Sodium in PDB 1jb7: Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex

The structure of Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex, PDB code: 1jb7 was solved by M.P.Horvath, S.C.Schultz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.86
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.100, 93.100, 421.800, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 24.6

The structure of Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex (pdb code 1jb7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex, PDB code: 1jb7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1001 b:31.6 occ:1.00 O6 G:DG9 2.3 37.8 1.0 O H:HOH500 2.4 50.5 1.0 O6 H:DG12 2.4 33.8 1.0 O2 G:DT7 2.5 29.7 1.0 O6 G:DG4 2.5 30.3 1.0 O6 H:DG1 2.7 31.7 1.0 O2 G:DT5 3.3 29.5 1.0 C6 G:DG9 3.3 39.2 1.0 C6 G:DG4 3.3 31.7 1.0 C6 H:DG12 3.4 36.6 1.0 C2 G:DT7 3.4 31.6 1.0 C6 H:DG1 3.5 34.1 1.0 N1 G:DG4 3.6 29.8 1.0 N1 G:DG9 3.7 37.4 1.0 N1 H:DG12 3.8 37.0 1.0 N3 G:DT7 3.8 32.3 1.0 NA H:NA1002 3.8 36.7 1.0 N1 H:DG1 3.9 35.4 1.0 C2 G:DT5 4.1 29.9 1.0 N3 G:DT5 4.2 28.8 1.0 O6 H:DG11 4.3 33.7 1.0 C5 G:DG4 4.6 30.6 1.0 C5 G:DG9 4.6 40.2 1.0 N1 G:DT7 4.6 34.4 1.0 O2 G:DT6 4.6 33.0 1.0 C5 H:DG1 4.7 34.4 1.0 C5 H:DG12 4.7 38.0 1.0 O G:HOH499 4.8 44.5 1.0 C6 H:DG11 4.8 36.6 1.0 C2 G:DG4 4.9 30.5 1.0 O6 G:DG10 4.9 36.5 1.0 O6 G:DG3 4.9 28.7 1.0

Sodium binding site 2 out of 4 in the Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1003 b:44.1 occ:1.00 O6 H:DG3 2.1 32.7 1.0 O6 G:DG11 2.3 43.4 1.0 O6 H:DG10 2.4 37.5 1.0 O6 G:DG2 2.4 35.9 1.0 O6 G:DG1 2.8 42.4 1.0 C6 H:DG3 3.2 33.8 1.0 C6 G:DG11 3.3 44.8 1.0 C6 H:DG10 3.4 39.1 1.0 C6 G:DG2 3.4 36.2 1.0 O6 H:DG2 3.4 33.4 1.0 N1 H:DG3 3.6 31.5 1.0 C6 G:DG1 3.6 42.2 1.0 N1 G:DG11 3.6 45.4 1.0 N1 H:DG10 3.6 38.5 1.0 O6 H:DG4 3.7 35.0 1.0 N1 G:DG2 3.7 35.9 1.0 O6 H:DG9 3.7 42.3 1.0 NA H:NA1004 4.0 40.1 1.0 C6 H:DG2 4.0 33.4 1.0 N1 G:DG1 4.0 41.8 1.0 N1 H:DG4 4.2 34.8 1.0 C6 H:DG4 4.3 36.2 1.0 NA H:NA1002 4.3 36.7 1.0 O6 G:DG10 4.3 36.5 1.0 N1 G:DG10 4.4 37.7 1.0 O6 G:DG12 4.5 40.4 1.0 C5 H:DG3 4.5 32.8 1.0 N1 H:DG2 4.5 33.0 1.0 C6 G:DG10 4.6 38.5 1.0 C5 G:DG11 4.6 44.9 1.0 C6 H:DG9 4.7 42.3 1.0 C5 G:DG1 4.7 42.2 1.0 C5 H:DG10 4.7 41.0 1.0 O6 G:DG3 4.7 28.7 1.0 C5 G:DG2 4.7 36.2 1.0 C5 H:DG2 4.8 33.4 1.0 C2 H:DG3 4.9 34.3 1.0 C2 H:DG10 5.0 39.4 1.0 C2 G:DG11 5.0 45.3 1.0

Sodium binding site 3 out of 4 in the Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1002 b:36.7 occ:1.00 O6 H:DG2 2.3 33.4 1.0 O6 G:DG3 2.3 28.7 1.0 O6 H:DG1 2.5 31.7 1.0 O6 G:DG10 2.5 36.5 1.0 O6 H:DG11 2.5 33.7 1.0 C6 H:DG2 3.2 33.4 1.0 C6 H:DG1 3.3 34.1 1.0 C6 G:DG10 3.3 38.5 1.0 C6 G:DG3 3.4 30.1 1.0 N1 G:DG10 3.5 37.7 1.0 N1 H:DG2 3.5 33.0 1.0 C6 H:DG11 3.5 36.6 1.0 O6 G:DG9 3.6 37.8 1.0 O6 G:DG4 3.7 30.3 1.0 N1 G:DG3 3.7 28.6 1.0 O6 G:DG2 3.7 35.9 1.0 N1 H:DG11 3.8 36.2 1.0 NA G:NA1001 3.8 31.6 1.0 N1 H:DG1 3.9 35.4 1.0 N1 G:DG4 4.0 29.8 1.0 C6 G:DG4 4.2 31.7 1.0 C6 G:DG2 4.3 36.2 1.0 NA G:NA1003 4.3 44.1 1.0 O6 H:DG12 4.4 33.8 1.0 C5 H:DG1 4.4 34.4 1.0 C6 G:DG9 4.5 39.2 1.0 C5 H:DG2 4.5 33.4 1.0 O6 H:DG10 4.5 37.5 1.0 C5 G:DG3 4.6 29.3 1.0 N1 H:DG10 4.7 38.5 1.0 C5 G:DG10 4.7 41.0 1.0 N1 G:DG2 4.7 35.9 1.0 O6 H:DG3 4.8 32.7 1.0 C2 G:DG10 4.8 39.7 1.0 C2 H:DG2 4.8 33.0 1.0 C6 H:DG10 4.8 39.1 1.0 C5 H:DG11 4.8 37.3 1.0 N7 H:DG1 5.0 33.5 1.0

Sodium binding site 4 out of 4 in the Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1004 b:40.1 occ:1.00 O6 G:DG12 2.3 40.4 1.0 O6 H:DG9 2.4 42.3 1.0 O6 H:DG4 2.5 35.0 1.0 O2 H:DT7 2.7 42.9 1.0 O6 G:DG1 2.7 42.4 1.0 O H:HOH501 2.9 45.5 1.0 C6 G:DG12 3.2 41.8 1.0 C6 H:DG9 3.4 42.3 1.0 C6 H:DG4 3.4 36.2 1.0 O2 H:DT5 3.4 39.9 1.0 C2 H:DT7 3.6 42.9 1.0 C6 G:DG1 3.6 42.2 1.0 N1 G:DG12 3.6 42.0 1.0 N1 H:DG9 3.7 42.4 1.0 N1 H:DG4 3.8 34.8 1.0 N3 H:DT7 3.9 41.4 1.0 N1 G:DG1 3.9 41.8 1.0 NA G:NA1003 4.0 44.1 1.0 O6 G:DG11 4.2 43.4 1.0 N3 H:DT5 4.2 40.0 1.0 C2 H:DT5 4.2 40.2 1.0 C5 G:DG12 4.5 42.8 1.0 C5 H:DG4 4.5 36.7 1.0 O H:HOH502 4.6 49.1 1.0 C6 G:DG11 4.6 44.8 1.0 O2 H:DT6 4.6 43.2 1.0 C5 H:DG9 4.6 43.0 1.0 O6 H:DG3 4.8 32.7 1.0 N1 H:DT7 4.8 43.4 1.0 C5 G:DG1 4.8 42.2 1.0 O6 H:DG10 4.9 37.5 1.0 N1 G:DG11 4.9 45.4 1.0 C2 G:DG12 4.9 42.9 1.0

M.P.Horvath, S.C.Schultz. Dna G-Quartets in A 1.86 A Resolution Structure of An Oxytricha Nova Telomeric Protein-Dna Complex. J.Mol.Biol. V. 310 367 2001.
ISSN: ISSN 0022-2836
PubMed: 11428895
DOI: 10.1006/JMBI.2001.4766