Sodium in PDB 1ph3: Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg

The structure of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg, PDB code: 1ph3 was solved by D.L.Theobald, S.C.Schultz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.82 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.636, 93.636, 423.111, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 26.3

The binding sites of Sodium atom in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg (pdb code 1ph3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg, PDB code: 1ph3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1001 b:48.4 occ:1.00 O6 G:DG9 2.5 52.0 1.0 O6 G:DG4 2.5 44.4 1.0 O G:HOH500 2.5 63.4 1.0 O2 G:DT7 2.5 47.8 1.0 O6 H:DG12 2.5 42.6 1.0 O6 H:DG1 2.8 43.5 1.0 C6 G:DG4 3.3 42.5 1.0 C6 G:DG9 3.4 51.1 1.0 C2 G:DT7 3.4 46.0 1.0 O2 G:DT5 3.5 38.2 1.0 C6 H:DG12 3.5 44.1 1.0 N1 G:DG4 3.5 42.2 1.0 C6 H:DG1 3.6 44.2 1.0 N1 G:DG9 3.7 48.9 1.0 N3 G:DT7 3.7 44.2 1.0 N1 H:DG12 3.8 45.2 1.0 N1 H:DG1 3.9 46.1 1.0 NA H:NA1002 3.9 45.6 1.0 N3 G:DT5 4.1 38.9 1.0 C2 G:DT5 4.2 39.1 1.0 O6 H:DG11 4.3 45.4 1.0 C5 G:DG4 4.5 40.8 1.0 N1 G:DT7 4.7 46.4 1.0 O2 G:DT6 4.7 41.5 1.0 C5 G:DG9 4.7 52.0 1.0 C5 H:DG1 4.7 46.1 1.0 C2 G:DG4 4.8 41.8 1.0 C5 H:DG12 4.8 46.3 1.0 C6 H:DG11 4.8 45.6 1.0 O G:HOH499 4.9 48.6 1.0 O6 G:DG3 4.9 40.0 1.0 O6 G:DG10 4.9 51.5 1.0 C2 G:DG9 5.0 48.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1002 b:45.6 occ:1.00 O6 H:DG2 2.3 45.8 1.0 O6 H:DG11 2.3 45.4 1.0 O6 G:DG10 2.4 51.5 1.0 O6 G:DG3 2.5 40.0 1.0 O6 H:DG1 2.7 43.5 1.0 C6 H:DG2 3.2 45.1 1.0 C6 G:DG10 3.2 49.9 1.0 N1 G:DG10 3.3 49.5 1.0 C6 H:DG11 3.4 45.6 1.0 C6 H:DG1 3.5 44.2 1.0 O6 G:DG9 3.6 52.0 1.0 O6 G:DG2 3.6 44.8 1.0 N1 H:DG2 3.6 44.3 1.0 C6 G:DG3 3.6 41.3 1.0 O6 G:DG4 3.8 44.4 1.0 N1 H:DG11 3.8 45.8 1.0 NA G:NA1001 3.9 48.4 1.0 N1 H:DG1 3.9 46.1 1.0 N1 G:DG3 4.0 39.8 1.0 N1 G:DG4 4.1 42.2 1.0 NA H:NA1003 4.2 55.0 1.0 C6 G:DG2 4.2 46.7 1.0 C6 G:DG4 4.3 42.5 1.0 C6 G:DG9 4.4 51.1 1.0 N1 H:DG10 4.5 48.4 1.0 O6 H:DG10 4.5 48.8 1.0 O6 H:DG12 4.5 42.6 1.0 C5 H:DG2 4.5 46.1 1.0 C5 G:DG10 4.6 52.1 1.0 C2 G:DG10 4.6 47.7 1.0 C5 H:DG1 4.6 46.1 1.0 O6 H:DG3 4.7 46.8 1.0 N1 G:DG2 4.7 45.9 1.0 C5 H:DG11 4.7 46.6 1.0 C6 H:DG10 4.7 49.4 1.0 C5 G:DG3 4.8 40.7 1.0 N1 G:DG9 4.9 48.9 1.0 C2 H:DG2 4.9 44.