Sodium in PDB 1pa6: 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: 1pa6 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)	29.79 / 2.45
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.110, 93.110, 422.680, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 26.8

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 1pa6). 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: 1pa6:
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:Na601 b:54.2 occ:1.00 O H:HOH500 2.2 88.0 1.0 O2 G:DT7 2.3 39.5 1.0 O6 H:DG12 2.5 60.0 1.0 O6 G:DG9 2.6 64.8 1.0 O6 G:DG4 2.8 47.6 1.0 O2 G:DT5 3.2 45.1 1.0 O6 H:DG1 3.2 44.9 1.0 C2 G:DT7 3.2 39.3 1.0 C6 H:DG12 3.4 58.9 1.0 C6 G:DG4 3.5 47.5 1.0 C6 G:DG9 3.5 64.5 1.0 N3 G:DT7 3.6 35.5 1.0 N1 G:DG4 3.7 48.2 1.0 N1 H:DG12 3.8 58.7 1.0 N1 G:DG9 3.9 64.0 1.0 C6 H:DG1 3.9 45.0 1.0 N3 G:DT5 3.9 47.4 1.0 C2 G:DT5 3.9 46.2 1.0 NA H:NA602 4.1 0.3 1.0 N1 H:DG1 4.2 44.8 1.0 O2 G:DT6 4.3 27.9 1.0 N1 G:DT7 4.5 40.4 1.0 O6 H:DG11 4.5 64.2 1.0 C5 G:DG4 4.6 44.9 1.0 C5 H:DG12 4.7 58.8 1.0 C5 G:DG9 4.8 64.6 1.0 O G:HOH499 4.9 42.3 1.0 C2 G:DG4 4.9 46.2 1.0 C4 G:DT7 4.9 36.5 1.0 C5 H:DG1 5.0 45.2 1.0 O4' G:DT8 5.0 58.0 1.0 C2 G:DT6 5.0 28.7 1.0 C1' G:DT7 5.0 42.5 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 G:Na603 b:63.4 occ:1.00 O6 G:DG11 2.1 64.1 1.0 O6 H:DG3 2.2 63.7 1.0 O6 H:DG10 2.3 71.0 1.0 O6 G:DG2 2.8 55.0 1.0 O6 G:DG1 2.9 60.4 1.0 C6 G:DG11 3.1 63.7 1.0 O6 H:DG2 3.2 53.4 1.0 C6 H:DG3 3.2 64.7 1.0 C6 H:DG10 3.3 71.2 1.0 N1 G:DG11 3.4 64.2 1.0 N1 H:DG3 3.6 65.4 1.0 N1 H:DG10 3.6 71.0 1.0 O6 H:DG4 3.7 52.9 1.0 C6 G:DG2 3.7 56.4 1.0 C6 G:DG1 3.8 58.8 1.0 C6 H:DG2 3.9 54.1 1.0 O6 H:DG9 3.9 60.8 1.0 N1 G:DG2 4.0 56.4 1.0 N1 G:DG1 4.2 59.5 1.0 N1 G:DG10 4.2 60.5 1.0 NA H:NA604 4.3 65.7 1.0 O6 G:DG10 4.3 61.8 1.0 NA H:NA602 4.3 0.3 1.0 C5 G:DG11 4.4 63.8 1.0 N1 H:DG2 4.4 52.3 1.0 O6 G:DG12 4.4 56.7 1.0 N1 H:DG4 4.5 54.5 1.0 C6 G:DG10 4.5 60.8 1.0 C6 H:DG4 4.5 54.3 1.0 C5 H:DG3 4.6 63.4 1.0 C5 H:DG10 4.7 70.4 