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), 0.260 (DCC)
R-Value Work:
0.214 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

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 | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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), 0.260 (DCC)
R-Value Work: 0.214 (Depositor), 0.220 (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

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

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.