3V6H | pdb_00003v6h

Replication of N2,3-Ethenoguanine by DNA Polymerases

PDB DOI: https://doi.org/10.2210/pdb3V6H/pdb
NAKB: 3V6H

Classification: TRANSFERASE/DNA
Organism(s): Saccharolobus solfataricus P2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-12-19 Released: 2012-04-25
Deposition Author(s): Zhao, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.267 (Depositor), 0.284 (DCC)
R-Value Work:
0.215 (Depositor), 0.230 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Replication of n(2) ,3-ethenoguanine by DNA polymerases.

Zhao, L., Christov, P.P., Kozekov, I.D., Pence, M.G., Pallan, P.S., Rizzo, C.J., Egli, M., Guengerich, F.P.

(2012) Angew Chem Int Ed Engl 51: 5466-5469

PubMed: 22488769 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.201109004
Primary Citation Related Structures:
3V6H, 3V6J, 3V6K

Organizational Affiliation

Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.

Macromolecule Content

Total Structure Weight: 100.1 kDa
Atom Count: 6,867
Modeled Residue Count: 738
Deposited Residue Count: 758
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	E [auth A], F [auth B]	348	Saccharolobus solfataricus P2	Mutation(s): 0 Gene Names: dbh, dpo4, SSO2448 EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W02 Go to UniProtKB: Q97W02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97W02
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(TPCPAPCP(EFG)PGPAPAPTPCPCPTPTPCPCPCPCPC)-3')	A [auth T], C	18	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(GPGGPGPGPAPAPGPGPAPTPTP*(DOC))-3')	B [auth P], D	13	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCP Query on DCP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	H [auth A], L [auth B]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₃ P₃ RGWHQCVHVJXOKC-SHYZEUOFSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain K [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] mmCIF format, chain G [auth D] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B]	G [auth D], K [auth A], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth D] Focus chain K [auth A] Focus chain N [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A]	I [auth A], J [auth A], M [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.267 (Depositor), 0.284 (DCC)
R-Value Work: 0.215 (Depositor), 0.230 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.532	α = 90
b = 111.267	β = 102.68
c = 98.942	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-04-25

Deposition Author(s):

Zhao, L.

Revision History (Full details and data files)

Version 1.0: 2012-04-25
Type: Initial release
Version 1.1: 2012-06-06
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description