Sodium in PDB 1ph5: Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttg(3DR)Gg

The structure of Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttg(3DR)Gg, PDB code: 1ph5 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)	39.70 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.349, 93.349, 423.232, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 25.8

The structure of Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttg(3DR)Gg also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttg(3DR)Gg (pdb code 1ph5). 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 Ggggttttg(3DR)Gg, PDB code: 1ph5:
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 Ggggttttg(3DR)Gg


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 Ggggttttg(3DR)Gg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1001 b:34.5 occ:1.00 O6 G:DG4 2.3 33.7 1.0 O6 G:DG9 2.4 41.1 1.0 O2 G:DT7 2.5 34.4 1.0 O6 H:DG12 2.6 36.7 1.0 O G:HOH500 2.8 53.1 1.0 O6 H:DG1 2.8 35.2 1.0 C6 G:DG4 3.2 34.5 1.0 C2 G:DT7 3.4 35.1 1.0 C6 G:DG9 3.4 42.0 1.0 N1 G:DG4 3.5 32.8 1.0 O2 G:DT5 3.5 31.9 1.0 C6 H:DG12 3.6 39.5 1.0 C6 H:DG1 3.7 37.0 1.0 NA H:NA1002 3.7 39.7 1.0 N3 G:DT7 3.8 34.9 1.0 N1 G:DG9 3.8 40.2 1.0 N1 H:DG12 3.9 40.1 1.0 N1 H:DG1 3.9 38.0 1.0 O6 H:DG11 4.2 37.2 1.0 N3 G:DT5 4.3 32.1 1.0 C2 G:DT5 4.3 32.7 1.0 C5 G:DG4 4.4 33.0 1.0 N1 G:DT7 4.6 37.3 1.0 O2 G:DT6 4.6 35.5 1.0 C5 G:DG9 4.7 43.4 1.0 C6 H:DG11 4.7 39.1 1.0 O6 G:DG10 4.7 40.0 1.0 O6 G:DG3 4.8 31.7 1.0 C2 G:DG4 4.8 32.8 1.0 C5 H:DG1 4.9 37.3 1.0 C5 H:DG12 4.9 40.3 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 Ggggttttg(3DR)Gg


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 Ggggttttg(3DR)Gg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1002 b:39.7 occ:1.00 O6 H:DG11 2.3 37.2 1.0 O6 H:DG2 2.4 36.6 1.0 O6 G:DG3 2.4 31.7 1.0 O6 G:DG10 2.5 40.0 1.0 O6 H:DG1 2.7 35.2 1.0 C6 G:DG10 3.3 42.0 1.0 C6 H:DG2 3.3 36.1 1.0 N1 G:DG10 3.3 41.1 1.0 C6 H:DG11 3.4 39.1 1.0 O6 G:DG4 3.5 33.7 1.0 O6 G:DG9 3.5 41.1 1.0 O6 G:DG2 3.6 38.3 1.0 C6 G:DG3 3.6 32.9 1.0 C6 H:DG1 3.6 37.0 1.0 N1 H:DG2 3.6 35.2 1.0 NA G:NA1001 3.7 34.5 1.0 N1 H:DG11 3.9 38.9 1.0 N1 G:DG4 4.0 32.8 1.0 N1 H:DG1 4.0 38.0 1.0 C6 G:DG4 4.1 34.5 1.0 N1 G:DG3 4.1 32.1 1.0 C6 G:DG2 4.1 38.9 1.0 NA H:NA1003 4.2 46.0 1.0 O6 H:DG12 4.5 36.7 1.0 C6 G:DG9 4.5 42.0 1.0 N1 H:DG10 4.5 41.2 1.0 O6 H:DG10 4.6 40.5 1.0 N1 G:DG2 4.6 38.8 1.0 C5 H:DG2 4.6 36.3 1.0 C5 G:DG10 4.6 43.7 1.0 C2 G:DG10 4.6 42.3 1.0 C5 H:DG11 4.7 39.8 1.0 O6 H:DG3 4.7 36.0 1.0 C5 H:DG1 4.8 37.3 1.0 C5 G:DG3 4.8 32.4 1.0 C6 H:DG10 4.8 42.3 1.0 C5 G:DG2 4.9 39.0 1.0 C2 H:DG2 5.0 35.6 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 Ggggttttg(3DR)Gg


