Sodium in PDB 1ph9: Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgagg

The structure of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgagg, PDB code: 1ph9 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)	29.75 / 2.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.972, 92.972, 422.119, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 26.4

The structure of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgagg 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 Ggggttttgagg (pdb code 1ph9). 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 Ggggttttgagg, PDB code: 1ph9:
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 Ggggttttgagg


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 Ggggttttgagg within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1001 b:47.7 occ:1.00 O H:HOH500 2.3 84.4 1.0 O2 G:DT7 2.3 38.5 1.0 O6 H:DG12 2.4 56.8 1.0 O6 G:DG9 2.7 63.7 1.0 O6 G:DG4 2.8 45.7 1.0 O6 H:DG1 3.2 44.6 1.0 O2 G:DT5 3.2 42.1 1.0 C2 G:DT7 3.2 39.8 1.0 C6 H:DG12 3.4 57.6 1.0 C6 G:DG4 3.5 46.0 1.0 N3 G:DT7 3.6 37.3 1.0 C6 G:DG9 3.6 63.4 1.0 N1 G:DG4 3.7 46.2 1.0 N1 H:DG12 3.8 57.7 1.0 N3 G:DT5 3.8 44.5 1.0 C6 H:DG1 3.9 45.6 1.0 N1 G:DG9 3.9 62.1 1.0 C2 G:DT5 3.9 44.2 1.0 N1 H:DG1 4.1 44.7 1.0 NA H:NA1002 4.2 97.8 1.0 O2 G:DT6 4.2 30.1 1.0 N1 G:DT7 4.5 40.2 1.0 O6 H:DG11 4.6 61.7 1.0 C5 G:DG4 4.7 44.9 1.0 C5 H:DG12 4.7 57.8 1.0 O G:HOH499 4.9 42.3 1.0 C5 G:DG9 4.9 63.9 1.0 C4 G:DT7 4.9 37.5 1.0 O4' G:DT8 4.9 56.3 1.0 C2 G:DG4 4.9 44.7 1.0 C2 G:DT6 4.9 30.5 1.0 C5 H:DG1 5.0 45.6 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 Ggggttttgagg


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 Ggggttttgagg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1002 b:97.8 occ:1.00 O6 H:DG2 2.3 51.5 1.0 O6 H:DG1 2.4 44.6 1.0 O6 G:DG10 2.5 60.9 1.0 O6 G:DG3 2.6 53.9 1.0 O6 H:DG11 2.6 61.7 1.0 C6 H:DG2 3.2 53.0 1.0 C6 H:DG1 3.3 45.6 1.0 C6 G:DG10 3.3 60.3 1.0 N1 G:DG10 3.4 59.7 1.0 N1 H:DG2 3.6 52.7 1.0 C6 H:DG11 3.6 61.6 1.0 C6 G:DG3 3.6 51.5 1.0 O6 G:DG2 3.7 55.0 1.0 O6 G:DG9 3.7 63.7 1.0 N1 H:DG1 3.7 44.7 1.0 O6 G:DG4 3.8 45.7 1.0 N1 G:DG4 4.0 46.2 1.0 N1 H:DG11 4.0 63.0 1.0 N1 G:DG3 4.1 50.5 1.0 NA G:NA1001 4.2 47.7 1.0 NA H:NA1003 4.3 61.6 1.0 C6 G:DG4 4.3 46.0 1.0 C6 G:DG2 4.4 55.8 1.0 C5 H:DG1 4.4 45.6 1.0 C5 H:DG2 4.5 53.3 1.0 C6 G:DG9 4.5 63.4 1.0 O6 H:DG12 4.6 56.8 1.0 O6 H:DG10 4.6 68.9 1.0 N1 H:DG10 4.7 69.4 1.0 C5 G:DG10 4.7 60.8 1.0 C2 G:DG10 4.7 59.1 1.0 O6 H:DG3 4.8 62.3 1.0 N1 G:DG2 4.8 56.1 1.0 C5 G:DG3 4.9 51.1 1.0 C2 H:DG2 4.9 51.5 1.0 C5 H:DG11 4.9 61.6 1.0 C6 H:DG10 4.9 69.7 1.0 N7 H:DG1 5.0 44.9 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 Ggggttttgagg


