4R6M

Crystal Structure of DNA Duplex Containing Two Consecutive Mercury-mediated Base Pairs

• PDB DOI: https://doi.org/10.2210/pdb4R6M/pdb
• NAKB: 4R6M

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


• Deposited: 2014-08-26 Released: 2015-09-02 
• Deposition Author(s): Xu, C.Y., Yu, F., Wang, L.H., Zhao, Y., Lin, T., Fan, C.H., He, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 
  0.240 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal Structure of DNA Duplex Containing Two Consecutive Mercury-mediated Base Pairs

Xu, C.Y., Yu, F., Wang, L.H., Zhao, Y., Lin, T., Fan, C.H., He, J.H.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.42 kDa 
• Atom Count: 1,242 
• Modelled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3')	A, C, E	10	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3')	B, D, F	10	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	G [auth B], H [auth B], I [auth D], J [auth D], K [auth E], L [auth F]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free:  0.240 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.785	α = 90
b = 70.785	β = 90
c = 108.037	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Xu, C.Y., Yu, F., Wang, L.H., Zhao, Y., Lin, T., Fan, C.H., He, J.H.

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations