Sodium in PDB 1ph7: Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgigg

The structure of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgigg, PDB code: 1ph7 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)	39.64 / 2.90
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.194, 93.194, 421.585, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 26.8

The structure of Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgigg 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 Ggggttttgigg (pdb code 1ph7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgigg, PDB code: 1ph7:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgigg


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 Ggggttttgigg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1002 b:37.7 occ:1.00 O6 H:DG2 2.2 33.8 1.0 O6 H:DG1 2.5 32.3 1.0 O6 H:DG11 2.5 34.5 1.0 O6 G:DG3 2.6 29.0 1.0 O6 G:DG10 2.7 37.2 1.0 C6 H:DG2 3.0 33.9 1.0 C6 H:DG1 3.3 34.7 1.0 N1 H:DG2 3.3 33.5 1.0 N1 G:DG10 3.3 38.3 1.0 C6 G:DG10 3.4 39.2 1.0 O6 G:DG9 3.6 38.3 1.0 C6 H:DG11 3.6 37.0 1.0 O6 G:DG4 3.6 31.0 1.0 C6 G:DG3 3.6 30.4 1.0 N1 H:DG1 3.8 35.8 1.0 O6 G:DG2 3.9 36.3 1.0 O6 H:DG12 3.9 34.4 1.0 N1 H:DG11 3.9 36.5 1.0 N1 G:DG3 4.0 29.0 1.0 N1 G:DG4 4.1 30.3 1.0 C6 G:DG4 4.2 32.0 1.0 C5 H:DG2 4.3 34.0 1.0 C5 H:DG1 4.4 34.8 1.0 O6 H:DG10 4.4 38.2 1.0 NA H:NA1003 4.5 45.0 1.0 C6 G:DG2 4.5 36.7 1.0 C6 G:DG9 4.5 39.6 1.0 C2 G:DG10 4.6 40.2 1.0 C2 H:DG2 4.6 33.4 1.0 N1 H:DG10 4.7 39.1 1.0 O6 H:DG3 4.7 33.2 1.0 C6 H:DG10 4.8 39.6 1.0 C5 G:DG10 4.8 41.3 1.0 C5 H:DG11 4.9 37.7 1.0 C6 H:DG12 4.9 37.1 1.0 C5 G:DG3 4.9 29.8 1.0 N7 H:DG1 4.9 34.1 1.0 N2 G:DG10 5.0 38.8 1.0 C2 H:DG1 5.0 36.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgigg


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 Ggggttttgigg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1003 b:45.0 occ:1.00 O6 G:DG11 2.2 43.8 1.0 O6 H:DG10 2.3 38.2 1.0 O6 H:DG3 2.7 33.2 1.0 O6 G:DG2 2.9 36.3 1.0 C6 G:DG11 3.0 45.2 1.0 N1 G:DG11 3.0 45.5 1.0 O6 G:DG1 3.1 42.8 1.0 C6 H:DG10 3.3 39.6 1.0 N1 H:DG3 3.3 32.3 1.0 C6 H:DG3 3.4 34.2 1.0 O6 H:DG4 3.4 35.5 1.0 O6 H:DG9 3.4 42.9 1.0 O6 H:DG2 3.4 33.8 1.0 O6 G:DG12 3.5 41.1 1.0 N1 H:DG10 3.6 39.1 1.0 C6 H:DG2 3.9 33.9 1.0 C6 G:DG2 4.0 36.7 1.0 NA H:NA1004 4.0 41.1 1.0 C6 G:DG1 4.1 42.6 1.0 C6 H:DG4 4.2 36.8 1.0 N1 G:DG2 4.3 36.0 1.0 C2 G:DG11 4.3 45.8 1.0 N1 G:DG10 4.3 38.3 1.0 C6 H:DG9 4.4 42.9 1.0 C5 G:DG11 4.4 45.5 1.0 N1 H:DG4 4.4 35.5 1.0 C6 G:DG12 4.4 42.3 1.0 N1 H:DG2 4.5 33.5 1.0 NA H:NA1002 4.5 37.7 1.0 O6 G:DG10 4.5 37.2 1.0 C2 H:DG3 4.6 34.9 1.0 C5 H:DG10 4.6 41.3 1.0 C5 H:DG2 4.7 34.0 1.0 C6 G:DG10 4.7 39.2 1.0 N1 G:DG1 4.7 42.4 1.0 N1 G:DG12 4.7 42.6 1.0 C5 H:DG3 4.8 33.4 1.0 N2 G:DG11 4.8 45.4 1.0 N2 H:DG3 4.9 33.6 1.0 O6 G:DG3 5.0 29.0 1.0 N1 H:DG9 5.0 42.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Oxytricha Nova Telomere End-Binding Protein Complexed with Noncognate Ssdna Ggggttttgigg


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 Ggggttttgigg within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1004 b:41.1 occ:1.00 O6 H:DG9 2.3 42.9 1.0 O6 G:DG12 2.3 41.1 1.0 O6 H:DG4 2.5 35.5 1.0 O2 H:DT7 2.9 43.5 1.0 O H:HOH501 3.0 45.7 1.0 O6 G:DG1 3.0 42.8 1.0 C6 H:DG9 3.2 42.9 1.0 C6 G:DG12 3.2 42.3 1.0 C6 H:DG4 3.5 36.8 1.0 N1 H:DG9 3.7 42.7 1.0 C2 H:DT7 3.7 43.4 1.0 N1 G:DG12 3.9 42.6 1.0 N3 H:DT7 3.9 41.9 1.0 C6 G:DG1 3.9 42.6 1.0 O2 H:DT5 4.0 40.8 1.0 NA H:NA1003 4.0 45.0 1.0 N1 H:DG4 4.0 35.5 1.0 C5 G:DG12 4.3 43.2 1.0 N3 H:DT5 4.3 40.6 1.0 N1 G:DG1 4.3 42.4 1.0 C5 H:DG9 4.4 43.4 1.0 C2 H:DT5 4.6 40.9 1.0 C5 H:DG4 4.6 37.2 1.0 O H:HOH502 4.6 49.4 1.0 O6 G:DG11 4.7 43.8 1.0 O2 H:DT6 4.7 43.7 1.0 N7 G:DG12 4.8 43.1 1.0 O6 H:DG10 4.9 38.2 1.0 N1 G:DG11 4.9 45.5 1.0 C6 G:DG11 4.9 45.2 1.0 N7 H:DG9 5.0 44.6 1.0 N1 H:DT7 5.0 43.7 1.0 C2 H:DG9 5.0 43.1 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