Sodium in PDB 1ph4: Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggcg

The structure of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggcg, PDB code: 1ph4 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)	28.12 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.450, 93.450, 422.558, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.1

The structure of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttggcg 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 Ggggttttggcg (pdb code 1ph4). 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 Ggggttttggcg, PDB code: 1ph4:
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 Ggggttttggcg


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 Ggggttttggcg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1001 b:48.2 occ:1.00 O6 G:DG9 2.4 52.6 1.0 O6 H:DG12 2.5 45.5 1.0 O6 G:DG4 2.5 44.2 1.0 O2 G:DT7 2.6 48.6 1.0 O H:HOH500 2.6 60.7 1.0 O6 H:DG1 2.8 47.9 1.0 C6 G:DG9 3.3 53.5 1.0 C6 G:DG4 3.3 43.8 1.0 C6 H:DG12 3.4 46.2 1.0 C2 G:DT7 3.5 48.6 1.0 O2 G:DT5 3.5 40.7 1.0 C6 H:DG1 3.6 49.3 1.0 N1 G:DG4 3.6 43.6 1.0 N1 G:DG9 3.7 50.8 1.0 N1 H:DG12 3.8 46.4 1.0 N3 G:DT7 3.8 47.9 1.0 NA H:NA1002 3.8 47.0 1.0 N1 H:DG1 3.9 49.3 1.0 N3 G:DT5 4.2 41.9 1.0 C2 G:DT5 4.3 43.0 1.0 O6 H:DG11 4.4 48.5 1.0 C5 G:DG4 4.6 42.6 1.0 C5 G:DG9 4.6 55.0 1.0 N1 G:DT7 4.7 50.9 1.0 O2 G:DT6 4.7 43.4 1.0 C5 H:DG12 4.7 46.5 1.0 C5 H:DG1 4.8 49.7 1.0 C2 G:DG4 4.9 43.8 1.0 C6 H:DG11 4.9 47.1 1.0 O6 G:DG3 4.9 41.3 1.0 O H:HOH499 4.9 49.3 1.0 O6 G:DG10 5.0 53.8 1.0 C2 G:DG9 5.0 51.3 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 Ggggttttggcg


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 Ggggttttggcg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1002 b:47.0 occ:1.00 O6 H:DG11 2.3 48.5 1.0 O6 H:DG2 2.4 48.2 1.0 O6 G:DG3 2.5 41.3 1.0 O6 G:DG10 2.5 53.8 1.0 O6 H:DG1 2.7 47.9 1.0 C6 H:DG2 3.3 48.1 1.0 C6 G:DG10 3.3 52.9 1.0 C6 H:DG11 3.4 47.1 1.0 N1 G:DG10 3.4 52.2 1.0 C6 G:DG3 3.5 42.2 1.0 C6 H:DG1 3.6 49.3 1.0 O6 G:DG9 3.6 52.6 1.0 N1 H:DG2 3.6 46.0 1.0 O6 G:DG2 3.6 46.5 1.0 O6 G:DG4 3.7 44.2 1.0 N1 H:DG11 3.7 46.7 1.0 NA G:NA1001 3.8 48.2 1.0 N1 G:DG3 3.9 42.5 1.0 N1 H:DG1 4.0 49.3 1.0 N1 G:DG4 4.1 43.6 1.0 C6 G:DG2 4.2 48.3 1.0 C6 G:DG4 4.3 43.8 1.0 O6 H:DG12 4.3 45.5 1.0 NA H:NA1003 4.3 56.5 1.0 C6 G:DG9 4.5 53.5 1.0 N1 H:DG10 4.5 49.5 1.0 O6 H:DG10 4.6 49.3 1.0 C5 H:DG2 4.6 48.7 1.0 N1 G:DG2 4.6 48.2 1.0 C5 H:DG11 4.7 47.6 1.0 C5 H:DG1 4.7 49.7 1.0 C5 G:DG10 4.7 54.7 1.0 O6 H:DG3 4.7 50.2 1.0 C2 G:DG10 4.7 51.5 1.0 C5 G:DG3 4.8 42.8 1.0 C6 H:DG10 4.8 50.5 1.0 C2 H:DG2 5.0 47.5 1.0 N1 G:DG9 5.0 50.8 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 Ggggttttggcg


