Sodium in PDB 1ph8: Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttgcgg

The structure of Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttgcgg, PDB code: 1ph8 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)	29.90 / 2.36
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.472, 93.472, 423.554, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 25.6

The structure of Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttgcgg 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 Ggggttttgcgg (pdb code 1ph8). 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 Ggggttttgcgg, PDB code: 1ph8:
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 Ggggttttgcgg


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 Ggggttttgcgg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1001 b:45.4 occ:1.00 O6 G:DG4 2.5 32.9 1.0 O G:HOH500 2.5 67.5 1.0 O2 G:DT7 2.5 46.1 1.0 O6 H:DG12 2.6 40.3 1.0 O6 G:DG9 2.6 54.1 1.0 O6 H:DG1 2.9 33.0 1.0 C6 G:DG4 3.2 33.3 1.0 C2 G:DT7 3.4 46.4 1.0 O2 G:DT5 3.5 39.9 1.0 C6 H:DG12 3.5 43.4 1.0 C6 G:DG9 3.5 54.2 1.0 N1 G:DG4 3.5 33.3 1.0 N3 G:DT7 3.7 45.0 1.0 N1 H:DG12 3.7 42.8 1.0 C6 H:DG1 3.8 35.9 1.0 N1 G:DG9 3.8 52.4 1.0 NA G:NA1002 3.8 48.0 1.0 N3 G:DT5 3.9 41.0 1.0 C2 G:DT5 4.1 41.4 1.0 N1 H:DG1 4.1 35.9 1.0 O6 H:DG11 4.2 40.7 1.0 C5 G:DG4 4.5 32.0 1.0 O2 G:DT6 4.5 35.8 1.0 N1 G:DT7 4.7 47.9 1.0 C2 G:DG4 4.8 32.7 1.0 C6 H:DG11 4.8 41.4 1.0 C5 H:DG12 4.8 44.7 1.0 C5 G:DG9 4.8 55.1 1.0 O G:HOH499 4.9 39.8 1.0 O6 G:DG10 4.9 52.9 1.0 C5 H:DG1 4.9 37.5 1.0 O6 G:DG3 5.0 35.8 1.0 C4 G:DT7 5.0 46.0 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 Ggggttttgcgg


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 Ggggttttgcgg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1002 b:48.0 occ:1.00 O6 H:DG2 2.3 42.9 1.0 O6 H:DG11 2.4 40.7 1.0 O6 G:DG3 2.4 35.8 1.0 O6 G:DG10 2.4 52.9 1.0 O6 H:DG1 2.6 33.0 1.0 C6 H:DG2 3.3 43.6 1.0 C6 G:DG10 3.3 52.5 1.0 C6 G:DG3 3.4 35.6 1.0 N1 G:DG10 3.5 51.3 1.0 C6 H:DG11 3.5 41.4 1.0 C6 H:DG1 3.5 35.9 1.0 O6 G:DG4 3.6 32.9 1.0 N1 H:DG2 3.6 42.8 1.0 O6 G:DG9 3.6 54.1 1.0 O6 G:DG2 3.7 41.4 1.0 NA G:NA1001 3.8 45.4 1.0 N1 G:DG4 3.9 33.3 1.0 N1 G:DG3 3.9 35.4 1.0 N1 H:DG11 4.0 40.7 1.0 N1 H:DG1 4.0 35.9 1.0 C6 G:DG4 4.1 33.3 1.0 NA H:NA1003 4.2 42.8 1.0 C6 G:DG2 4.3 41.8 1.0 O6 H:DG12 4.5 40.3 1.0 O6 H:DG10 4.5 44.9 1.0 C6 G:DG9 4.5 54.2 1.0 C5 H:DG2 4.6 45.0 1.0 N1 H:DG10 4.6 43.3 1.0 C5 G:DG10 4.6 53.8 1.0 C5 H:DG1 4.7 37.5 1.0 C5 G:DG3 4.7 36.3 1.0 C5 H:DG11 4.7 42.7 1.0 O6 H:DG3 4.7 47.8 1.0 N1 G:DG2 4.7 41.5 1.0 C2 G:DG10 4.8 50.7 1.0 C6 H:DG10 4.8 44.7 1.0 C2 H:DG2 4.9 43.8 1.0 C2 G:DG4 5.0 32.7 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 Ggggttttgcgg