1.0 C5 H:DG2 4.7 54.2 1.0 O6 G:DG3 4.7 55.4 1.0 C6 H:DG9 4.8 60.3 1.0 C2 G:DG11 4.8 64.4 1.0 C5 G:DG1 4.9 58.7 1.0 C2 H:DG3 4.9 65.0 1.0 C2 H:DG10 4.9 70.7 1.0 C2 G:DG10 5.0 59.5 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:Na602 b:0.3 occ:1.00 O6 H:DG1 2.3 44.9 1.0 O6 H:DG2 2.3 53.4 1.0 O6 G:DG10 2.4 61.8 1.0 O6 H:DG11 2.6 64.2 1.0 O6 G:DG3 2.6 55.4 1.0 C6 H:DG1 3.2 45.0 1.0 C6 G:DG10 3.2 60.8 1.0 C6 H:DG2 3.2 54.1 1.0 N1 G:DG10 3.3 60.5 1.0 O6 G:DG2 3.6 55.0 1.0 O6 G:DG9 3.6 64.8 1.0 C6 H:DG11 3.6 63.0 1.0 N1 H:DG2 3.6 52.3 1.0 C6 G:DG3 3.6 52.7 1.0 N1 H:DG1 3.7 44.8 1.0 O6 G:DG4 3.7 47.6 1.0 N1 H:DG11 3.9 63.8 1.0 N1 G:DG4 4.0 48.2 1.0 N1 G:DG3 4.0 52.1 1.0 NA G:NA601 4.1 54.2 1.0 C6 G:DG4 4.3 47.5 1.0 C6 G:DG2 4.3 56.4 1.0 NA G:NA603 4.3 63.4 1.0 C5 H:DG1 4.4 45.2 1.0 C6 G:DG9 4.4 64.5 1.0 C5 H:DG2 4.5 54.2 1.0 O6 H:DG10 4.5 71.0 1.0 O6 H:DG12 4.6 60.0 1.0 C5 G:DG10 4.6 60.4 1.0 N1 H:DG10 4.6 71.0 1.0 C2 G:DG10 4.6 59.5 1.0 N1 G:DG2 4.8 56.4 1.0 O6 H:DG3 4.8 63.7 1.0 C6 H:DG10 4.8 71.2 1.0 C5 G:DG3 4.9 51.4 1.0 C2 H:DG2 4.9 52.2 1.0 N7 H:DG1 4.9 45.2 1.0 C5 H:DG11 4.9 62.9 1.0 N1 G:DG9 4.9 64.0 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:Na604 b:65.7 occ:1.00 O6 G:DG12 2.5 56.7 1.0 O6 H:DG4 2.5 52.9 1.0 O2 H:DT7 2.6 52.2 1.0 O6 H:DG9 2.7 60.8 1.0 O6 G:DG1 2.9 60.4 1.0 O H:HOH501 3.0 49.7 1.0 O2 H:DT5 3.2 62.9 1.0 C6 H:DG4 3.3 54.3 1.0 C6 G:DG12 3.4 54.8 1.0 C2 H:DT7 3.4 52.1 1.0 N3 H:DT7 3.6 50.9 1.0 N1 G:DG12 3.6 53.2 1.0 C6 H:DG9 3.7 60.3 1.0 C6 G:DG1 3.7 58.8 1.0 N1 H:DG4 3.8 54.5 1.0 C2 H:DT5 4.0 62.8 1.0 N3 H:DT5 4.0 63.4 1.0 N1 H:DG9 4.0 59.5 1.0 N1 G:DG1 4.1 59.5 1.0 NA G:NA603 4.3 63.4 1.0 O2 H:DT6 4.4 68.3 1.0 C5 H:DG4 4.4 54.6 1.0 O6 G:DG11 4.5 64.1 1.0 O H:HOH502 4.5 41.3 1.0 C5 G:DG12 4.7 55.3 1.0 N1 H:DT7 4.7 53.4 1.0 C5 G:DG1 4.8 58.7 1.0 O6 H:DG3 4.9 63.7 1.0 C5 H:DG9 4.9 61.4 1.0 C6 G:DG11 4.9 63.7 1.0 C2 G:DG12 4.9 52.6 1.0 C4 H:DT7 5.0 51.0 1.0 C2 H:DT6 5.0 68.0 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