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1003 b:55.0 occ:1.00 O6 H:DG3 2.2 46.8 1.0 O6 G:DG11 2.2 55.4 1.0 O6 H:DG10 2.3 48.8 1.0 O6 G:DG2 2.5 44.8 1.0 O6 G:DG1 2.9 50.8 1.0 C6 H:DG3 3.2 47.7 1.0 C6 H:DG10 3.2 49.4 1.0 C6 G:DG11 3.2 54.8 1.0 O6 H:DG2 3.3 45.8 1.0 N1 H:DG10 3.5 48.4 1.0 C6 G:DG2 3.5 46.7 1.0 N1 H:DG3 3.5 44.6 1.0 N1 G:DG11 3.5 55.6 1.0 C6 G:DG1 3.7 51.4 1.0 N1 G:DG2 3.8 45.9 1.0 O6 H:DG4 3.8 45.8 1.0 O6 H:DG9 3.8 52.4 1.0 C6 H:DG2 3.9 45.1 1.0 NA H:NA1004 4.0 58.4 1.0 N1 G:DG1 4.1 50.5 1.0 NA H:NA1002 4.2 45.6 1.0 N1 G:DG10 4.2 49.5 1.0 O6 G:DG10 4.3 51.5 1.0 N1 H:DG4 4.4 46.1 1.0 N1 H:DG2 4.5 44.3 1.0 O6 G:DG12 4.5 49.6 1.0 C6 H:DG4 4.5 46.5 1.0 C6 G:DG10 4.5 49.9 1.0 C5 H:DG3 4.6 45.6 1.0 C5 H:DG10 4.6 50.1 1.0 C5 G:DG11 4.6 55.3 1.0 C5 H:DG2 4.7 46.1 1.0 C6 H:DG9 4.7 51.8 1.0 C5 G:DG1 4.7 51.1 1.0 C5 G:DG2 4.8 45.6 1.0 C2 H:DG10 4.8 49.2 1.0 O6 G:DG3 4.8 40.0 1.0 C2 H:DG3 4.8 45.0 1.0 C2 G:DG11 4.9 55.4 1.0 C2 G:DG10 5.0 47.7 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggtg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1004 b:58.4 occ:1.00 O6 G:DG12 2.2 49.6 1.0 O6 H:DG9 2.4 52.4 1.0 O6 H:DG4 2.5 45.8 1.0 O6 G:DG1 2.7 50.8 1.0 O2 H:DT7 2.8 50.3 1.0 O H:HOH501 2.9 53.1 1.0 C6 G:DG12 3.2 52.8 1.0 C6 H:DG9 3.4 51.8 1.0 C6 H:DG4 3.4 46.5 1.0 N1 G:DG12 3.5 52.3 1.0 C6 G:DG1 3.6 51.4 1.0 O2 H:DT5 3.6 56.1 1.0 C2 H:DT7 3.7 50.8 1.0 N1 H:DG9 3.8 52.6 1.0 N1 G:DG1 3.9 50.5 1.0 N1 H:DG4 3.9 46.1 1.0 N3 H:DT7 4.0 49.7 1.0 NA H:NA1003 4.0 55.0 1.0 O6 G:DG11 4.1 55.4 1.0 N3 H:DT5 4.2 55.4 1.0 C2 H:DT5 4.3 54.5 1.0 C5 G:DG12 4.5 52.5 1.0 C6 G:DG11 4.5 54.8 1.0 O H:HOH502 4.6 58.2 1.0 C5 H:DG4 4.6 47.9 1.0 C5 H:DG9 4.7 53.8 1.0 O6 H:DG10 4.7 48.8 1.0 C5 G:DG1 4.8 51.1 1.0 N1 G:DG11 4.8 55.6 1.0 O2 H:DT6 4.8 56.4 1.0 O6 H:DG3 4.9 46.8 1.0 C2 G:DG12 4.9 53.0 1.0 N1 H:DT7 4.9 51.8 1.0

D.L.Theobald, S.C.Schultz. Nucleotide Shuffling and Ssdna Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes Embo J. V. 22 4314 2003.
ISSN: ISSN 0261-4189
PubMed: 12912928
DOI: 10.1093/EMBOJ/CDG415