human immunodeficiency virus 1 (2)
	Mus musculus (2)
	Saccharolobus solfataricus P2 (2)
	synthetic construct (1)

Taxonomy

	Archaea (2)
	Eukaryota (2)
	Riboviria (2)
	other sequences (1)

Experimental Method

	SOLUTION NMR (7)
	X-RAY DIFFRACTION (4)

Polymer Entity Type

	DNA (11)
	Protein (4)

Refinement Resolution (Å)

	2.0 - 2.5 (1)
	2.5 - 3.0 (1)
	3.0 - 3.5 (2)

Release Date

	1995 - 1999 (2)
	2000 - 2004 (5)
	2005 - 2009 (3)
	2010 - 2014 (1)

Enzyme Classification Name

Transferases (4)

Symmetry Type

Asymmetric (4)

SCOP Classification

	All beta proteins (2)
	Multi-domain proteins (alpha and beta) (4)
	Alpha and beta proteins (a+b) (2)
	Alpha and beta proteins (a/b) (2)

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1 to 11 of 11 Structures

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1BPS \| pdb_00001bps	Download File View File

MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

Schwartz, J.S., Rice, J.S., Luxon, B.A., Sayer, J.M., Xie, G., Yeh, H.J.C., Liu, X., Jerina, D.M., Gorenstein, D.G.

(1997) Biochemistry 36: 11069-11076

Released	1998-08-19
Method	SOLUTION NMR
Organisms	synthetic construct
Macromolecule	DNA (5'-D(CPTPCPGPGPGPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPCP(BAP)APCPGPAPG)-3') (nucleic acid)
Unique Ligands	BAP

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1DXA \| pdb_00001dxa	Download File View File

BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

Yeh, H.J.C., Sayer, J.M., Liu, X., Altieri, A.S., Byrd, R.A., Lakshman, M.K., Yagi, H., Schurter, E.J., Gorenstein, D.G., Jerina, D.M.

(1995) Biochemistry 34: 13570-13581

Released	1995-12-07
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(CPTPCPGPGPGPAPCPC)-3') (nucleic acid) DNA (5'-D(GPGPTPCPAPCPGPAPG)-3') (nucleic acid)
Unique Ligands	BAP

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1FYY \| pdb_00001fyy	Download File View File

HPRT GENE MUTATION HOTSPOT WITH A BPDE2(10R) ADDUCT

Volk, D.E., Rice, J.S., Luxon, B.A., Yeh, H.J.C., Liang, C., Xie, G., Sayer, J.M., Jerina, D.M., Gorenstein, D.G.

(2000) Biochemistry 39: 14040-14053

Released	2000-12-06
Method	SOLUTION NMR
Macromolecule	5'-D(TPGPCPCPCPTPTPGPAPCPTPA)-3' (nucleic acid) HPRT DNA WITH BENZO[A]PYRENE-ADDUCTED DA7 (nucleic acid)
Unique Ligands	BAP

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1JDG \| pdb_00001jdg	Download File View File

Solution Structure of a Trans-Opened (10S)-dA Adduct of (+)-(7S,8R,9S,10R)-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully Complementary DNA Duplex

Pradhan, P., Tirumala, S., Liu, X., Sayer, J.M., Jerina, D.M., Yeh, H.J.C.

(2001) Biochemistry 40: 5870-5881

Released	2001-07-04
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPTPCPGPTPGPAPCPCPG)-3' (nucleic acid) 5'-D(CPGPGPTPCP(BPA)APCPGPAPGPG)-3' (nucleic acid)
Unique Ligands	BPA

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1N5Y \| pdb_00001n5y	Download File View File

HIV-1 Reverse Transcriptase Crosslinked to Post-Translocation AZTMP-Terminated DNA (Complex P)

Sarafianos, S.G., Clark Jr., A.D., Das, K., Tuske, S., Birktoft, J.J., Ilankumaran, P., Ramesha, A.R., Sayer, J.M., Jerina, D.M., Boyer, P.L., Hughes, S.H., Arnold, E.

(2002) EMBO J 21: 6614-6624

Released	2003-01-28
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Human immunodeficiency virus 1 Mus musculus
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MG

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1N6Q \| pdb_00001n6q	Download File View File

HIV-1 Reverse Transcriptase Crosslinked to pre-translocation AZTMP-terminated DNA (complex N)

Sarafianos, S.G., Clark Jr., A.D., Das, K., Tuske, S., Birktoft, J.J., Ilankumaran, I., Ramesha, A.R., Sayer, J.M., Jerina, D.M., Boyer, P.L., Hughes, S.H., Arnold, E.

