Sodium in PDB 1p4y: Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions

The structure of Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions, PDB code: 1p4y was solved by F.A.Hays, J.M.Vargason, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.50 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.513, 24.179, 37.004, 90.00, 110.01, 90.00
R / Rfree (%)	22.9 / 26

The binding sites of Sodium atom in the Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions (pdb code 1p4y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions, PDB code: 1p4y:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na21 b:1.0 occ:1.00 O A:HOH25 2.5 1.0 1.0 O A:HOH109 2.5 8.7 1.0 O A:HOH56 2.7 18.8 1.0 O A:HOH24 2.8 4.6 1.0 NA A:NA49 3.4 11.9 1.0 O A:HOH95 4.1 9.9 1.0 N2 A:DG10 4.5 8.6 1.0 N2 A:DG9 4.5 9.8 1.0 O A:HOH88 4.7 9.7 1.0

Sodium binding site 2 out of 4 in the Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na36 b:9.8 occ:1.00 O5' A:DC1 2.5 5.3 1.0 O A:HOH82 2.6 13.7 1.0 C6 A:DC1 3.3 5.8 1.0 C5' A:DC1 3.4 5.1 1.0 N4 A:DC2 3.6 7.0 1.0 O4' A:DC1 3.9 5.1 1.0 C5 A:DC1 3.9 5.9 1.0 N1 A:DC1 4.2 5.6 1.0 C4' A:DC1 4.2 5.3 1.0 C5 A:DC2 4.2 7.0 1.0 C4 A:DC2 4.3 7.1 1.0 C1' A:DC1 4.4 5.5 1.0 C2' A:DC1 4.6 5.4 1.0 O A:HOH33 4.9 2.0 1.0 C3' A:DC1 4.9 5.4 1.0

Sodium binding site 3 out of 4 in the Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions within 5.0Å range: probe atom residue distance (Å) B Occ A:Na49 b:11.9 occ:1.00 O A:HOH56 2.6 18.8 1.0 N3 A:DG10 2.9 9.0 1.0 NA A:NA21 3.4 1.0 1.0 N2 A:DG10 3.4 8.6 1.0 C2 A:DG10 3.6 8.9 1.0 O4' A:DG10 3.8 9.1 1.0 C1' A:DG10 3.9 9.2 1.0 O A:HOH24 4.0 4.6 1.0 C4 A:DG10 4.0 9.2 1.0 O A:HOH95 4.2 9.9 1.0 N9 A:DG10 4.4 9.2 1.0 O A:HOH109 4.6 8.7 1.0 O A:HOH25 4.6 1.0 1.0 O A:HOH47 4.7 20.8 1.0 N2 A:DG9 4.8 9.8 1.0 C4' A:DG10 4.9 9.2 1.0 N1 A:DG10 5.0 9.2 1.0

Sodium binding site 4 out of 4 in the Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Effect of Sequence on the Conformational Geometry of Dna Holliday Junctions within 5.0Å range: probe atom residue distance (Å) B Occ B:Na55 b:11.6 occ:1.00 O4' B:DG19 2.6 10.3 1.0 O B:HOH75 2.8 19.4 1.0 C4' B:DG19 3.2 10.1 1.0 C1' B:DG19 3.4 10.5 1.0 N3 B:DG19 3.7 10.6 1.0 O3' B:DG19 3.9 10.8 1.0 C3' B:DG19 4.1 10.3 1.0 C5' B:DG19 4.2 9.3 1.0 N9 B:DG19 4.3 10.5 1.0 O A:HOH71 4.3 6.0 1.0 O B:HOH79 4.3 12.4 1.0 C4 B:DG19 4.3 10.6 1.0 C2' B:DG19 4.5 10.4 1.0 O A:HOH51 4.5 24.6 1.0 C2 B:DG19 4.6 10.7 1.0 O4' B:DG20 4.6 10.1 1.0 N2 B:DG19 4.7 10.8 1.0 O2 B:DC18 4.9 5.4 1.0 C5' B:DG20 4.9 10.3 1.0

F.A.Hays, J.M.Vargason, P.S.Ho. Effect of Sequence on the Conformation of Dna Holliday Junctions Biochemistry V. 42 9586 2003.
ISSN: ISSN 0006-2960
PubMed: 12911300
DOI: 10.1021/BI0346603