Summary information

PDB id
4r47
Class
DNA
Method
X-ray (1.85 Å)
Summary
Racemic crystal structure of a bimolecular DNA g-quadruplex (p21-n)
Reference
Mandal PK, Collie GW, Kauffmann B, Huc I (2014): "Racemic DNA crystallography." Angew.Chem.Int.Ed.Engl., 53, 14424-14427. doi: 10.1002/anie.201409014.
Abstract
Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UDDU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.258 type=other  nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.159 type=planar nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.130 type=planar nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
 4 glyco-bond=-ss- sugar=---. groove=w-n- planarity=0.267 type=bowl   nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
 4  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012
  step#1  mm(<>,outward)  area=13.22 rise=3.47 twist=18.1
  step#2  pp(><,inward)   area=18.49 rise=3.57 twist=36.6
  step#3  mm(<>,outward)  area=14.06 rise=3.49 twist=17.3
  strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1001,A.DG1002,A.DG1003,A.DG1004
  strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG2004,B.DG2003,B.DG2002,B.DG2001
  strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG1012,A.DG1011,A.DG1010,A.DG1009
  strand#4 DNA glyco-bond=s-s- sugar=---. nts=4 GGGG B.DG2009,B.DG2010,B.DG2011,B.DG2012

Download PDB file
Interactive view in 3Dmol.js
3 stacking diagrams 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
  step#1  mm(<>,outward)  area=13.22 rise=3.47 twist=18.1

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
  step#2  pp(><,inward)   area=18.49 rise=3.57 twist=36.6

Download PDB file
Interactive view in 3Dmol.js

 
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
 4  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012
  step#3  mm(<>,outward)  area=14.06 rise=3.49 twist=17.3

Download PDB file
Interactive view in 3Dmol.js

List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011
 4  glyco-bond=-ss- sugar=---. groove=w-n- WC-->Major nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012
  step#1  mm(<>,outward)  area=13.22 rise=3.47 twist=18.1
  step#2  pp(><,inward)   area=18.49 rise=3.57 twist=36.6
  step#3  mm(<>,outward)  area=14.06 rise=3.49 twist=17.3
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1001,A.DG1002,A.DG1003,A.DG1004
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG2004,B.DG2003,B.DG2002,B.DG2001
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG1012,A.DG1011,A.DG1010,A.DG1009
  strand#4  U DNA glyco-bond=s-s- sugar=---. nts=4 GGGG B.DG2009,B.DG2010,B.DG2011,B.DG2012
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT1005,A.DT1006,A.DT1007,A.DT1008
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT2005,B.DT2006,B.DT2007,B.DT2008

Download PDB file
Interactive view in 3Dmol.js