(2002) EMBO J 21: 6614-6624

Released	2003-01-14
Method	X-RAY DIFFRACTION 3 Å
Organisms	Human immunodeficiency virus 1 Mus musculus
Macromolecule	Unique protein chains: 4 Unique nucleic acid chains: 2
Unique Ligands	MG

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1N8C \| pdb_00001n8c	Download File View File

Solution Structure of a Cis-Opened (10R)-N6-Deoxyadenosine Adduct of (9S,10R)-(9,10)-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex

Volk, D.E., Thiviyanathan, V., Rice, J.S., Luxon, B.A., Shah, J.H., Yagi, H., Sayer, J.M., Yeh, H.J.C., Jerina, D.M., Gorenstein, D.G.

(2003) Biochemistry 42: 1410-1420

Released	2003-02-14
Method	SOLUTION NMR
Macromolecule	5'-D(CPCPTPCPGPTPGPAPCPCPG)-3' (nucleic acid) 5'-D(CPGPGPTPCPAPCPGPAPGPG)-3' (nucleic acid)
Unique Ligands	TBC

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2IA6 \| pdb_00002ia6	Download File View File

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

Bauer, J., Ling, H., Sayer, J.M., Xing, G., Yagi, H., Jerina, D.M.

(2007) Proc Natl Acad Sci U S A 104: 14905-14910

Released	2007-09-11
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPA)-3' (nucleic acid) 5'-D(TPCPAPTPGPAPAPTPCPCPTPTPCPCPCPCPC)-3' (nucleic acid)
Unique Ligands	ATP, BAP, CA, EDO, GOL, PO4

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2IBK \| pdb_00002ibk	Download File View File

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

Bauer, J., Ling, H., Sayer, J.M., Xing, G., Yagi, H., Jerina, D.M.

(2007) Proc Natl Acad Sci U S A 104: 14905-14910

Released	2007-09-11
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Saccharolobus solfataricus P2
Macromolecule	DNA polymerase IV (protein) 5'-D(GPGPGPGPGPAPAPGPGPAPTPTPAPT)-3' (nucleic acid) 5'-D(TPCPAPTPGPAPAPTPCPCPTPTPCPCPCPCP*C)-3' (nucleic acid)
Unique Ligands	BAP, CA, EDO, GOL, POP

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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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2ROU \| pdb_00002rou	Download File View File

Stereospecific Conformations of N2-dG 1R-trans-anti-Benzo[c]phenanthrene DNA Adducts: 3'-Intercalation of the 1R Adduct and 5'-Minor Groove Orientation of the 1S Adduct in an Iterated (CG)3 Repeat

Wang, Y., Kroth, H., Yagi, H., Sayer, J.M., Kumar, S., Jerina, D.M., Stone, M.P.

(2008) Chem Res Toxicol 21: 1348-1358

Released	2009-03-03
Method	SOLUTION NMR
Macromolecule	DNA (5'-D(DAPDTPDCPDGPDCPDGPDCPDGPDGPDCPDAPDTPDG)-3') (nucleic acid) DNA (5'-D(DCPDAPDTPDGPDCPDCPDGPDCPDGPDCPDGPDAPDT)-3') (nucleic acid)
Unique Ligands	BPJ

1 to 11 of 11 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

1BPS | pdb_00001bps

MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

1DXA | pdb_00001dxa

BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA

1FYY | pdb_00001fyy

HPRT GENE MUTATION HOTSPOT WITH A BPDE2(10R) ADDUCT

1JDG | pdb_00001jdg

Solution Structure of a Trans-Opened (10S)-dA Adduct of (+)-(7S,8R,9S,10R)-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully Complementary DNA Duplex

1N5Y | pdb_00001n5y

HIV-1 Reverse Transcriptase Crosslinked to Post-Translocation AZTMP-Terminated DNA (Complex P)

1N6Q | pdb_00001n6q

HIV-1 Reverse Transcriptase Crosslinked to pre-translocation AZTMP-terminated DNA (complex N)

1N8C | pdb_00001n8c

Solution Structure of a Cis-Opened (10R)-N6-Deoxyadenosine Adduct of (9S,10R)-(9,10)-Epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a DNA Duplex

2IA6 | pdb_00002ia6

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

2IBK | pdb_00002ibk

Bypass of Major Benzopyrene-dG Adduct by Y-Family DNA Polymerase with Unique Structural Gap

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

2ROU | pdb_00002rou

Stereospecific Conformations of N2-dG 1R-trans-anti-Benzo[c]phenanthrene DNA Adducts: 3'-Intercalation of the 1R Adduct and 5'-Minor Groove Orientation of the 1S Adduct in an Iterated (CG)3 Repeat

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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

1BPS | pdb_00001bps

1DXA | pdb_00001dxa

1FYY | pdb_00001fyy

1JDG | pdb_00001jdg

1N5Y | pdb_00001n5y

1N6Q | pdb_00001n6q

1N8C | pdb_00001n8c

2IA6 | pdb_00002ia6

2IBK | pdb_00002ibk

2LZK | pdb_00002lzk

2ROU | pdb_00002rou