2RVP | pdb_00002rvp

Solution structure of DNA Containing Metallo-Base-Pair

• PDB DOI: https://doi.org/10.2210/pdb2RVP/pdb
• BMRB: 11608
• NAKB: 2RVP

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


• Deposited: 2016-03-22 Released: 2016-08-31 
• Deposition Author(s): Dairaku, T., Furuita, K., Sato, H., Sebera, J., Nakashima, K., Kondo, J., Yamanaka, D., Kondo, Y., Okamoto, I., Ono, A., Sychrovsky, V., Kojima, C., Tanaka, Y.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.

Dairaku, T., Furuita, K., Sato, H., Sebera, J., Nakashima, K., Kondo, J., Yamanaka, D., Kondo, Y., Okamoto, I., Ono, A., Sychrovsky, V., Kojima, C., Tanaka, Y.

(2016) Chemistry 22: 13028-13031

• PubMed: 27505707 
• DOI: https://doi.org/10.1002/chem.201603048
• Primary Citation Related Structures: 
  2RVP


• PubMed Abstract: 
  

  The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the C-Ag(I) -C base pair evidenced the N3-Ag(I) -N3 linkage in C-Ag(I) -C. The triplet resonances of the N4 atoms in C-Ag(I) -C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2 ), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I) -DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I) -C (-18.3±3.0°). The (109) Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (δ((109) Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I) -C base pair.

---

Organizational Affiliation: 
• School of Pharmaceutical Sciences, Ohu University, 31-1 Misumido, Tomita-machi, Koriyama, Fukushima, 963-8611, Japan. [e-mail].
Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan. [e-mail].
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Application, Bruker BioSpin K. K., 3-9 Moriya-cho, Kanagawa-ku, Yokohama, Kanagawa, 221-0022, Japan.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, 16610, Praha 6, Czech Republic.
Faculty of Phamaceutical Scienes, Tokushima Bunri University, Yamashiro-cho, Tokushima, 770-8514, Japan.
Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo, 102-8554, Japan.
Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
Department of Material & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, Kanagawa, 221-8686, Japan.
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 2, 16610, Praha 6, Czech Republic. [e-mail].
Czech Technical University in Prague, Faculty of Electrical Engineering, Department of Electrotechnology, Technická 2, 166 27, Praha 6, Czech Republic. [e-mail].
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. [e-mail].
Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan. [e-mail].
Faculty of Phamaceutical Scienes, Tokushima Bunri University, Yamashiro-cho, Tokushima, 770-8514, Japan. [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.24 kDa 
• Atom Count: 607 
• Modeled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*AP*TP*AP*TP*AP*CP*TP*TP*AP*AP*TP*TP*A)-3')	A [auth 1]	15	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*AP*TP*TP*AP*AP*CP*TP*AP*TP*AP*TP*TP*A)-3')	B [auth 2]	15	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG	C [auth 1]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Dairaku, T., Furuita, K., Sato, H., Sebera, J., Nakashima, K., Kondo, J., Yamanaka, D., Kondo, Y., Okamoto, I., Ono, A., Sychrovsky, V., Kojima, C., Tanaka, Y.

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references