Potassium in PDB 4r47: Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N)

The structure of Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N), PDB code: 4r47 was solved by P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.28 / 1.85
Space group	P 1 21/n 1
Cell size a, b, c (Å), α, β, γ (°)	28.500, 47.300, 46.800, 90.00, 97.02, 90.00
R / Rfree (%)	28.3 / 30.4

The structure of Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N) also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Potassium atom in the Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N) (pdb code 4r47). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N), PDB code: 4r47:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N) within 5.0Å range: probe atom residue distance (Å) B Occ A:K1101 b:5.5 occ:1.00 O6 A:DG1001 2.7 4.8 1.0 O6 A:DG1012 2.7 6.5 1.0 O6 B:DG2010 2.7 6.0 1.0 O6 A:DG1011 2.8 6.8 1.0 O6 B:DG2003 2.8 5.4 1.0 O6 B:DG2004 2.8 5.0 1.0 O6 B:DG2009 2.9 6.8 1.0 O6 A:DG1002 2.9 4.6 1.0 K A:K1103 3.3 5.5 1.0 K B:K2101 3.5 8.4 1.0 C6 A:DG1011 3.6 7.2 1.0 C6 B:DG2003 3.6 5.7 1.0 C6 A:DG1001 3.6 5.0 1.0 C6 B:DG2010 3.7 7.0 1.0 C6 A:DG1012 3.7 7.0 1.0 C6 B:DG2004 3.7 5.4 1.0 C6 B:DG2009 3.8 7.4 1.0 C6 A:DG1002 3.8 4.8 1.0 N1 A:DG1011 3.9 6.8 1.0 N1 B:DG2003 3.9 5.7 1.0 N1 A:DG1001 4.0 4.9 1.0 N1 B:DG2004 4.0 5.2 1.0 N1 B:DG2010 4.0 6.4 1.0 N1 A:DG1012 4.0 6.8 1.0 N1 A:DG1002 4.1 4.5 1.0 N1 B:DG2009 4.2 6.9 1.0 C5 A:DG1011 4.7 7.3 1.0 C5 B:DG2003 4.8 6.0 1.0 C5 A:DG1001 4.9 5.0 1.0 C5 B:DG2010 4.9 7.1 1.0 C5 B:DG2009 4.9 7.3 1.0

Potassium binding site 2 out of 5 in the Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N) within 5.0Å range: probe atom residue distance (Å) B Occ A:K1102 b:6.1 occ:1.00 O6 B:DG2001 2.7 7.1 1.0 O6 B:DG2012 2.8 8.0 1.0 O6 B:DG2011 2.8 6.5 1.0 O6 A:DG1004 2.8 8.3 1.0 O6 A:DG1009 2.8 7.0 1.0 O6 A:DG1010 2.8 7.3 1.0 O6 A:DG1003 2.9 5.1 1.0 O6 B:DG2002 2.9 5.9 1.0 K A:K1103 3.4 5.5 1.0 C6 B:DG2011 3.6 7.3 1.0 C6 B:DG2001 3.6 7.2 1.0 K A:K1104 3.7 12.5 1.0 C6 A:DG1003 3.7 5.2 1.0 C6 A:DG1009 3.7 7.8 1.0 C6 A:DG1010 3.7 7.8 1.0 C6 B:DG2012 3.7 8.7 1.0 C6 A:DG1004 3.7 8.2 1.0 C6 B:DG2002 3.9 6.2 1.0 N1 B:DG2011 3.9 7.2 1.0 N1 B:DG2001 3.9 7.4 1.0 N1 A:DG1003 4.0 4.9 1.0 N1 A:DG1004 4.0 7.9 1.0 N1 A:DG1009 4.0 7.7 1.0 N1 A:DG1010 4.1 7.5 1.0 N1 B:DG2012 4.1 8.7 1.0 N1 B:DG2002 4.2 6.3 1.0 C5 B:DG2011 4.7 7.9 1.0 C5 A:DG1003 4.8 5.2 1.0 C5 B:DG2001 4.9 7.5 1.0 C5 A:DG1009 4.9 8.0 1.0 C5 A:DG1010 5.0 7.9 1.0 C5 B:DG2012 5.0 9.3 1.0