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 Ggggttttgagg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1003 b:61.6 occ:1.00 O6 H:DG3 2.2 62.3 1.0 O6 G:DG11 2.3 62.6 1.0 O6 H:DG10 2.4 68.9 1.0 O6 G:DG2 2.7 55.0 1.0 O6 G:DG1 2.8 57.5 1.0 O6 H:DG2 3.2 51.5 1.0 C6 H:DG3 3.2 62.9 1.0 C6 G:DG11 3.2 62.5 1.0 C6 H:DG10 3.3 69.7 1.0 N1 G:DG11 3.5 63.1 1.0 N1 H:DG10 3.6 69.4 1.0 N1 H:DG3 3.6 63.2 1.0 C6 G:DG2 3.6 55.8 1.0 C6 G:DG1 3.7 57.5 1.0 O6 H:DG4 3.8 52.5 1.0 C6 H:DG2 3.8 53.0 1.0 N1 G:DG2 3.8 56.1 1.0 O6 H:DG9 4.1 61.2 1.0 N1 G:DG10 4.2 59.7 1.0 N1 G:DG1 4.2 58.4 1.0 O6 G:DG10 4.2 60.9 1.0 NA H:NA1002 4.3 97.8 1.0 NA H:NA1004 4.3 63.7 1.0 N1 H:DG2 4.4 52.7 1.0 N1 H:DG4 4.4 53.6 1.0 C6 G:DG10 4.5 60.3 1.0 C6 H:DG4 4.5 53.5 1.0 C5 H:DG3 4.6 62.2 1.0 O6 G:DG12 4.6 54.5 1.0 C5 G:DG11 4.6 62.7 1.0 C5 H:DG2 4.7 53.3 1.0 C5 H:DG10 4.7 69.6 1.0 O6 G:DG3 4.7 53.9 1.0 C5 G:DG1 4.8 58.2 1.0 C2 G:DG11 4.9 62.5 1.0 C2 H:DG10 4.9 69.9 1.0 C6 H:DG9 4.9 60.3 1.0 C2 H:DG3 4.9 63.5 1.0 C5 G:DG2 5.0 55.4 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 Ggggttttgagg


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 Ggggttttgagg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1004 b:63.7 occ:1.00 O6 G:DG12 2.4 54.5 1.0 O2 H:DT7 2.6 51.2 1.0 O6 H:DG4 2.6 52.5 1.0 O6 H:DG9 2.6 61.2 1.0 O H:HOH501 2.9 45.5 1.0 O6 G:DG1 3.0 57.5 1.0 O2 H:DT5 3.3 61.4 1.0 C6 G:DG12 3.4 54.3 1.0 C6 H:DG4 3.4 53.5 1.0 C2 H:DT7 3.5 50.8 1.0 C6 H:DG9 3.6 60.3 1.0 N1 G:DG12 3.6 53.3 1.0 N3 H:DT7 3.7 50.0 1.0 C6 G:DG1 3.7 57.5 1.0 N1 H:DG4 3.8 53.6 1.0 N3 H:DT5 4.0 61.6 1.0 N1 H:DG9 4.0 59.7 1.0 C2 H:DT5 4.0 61.8 1.0 N1 G:DG1 4.1 58.4 1.0 NA H:NA1003 4.3 61.6 1.0 O2 H:DT6 4.3 65.2 1.0 O H:HOH502 4.4 36.8 1.0 O6 G:DG11 4.5 62.6 1.0 C5 H:DG4 4.5 53.7 1.0 C5 G:DG12 4.7 55.4 1.0 N1 H:DT7 4.8 52.5 1.0 C5 G:DG1 4.8 58.2 1.0 C5 H:DG9 4.9 61.2 1.0 C6 G:DG11 4.9 62.5 1.0 C2 G:DG12 4.9 53.5 1.0 C2 H:DT6 4.9 65.9 1.0 O6 H:DG3 5.0 62.3 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