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 Ggggttttgcgg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1004 b:48.4 occ:1.00 O6 H:DG9 2.3 55.6 1.0 O6 G:DG12 2.5 42.3 1.0 O6 G:DG1 2.6 34.4 1.0 O2 H:DT7 2.6 43.5 1.0 O6 H:DG4 2.7 48.6 1.0 O H:HOH501 3.0 42.1 1.0 C6 H:DG9 3.3 56.1 1.0 C6 G:DG1 3.4 33.7 1.0 C6 G:DG12 3.5 44.3 1.0 C6 H:DG4 3.5 46.9 1.0 C2 H:DT7 3.5 45.9 1.0 N1 G:DG1 3.7 34.0 1.0 N1 G:DG12 3.7 44.0 1.0 N1 H:DG9 3.7 56.9 1.0 N1 H:DG4 3.8 46.0 1.0 O2 H:DT5 3.8 56.5 1.0 N3 H:DT7 3.9 45.1 1.0 NA H:NA1003 4.0 42.8 1.0 O6 G:DG11 4.3 47.7 1.0 C5 H:DG9 4.5 57.7 1.0 C5 G:DG1 4.6 33.8 1.0 O H:HOH502 4.6 53.4 1.0 C2 H:DT5 4.6 55.1 1.0 N3 H:DT5 4.6 54.3 1.0 N1 H:DT7 4.7 47.4 1.0 C6 G:DG11 4.7 47.7 1.0 C5 H:DG4 4.7 46.9 1.0 O2 H:DT6 4.7 53.4 1.0 O6 H:DG10 4.7 44.9 1.0 O6 H:DG3 4.7 47.8 1.0 C5 G:DG12 4.8 46.0 1.0 N1 G:DG11 4.9 47.6 1.0 C2 G:DG1 4.9 33.6 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 Ggggttttgcgg


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 Ggggttttgcgg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1003 b:42.8 occ:1.00 O6 H:DG3 2.2 47.8 1.0 O6 G:DG2 2.3 41.4 1.0 O6 H:DG10 2.3 44.9 1.0 O6 G:DG11 2.5 47.7 1.0 O6 G:DG1 2.8 34.4 1.0 C6 H:DG10 3.2 44.7 1.0 C6 H:DG3 3.3 48.1 1.0 C6 G:DG2 3.3 41.8 1.0 O6 H:DG2 3.3 42.9 1.0 N1 H:DG10 3.4 43.3 1.0 C6 G:DG11 3.5 47.7 1.0 C6 G:DG1 3.6 33.7 1.0 N1 G:DG2 3.6 41.5 1.0 N1 G:DG11 3.7 47.6 1.0 N1 H:DG3 3.7 47.8 1.0 O6 H:DG9 3.9 55.6 1.0 C6 H:DG2 3.9 43.6 1.0 NA G:NA1004 4.0 48.4 1.0 N1 G:DG1 4.0 34.0 1.0 O6 H:DG4 4.0 48.6 1.0 O6 G:DG10 4.1 52.9 1.0 NA G:NA1002 4.2 48.0 1.0 N1 G:DG10 4.3 51.3 1.0 C6 G:DG10 4.4 52.5 1.0 N1 H:DG4 4.5 46.0 1.0 N1 H:DG2 4.5 42.8 1.0 C5 H:DG3 4.5 48.9 1.0 O6 G:DG3 4.5 35.8 1.0 C5 H:DG10 4.6 44.4 1.0 C5 G:DG2 4.6 41.0 1.0 C5 G:DG1 4.6 33.8 1.0 C6 H:DG4 4.7 46.9 1.0 O6 G:DG12 4.7 42.3 1.0 C5 H:DG2 4.8 45.0 1.0 C6 H:DG9 4.8 56.1 1.0 C2 H:DG10 4.8 43.2 1.0 C5 G:DG11 4.9 48.5 1.0 C2 G:DG2 5.0 42.0 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