7EAY | pdb_00007eay

DNA containing Cu(II)-mediated 4-N-carboxymethylcytosine base pairs

PDB DOI: https://doi.org/10.2210/pdb7EAY/pdb
NAKB: 7EAY

Classification: DNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2021-03-08 Released: 2022-03-09
Deposition Author(s): Kondo, J., Terashima, A., Yoshimura, A., Tada, Y., Ono, A.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.253 (Depositor), 0.267 (DCC)
R-Value Work:
0.214 (Depositor), 0.235 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7EAY

This is version 1.1 of the entry. See complete history.

Literature

DNA containing Cu(II)-mediated 4-N-carboxymethylcytosine base pairs

Kondo, J., Terashima, A., Yoshimura, A., Tada, Y., Ono, A.

To be published.

Macromolecule Content

Total Structure Weight: 48.6 kDa
Atom Count: 3,208
Modeled Residue Count: 144
Deposited Residue Count: 144
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(GPGPAPCPCP(J0X)P(J0X)PGPGPTPCPC)-3')	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NCO Query on NCO Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain TA [auth K] SDF format, chain T [auth C] SDF format, chain SA [auth K] SDF format, chain PA [auth J] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain NA [auth I] SDF format, chain MA [auth I] SDF format, chain LA [auth I] SDF format, chain HA [auth G] SDF format, chain GA [auth G] SDF format, chain CA [auth E] SDF format, chain BA [auth E] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain SA [auth K] MOL2 format, chain PA [auth J] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth I] MOL2 format, chain MA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain HA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain SA [auth K] mmCIF format, chain PA [auth J] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth I] mmCIF format, chain MA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain HA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] CA [auth E] GA [auth G] HA [auth G] AA [auth E], BA [auth E], CA [auth E], GA [auth G], HA [auth G], LA [auth I], MA [auth I], NA [auth I], O [auth A], P [auth A], PA [auth J], SA [auth K], T [auth C], TA [auth K], U [auth C], V [auth C], Z [auth E]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth J] Focus chain SA [auth K] Focus chain T [auth C] Focus chain TA [auth K] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth J] Focus chain SA [auth K] Focus chain T [auth C] Focus chain TA [auth K] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth E]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain S [auth C] SDF format, chain RA [auth K] SDF format, chain R [auth C] SDF format, chain QA [auth K] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain KA [auth I] SDF format, chain JA [auth I] SDF format, chain FA [auth G] SDF format, chain EA [auth G] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth K] MOL2 format, chain R [auth C] MOL2 format, chain QA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain FA [auth G] MOL2 format, chain EA [auth G] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth K] mmCIF format, chain R [auth C] mmCIF format, chain QA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain FA [auth G] mmCIF format, chain EA [auth G]	EA [auth G] FA [auth G] JA [auth I] KA [auth I] M [auth A] EA [auth G], FA [auth G], JA [auth I], KA [auth I], M [auth A], N [auth A], QA [auth K], R [auth C], RA [auth K], S [auth C], X [auth E], Y [auth E]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Focus chain FA [auth G] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain QA [auth K] Focus chain R [auth C] Focus chain RA [auth K] Focus chain S [auth C] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain EA [auth G] Focus chain FA [auth G] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain QA [auth K] Focus chain R [auth C] Focus chain RA [auth K] Focus chain S [auth C] Focus chain X [auth E] Focus chain Y [auth E]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain W [auth D] MOL2 format, chain W [auth D] mmCIF format, chain W [auth D]	W [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain W [auth D] Interactions & Density Focus chain W [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain OA [auth I] SDF format, chain IA [auth H] SDF format, chain DA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain OA [auth I] MOL2 format, chain IA [auth H] MOL2 format, chain DA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain OA [auth I] mmCIF format, chain IA [auth H] mmCIF format, chain DA [auth E]	DA [auth E], IA [auth H], OA [auth I], Q [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain IA [auth H] Focus chain OA [auth I] Focus chain Q [auth A] Interactions & Density Focus chain DA [auth E] Focus chain IA [auth H] Focus chain OA [auth I] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253 (Depositor), 0.267 (DCC)
R-Value Work: 0.214 (Depositor), 0.235 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.923	α = 90
b = 155.333	β = 90
c = 80.627	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
SOLVE	phasing
PHENIX	refinement
XSCALE	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24245037

Revision History (Full details and data files)

Version 1.0: 2022-03-09
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.