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 Ggggttttggcg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1003 b:56.5 occ:1.00 O6 G:DG11 2.2 56.1 1.0 O6 H:DG3 2.2 50.2 1.0 O6 H:DG10 2.3 49.3 1.0 O6 G:DG2 2.6 46.5 1.0 O6 G:DG1 2.9 53.4 1.0 C6 G:DG11 3.2 56.9 1.0 C6 H:DG10 3.2 50.5 1.0 C6 H:DG3 3.2 50.1 1.0 N1 H:DG10 3.5 49.5 1.0 O6 H:DG2 3.5 48.2 1.0 N1 G:DG11 3.5 58.6 1.0 N1 H:DG3 3.6 49.4 1.0 C6 G:DG2 3.6 48.3 1.0 C6 G:DG1 3.7 52.8 1.0 O6 H:DG9 3.7 55.6 1.0 O6 H:DG4 3.8 47.6 1.0 N1 G:DG2 3.8 48.2 1.0 NA H:NA1004 3.9 61.1 1.0 C6 H:DG2 4.1 48.1 1.0 N1 G:DG1 4.1 50.8 1.0 N1 G:DG10 4.2 52.2 1.0 O6 G:DG10 4.3 53.8 1.0 N1 H:DG4 4.3 48.5 1.0 NA H:NA1002 4.3 47.0 1.0 O6 G:DG12 4.4 51.7 1.0 C6 H:DG4 4.4 49.1 1.0 C6 G:DG10 4.5 52.9 1.0 C5 G:DG11 4.5 58.2 1.0 C5 H:DG3 4.6 50.2 1.0 C5 H:DG10 4.6 51.6 1.0 C6 H:DG9 4.6 54.5 1.0 N1 H:DG2 4.6 46.0 1.0 C5 G:DG1 4.8 52.2 1.0 C2 H:DG10 4.8 50.6 1.0 C5 H:DG2 4.8 48.7 1.0 C2 G:DG11 4.9 58.9 1.0 O6 G:DG3 4.9 41.3 1.0 C5 G:DG2 4.9 48.0 1.0 C2 H:DG3 4.9 50.7 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 Ggggttttggcg


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 Ggggttttggcg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1004 b:61.1 occ:1.00 O6 G:DG12 2.2 51.7 1.0 O6 H:DG4 2.4 47.6 1.0 O6 H:DG9 2.5 55.6 1.0 O6 G:DG1 2.7 53.4 1.0 O2 H:DT7 2.8 51.5 1.0 O H:HOH501 3.0 58.7 1.0 C6 G:DG12 3.2 55.8 1.0 C6 H:DG4 3.3 49.1 1.0 C6 H:DG9 3.4 54.5 1.0 O2 H:DT5 3.5 59.4 1.0 N1 G:DG12 3.6 55.4 1.0 C6 G:DG1 3.6 52.8 1.0 C2 H:DT7 3.7 51.9 1.0 N1 H:DG9 3.7 55.1 1.0 N1 H:DG4 3.8 48.5 1.0 N1 G:DG1 3.9 50.8 1.0 NA H:NA1003 3.9 56.5 1.0 N3 H:DT7 4.0 51.0 1.0 O6 G:DG11 4.1 56.1 1.0 N3 H:DT5 4.2 59.4 1.0 C2 H:DT5 4.3 59.0 1.0 C5 G:DG12 4.5 56.6 1.0 C5 H:DG4 4.5 50.3 1.0 C6 G:DG11 4.6 56.9 1.0 O H:HOH502 4.7 59.6 1.0 C5 H:DG9 4.7 55.7 1.0 O6 H:DG10 4.7 49.3 1.0 O6 H:DG3 4.8 50.2 1.0 O2 H:DT6 4.8 59.9 1.0 N1 G:DG11 4.8 58.6 1.0 C5 G:DG1 4.8 52.2 1.0 C2 G:DG12 4.9 56.9 1.0 N1 H:DT7 4.9 54.0 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