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 Ggggttttg(3DR)Gg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1003 b:46.0 occ:1.00 O6 H:DG3 2.2 36.0 1.0 O6 H:DG10 2.3 40.5 1.0 O6 G:DG11 2.3 46.0 1.0 O6 G:DG2 2.4 38.3 1.0 O6 G:DG1 2.8 45.0 1.0 C6 H:DG10 3.2 42.3 1.0 O6 H:DG2 3.2 36.6 1.0 C6 H:DG3 3.3 35.9 1.0 C6 G:DG11 3.3 47.2 1.0 C6 G:DG2 3.3 38.9 1.0 N1 H:DG10 3.4 41.2 1.0 N1 G:DG2 3.6 38.8 1.0 N1 G:DG11 3.6 48.0 1.0 C6 G:DG1 3.6 45.1 1.0 N1 H:DG3 3.7 35.1 1.0 O6 H:DG9 3.8 45.1 1.0 C6 H:DG2 3.9 36.1 1.0 O6 H:DG4 3.9 38.4 1.0 NA H:NA1004 3.9 43.6 1.0 N1 G:DG1 4.1 45.0 1.0 N1 G:DG10 4.2 41.1 1.0 NA H:NA1002 4.2 39.7 1.0 O6 G:DG10 4.3 40.0 1.0 N1 H:DG2 4.5 35.2 1.0 C6 G:DG10 4.5 42.0 1.0 N1 H:DG4 4.5 37.7 1.0 C5 H:DG10 4.6 43.4 1.0 C5 H:DG3 4.6 35.6 1.0 C6 H:DG4 4.6 38.7 1.0 C5 G:DG11 4.6 47.7 1.0 O6 G:DG12 4.7 43.6 1.0 C5 G:DG2 4.7 39.0 1.0 C5 G:DG1 4.7 44.9 1.0 C6 H:DG9 4.7 45.5 1.0 C2 H:DG10 4.7 42.4 1.0 C5 H:DG2 4.8 36.3 1.0 O6 G:DG3 4.8 31.7 1.0 C2 G:DG2 4.9 38.0 1.0 C2 G:DG10 5.0 42.3 1.0 C2 G:DG11 5.0 48.1 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 Ggggttttg(3DR)Gg


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 Ggggttttg(3DR)Gg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1004 b:43.6 occ:1.00 O6 H:DG9 2.2 45.1 1.0 O6 G:DG12 2.4 43.6 1.0 O6 H:DG4 2.6 38.4 1.0 O6 G:DG1 2.7 45.0 1.0 O2 H:DT7 2.8 45.4 1.0 O H:HOH501 3.0 47.6 1.0 C6 H:DG9 3.2 45.5 1.0 C6 G:DG12 3.3 44.8 1.0 C6 H:DG4 3.5 38.7 1.0 C6 G:DG1 3.6 45.1 1.0 N1 H:DG9 3.6 45.0 1.0 N1 G:DG12 3.7 45.0 1.0 C2 H:DT7 3.7 45.5 1.0 O2 H:DT5 3.7 43.5 1.0 N1 G:DG1 3.9 45.0 1.0 N1 H:DG4 3.9 37.7 1.0 NA H:NA1003 3.9 46.0 1.0 O6 G:DG11 4.0 46.0 1.0 N3 H:DT7 4.1 43.9 1.0 N3 H:DT5 4.4 43.3 1.0 C2 H:DT5 4.4 43.3 1.0 C6 G:DG11 4.4 47.2 1.0 C5 H:DG9 4.5 46.1 1.0 O H:HOH502 4.5 51.4 1.0 O6 H:DG10 4.6 40.5 1.0 C5 G:DG12 4.7 45.8 1.0 N1 G:DG11 4.7 48.0 1.0 C5 H:DG4 4.7 39.5 1.0 O6 H:DG3 4.8 36.0 1.0 C5 G:DG1 4.8 44.9 1.0 N1 H:DT7 4.8 46.5 1.0 O2 H:DT6 4.9 46.0 1.0 C2 H:DG9 5.0 45.4 1.0 C2 G:DG12 5.0 45.7 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