Potassium binding site 3 out of 5 in the Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N) within 5.0Å range: probe atom residue distance (Å) B Occ A:K1103 b:5.5 occ:1.00 O6 A:DG1002 2.6 4.6 1.0 O6 B:DG2010 2.7 6.0 1.0 O6 B:DG2003 2.8 5.4 1.0 O6 A:DG1003 2.8 5.1 1.0 O6 B:DG2002 2.8 5.9 1.0 O6 A:DG1010 2.8 7.3 1.0 O6 A:DG1011 2.9 6.8 1.0 O6 B:DG2011 2.9 6.5 1.0 K A:K1101 3.3 5.5 1.0 K A:K1102 3.4 6.1 1.0 C6 A:DG1002 3.5 4.8 1.0 C6 B:DG2010 3.6 7.0 1.0 C6 B:DG2002 3.6 6.2 1.0 C6 A:DG1010 3.7 7.8 1.0 C6 B:DG2003 3.8 5.7 1.0 C6 A:DG1003 3.8 5.2 1.0 N1 A:DG1002 3.8 4.5 1.0 C6 A:DG1011 3.9 7.2 1.0 N1 B:DG2010 3.9 6.4 1.0 C6 B:DG2011 3.9 7.3 1.0 N1 A:DG1010 3.9 7.5 1.0 N1 B:DG2002 3.9 6.3 1.0 N1 A:DG1011 4.1 6.8 1.0 N1 B:DG2011 4.2 7.2 1.0 N1 B:DG2003 4.2 5.7 1.0 N1 A:DG1003 4.3 4.9 1.0 C5 A:DG1002 4.7 4.8 1.0 C5 B:DG2010 4.8 7.1 1.0 C5 B:DG2002 4.8 6.6 1.0 C5 A:DG1010 4.9 7.9 1.0

Potassium binding site 4 out of 5 in the Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N) within 5.0Å range: probe atom residue distance (Å) B Occ A:K1104 b:12.5 occ:1.00 O A:HOH1236 2.6 12.0 1.0 O2 A:DT1007 2.7 8.3 1.0 O2 A:DT1005 2.8 14.6 1.0 O6 B:DG2012 2.9 8.0 1.0 O A:HOH1208 3.0 16.5 1.0 O6 A:DG1009 3.0 7.0 1.0 O6 A:DG1004 3.1 8.3 1.0 O6 B:DG2001 3.2 7.1 1.0 C6 B:DG2012 3.6 8.7 1.0 C2 A:DT1007 3.7 8.9 1.0 K A:K1102 3.7 6.1 1.0 C2 A:DT1005 3.7 14.7 1.0 C6 A:DG1009 3.8 7.8 1.0 N3 A:DT1005 3.8 16.1 1.0 C6 A:DG1004 3.8 8.2 1.0 N3 A:DT1007 3.9 9.0 1.0 N1 B:DG2012 4.0 8.7 1.0 C6 B:DG2001 4.0 7.2 1.0 N1 A:DG1009 4.1 7.7 1.0 O2 A:DT1006 4.2 11.5 1.0 N1 A:DG1004 4.3 7.9 1.0 N1 B:DG2001 4.3 7.4 1.0 C5 B:DG2012 4.7 9.3 1.0 C2 A:DT1006 4.8 10.8 1.0 C5 A:DG1004 4.8 8.0 1.0 N1 A:DT1007 4.9 9.3 1.0 N3 A:DT1006 5.0 10.8 1.0 N1 A:DT1005 5.0 14.8 1.0

Potassium binding site 5 out of 5 in the Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Racemic Crystal Structure of A Bimolecular Dna G-Quadruplex (P21/N) within 5.0Å range: probe atom residue distance (Å) B Occ B:K2101 b:8.4 occ:1.00 O2 B:DT2007 2.7 6.0 1.0 O6 B:DG2009 2.8 6.8 1.0 O6 A:DG1012 2.8 6.5 1.0 O B:HOH2222 2.8 10.8 1.0 O B:HOH2242 2.9 10.0 1.0 O6 B:DG2004 2.9 5.0 1.0 O2 B:DT2005 3.0 8.5 1.0 O6 A:DG1001 3.0 4.8 1.0 K A:K1101 3.5 5.5 1.0 C6 A:DG1012 3.5 7.0 1.0 C2 B:DT2007 3.6 6.5 1.0 C6 B:DG2009 3.6 7.4 1.0 C6 B:DG2004 3.7 5.4 1.0 C6 A:DG1001 3.8 5.0 1.0 C2 B:DT2005 3.8 9.1 1.0 N1 B:DG2009 3.9 6.9 1.0 N1 A:DG1012 3.9 6.8 1.0 N3 B:DT2007 3.9 6.6 1.0 N3 B:DT2005 3.9 9.2 1.0 N1 A:DG1001 4.1 4.9 1.0 N1 B:DG2004 4.2 5.2 1.0 O2 B:DT2006 4.4 8.4 1.0 C5 A:DG1012 4.6 7.3 1.0 C5 B:DG2004 4.8 5.7 1.0 N1 B:DT2007 4.8 6.7 1.0 O B:HOH2205 4.8 11.8 1.0 C5 B:DG2009 4.9 7.3 1.0 C2 B:DT2006 5.0 9.2 1.0

P.K.Mandal, G.W.Collie, B.Kauffmann, I.Huc. Racemic Dna Crystallography. Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25358289
DOI: 10.1002/ANIE.201409014