3GO3

Interactions of an echinomycin-DNA complex with manganese(II) ions

• PDB DOI: https://doi.org/10.2210/pdb3GO3/pdb
• NAKB: 3GO3

• Classification: DNA/ANTIBIOTIC
• Organism(s): Streptomyces echinatus
• Mutation(s): Yes 


• Deposited: 2009-03-18 Released: 2009-03-31 
• Deposition Author(s): Pfoh, R., Cuesta-Seijo, J.A., Sheldrick, G.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.196 
• R-Value Observed: 0.162 

Literature

Interaction of an Echinomycin-DNA Complex with Manganese Ion

Pfoh, R., Cuesta-Seijo, J.A., Sheldrick, G.M.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 660

• PubMed: 19574634 
• DOI: https://doi.org/10.1107/S1744309109019654
• Primary Citation of Related Structures:  
  3GO3


• PubMed Abstract: 
  

  The crystal structure of an echinomycin-d(ACGTACGT) duplex interacting with manganese(II) was solved by Mn-SAD using in-house data and refined to 1.1 A resolution against synchrotron data. This complex crystallizes in a different space group compared with related complexes and shows a different mode of base pairing next to the bis-intercalation site, suggesting that the energy difference between Hoogsteen and Watson-Crick pairing is rather small. The binding of manganese to N7 of guanine is only possible because of DNA unwinding induced by the echinomycin, which might help to explain the mode of action of the drug.

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Organizational Affiliation: 

Department of Structural Chemistry, University of Göttingen, 37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.38 kDa 
• Atom Count: 565 
• Modelled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ECHINOMYCIN	C, D	8	Streptomyces echinatus	Mutation(s): 2

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*GP*TP*AP*CP*GP*T)-3'	A, B	8	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUI	H [auth C], I [auth C], J [auth D], K [auth D]	2-CARBOXYQUINOXALINE C9 H6 N2 O2 UPUZGXILYFKSGE-UHFFFAOYSA-N
PEG	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN	E [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MVA	C, D	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000491	C, D	Echinomycin	Cyclic depsipeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.196 
• R-Value Observed: 0.162 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.544	α = 90
b = 26.544	β = 90
c = 162.129	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
SHELXL-97	refinement
XDS	data reduction
SAINT	data reduction
SADABS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Pfoh, R., Cuesta-Seijo, J.A., Sheldrick, G.M.

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-06-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2012-12-12
  Changes: Other