Sodium in PDB 1ph2: Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttg

The structure of Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttg, PDB code: 1ph2 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)	29.96 / 3.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.650, 93.650, 423.038, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 26.9

The structure of Crystal Structure of the Oxytricha Nova Telomere End- Binding Protein Complexed with Noncognate Ssdna Ggggttttg 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 (pdb code 1ph2). 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, PDB code: 1ph2:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1001 b:32.7 occ:1.00 O6 G:DG4 2.6 27.3 1.0 O6 H:DG12 2.7 35.9 1.0 O2 G:DT7 2.9 39.7 1.0 O G:HOH500 2.9 44.3 1.0 O6 G:DG9 2.9 35.0 1.0 O6 H:DG1 3.0 30.8 1.0 O2 G:DT5 3.2 23.4 1.0 C6 G:DG4 3.3 25.6 1.0 N1 G:DG4 3.4 24.5 1.0 C6 H:DG12 3.5 39.0 1.0 N1 H:DG12 3.6 39.2 1.0 C2 G:DT7 3.6 38.5 1.0 N3 G:DT7 3.7 37.1 1.0 NA H:NA1002 3.7 52.1 1.0 N3 G:DT5 3.8 29.8 1.0 C6 G:DG9 3.8 37.2 1.0 C2 G:DT5 3.9 29.2 1.0 C6 H:DG1 3.9 31.3 1.0 N1 G:DG9 4.1 34.4 1.0 N1 H:DG1 4.2 30.6 1.0 C5 G:DG4 4.5 25.4 1.0 O6 H:DG11 4.5 38.6 1.0 C2 G:DG4 4.6 25.6 1.0 O2 G:DT6 4.7 31.0 1.0 C2 H:DG12 4.8 41.2 1.0 C5 H:DG12 4.8 41.1 1.0 N1 G:DT7 4.8 38.2 1.0 C4 G:DT7 4.9 36.3 1.0 C4 G:DT5 5.0 31.2 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1003 b:18.5 occ:1.00 O6 H:DG10 2.7 39.0 1.0 O6 H:DG3 2.7 38.8 1.0 O6 G:DG11 2.7 51.8 1.0 O6 G:DG2 2.9 32.2 1.0 O6 G:DG1 3.0 45.3 1.0 O6 H:DG2 3.2 34.7 1.0 N1 G:DG11 3.4 48.3 1.0 N1 H:DG3 3.4 39.1 1.0 C6 G:DG11 3.5 49.5 1.0 C6 H:DG3 3.5 41.0 1.0 C6 H:DG10 3.5 39.5 1.0 N1 H:DG10 3.6 37.8 1.0 C6 G:DG2 3.8 31.8 1.0 O6 H:DG4 3.8 43.4 1.0 C6 H:DG2 3.9 35.7 1.0 C6 G:DG1 3.9 43.8 1.0 N1 G:DG2 3.9 30.6 1.0 O6 H:DG9 4.0 49.8 1.0 NA H:NA1004 4.0 45.6 1.0 N1 G:DG10 4.1 47.2 1.0 N1 G:DG1 4.3 43.1 1.0 O6 G:DG10 4.3 50.5 1.0 N1 H:DG2 4.4 35.0 1.0 NA H:NA1002 4.5 52.1 1.0 C6 G:DG10 4.5 50.0 1.0 N1 H:DG4 4.5 41.6 1.0 C6 H:DG4 4.6 42.6 1.0 O6 G:DG12 4.7 45.1 1.0 C2 G:DG11 4.7 48.7 1.0 C5 H:DG2 4.7 36.7 1.0 C2 H:DG3 4.7 38.7 1.0 C2 G:DG10 4.8 46.6 1.0 C6 H:DG9 4.8 49.3 1.0 C5 G:DG11 4.9 49.3 1.0 C2 H:DG10 4.9 38.1 1.0 O6 G:DG3 4.9 24.5 1.0 C5 H:DG3 4.9 42.0 1.0 C5 H:DG10 4.9 40.0 1.0 N2 G:DG10 4.9 43.9 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1002 b:52.1 occ:1.00 O6 H:DG2 2.6 34.7 1.0 O6 H:DG1 2.6 30.8 1.0 O6 G:DG3 2.6 24.5 1.0 O6 H:DG11 2.7 38.6 1.0 O6 G:DG10 2.8 50.5 1.0 C6 H:DG2 3.4 35.7 1.0 N1 H:DG2 3.5 35.0 1.0 C6 H:DG1 3.5 31.3 1.0 O6 G:DG9 3.6 35.0 1.0 C6 G:DG3 3.6 24.6 1.0 C6 G:DG10 3.6 50.0 1.0 N1 G:DG10 3.6 47.2 1.0 O6 G:DG4 3.7 27.3 1.0 N1 G:DG4 3.7 24.5 1.0 C6 H:DG11 3.7 37.9 1.0 NA G:NA1001 3.7 32.7 1.0 O6 G:DG2 3.9 32.2 1.0 N1 H:DG1 3.9 30.6 1.0 N1 G:DG3 3.9 22.9 1.0 N1 H:DG11 4.0 36.1 1.0 C6 G:DG4 4.1 25.6 1.0 C6 G:DG2 4.4 31.8 1.0 O6 H:DG12 4.4 35.9 1.0 NA G:NA1003 4.5 18.5 1.0 C6 G:DG9 4.5 37.2 1.0 C5 H:DG1 4.7 33.6 1.0 N1 G:DG2 4.7 30.6 1.0 C5 H:DG2 4.7 36.7 1.0 C2 H:DG2 4.7 35.1 1.0 C2 G:DG4 4.8 25.6 1.0 N2 G:DG4 4.8 23.1 1.0 C5 G:DG3 4.9 26.1 1.0 C2 G:DG10 4.9 46.6 1.0 O6 H:DG3 4.9 38.8 1.0 N1 H:DG10 4.9 37.8 1.0 N1 G:DG9 5.0 34.4 1.0 C5 G:DG10 5.0 51.3 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1004 b:45.6 occ:1.00 O6 H:DG9 2.7 49.8 1.0 O6 G:DG1 2.8 45.3 1.0 O6 G:DG12 2.8 45.1 1.0 O6 H:DG4 2.8 43.4 1.0 O2 H:DT7 2.8 40.9 1.0 O H:HOH501 2.9 32.5 1.0 O2 H:DT5 3.5 53.1 1.0 C6 G:DG1 3.5 43.8 1.0 C6 H:DG4 3.5 42.6 1.0 C6 G:DG12 3.6 46.3 1.0 C2 H:DT7 3.6 40.3 1.0 C6 H:DG9 3.6 49.3 1.0 N1 G:DG12 3.7 46.1 1.0 N1 H:DG4 3.7 41.6 1.0 N1 G:DG1 3.7 43.1 1.0 N3 H:DT7 3.9 39.6 1.0 N1 H:DG9 3.9 48.4 1.0 NA G:NA1003 4.0 18.5 1.0 N3 H:DT5 4.2 53.4 1.0 C2 H:DT5 4.2 52.9 1.0 O6 G:DG11 4.3 51.8 1.0 O2 H:DT6 4.6 58.0 1.0 C5 G:DG1 4.7 43.1 1.0 C5 H:DG4 4.7 43.0 1.0 N1 H:DT7 4.8 41.2 1.0 C6 G:DG11 4.8 49.5 1.0 N1 G:DG11 4.8 48.3 1.0 C5 H:DG9 4.9 50.5 1.0 C2 H:DG4 4.9 41.2 1.0 C2 G:DG12 4.9 47.1 1.0 O H:HOH502 4.9 30.1 1.0 C2 G:DG1 5.0 42.7 1.0 C5 G:DG12 5.0 46.4 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