Sodium in PDB 8d79: Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX

The structure of Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX, PDB code: 8d79 was solved by E.V.Chen, D.Beseiso, L.A.Yatsunyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.97 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.284, 34.716, 34.397, 90, 106.54, 90
R / Rfree (%)	24.1 / 25.3

The binding sites of Sodium atom in the Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX (pdb code 8d79). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX, PDB code: 8d79:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX


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 A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:48.0 occ:1.00 O6 A:DG9 2.6 58.4 1.0 O6 A:DG14 2.6 48.2 1.0 O6 A:DG21 2.7 59.3 1.0 O6 A:DG20 2.7 53.1 1.0 O6 A:DG15 2.7 50.3 1.0 O6 A:DG3 2.7 49.1 1.0 O6 A:DG2 2.8 47.8 1.0 O6 A:DG8 2.8 47.9 1.0 NA A:NA102 3.2 50.4 1.0 NA A:NA104 3.2 47.0 0.5 C6 A:DG9 3.5 52.7 1.0 C6 A:DG14 3.5 52.8 1.0 C6 A:DG20 3.5 50.8 1.0 C6 A:DG21 3.5 50.4 1.0 C6 A:DG15 3.5 55.5 1.0 C6 A:DG3 3.5 51.7 1.0 C6 A:DG2 3.6 54.5 1.0 C6 A:DG8 3.7 48.6 1.0 N1 A:DG9 3.8 61.9 1.0 N1 A:DG14 3.8 49.3 1.0 N1 A:DG21 3.8 50.2 1.0 N1 A:DG3 3.8 49.7 1.0 N1 A:DG15 3.8 50.9 1.0 N1 A:DG20 3.9 51.2 1.0 N1 A:DG2 3.9 48.6 1.0 N1 A:DG8 4.0 49.1 1.0 C5 A:DG14 4.7 53.4 1.0 C5 A:DG20 4.7 56.5 1.0 C5 A:DG15 4.7 60.1 1.0 C5 A:DG9 4.7 53.1 1.0 C5 A:DG21 4.7 50.7 1.0 C5 A:DG3 4.8 57.3 1.0 C5 A:DG2 4.8 54.1 1.0 C5 A:DG8 4.9 52.5 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX


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 A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:50.4 occ:1.00 O6 A:DG10 2.6 56.9 1.0 O6 A:DG15 2.6 50.3 1.0 O6 A:DG3 2.6 49.1 1.0 O6 A:DG21 2.7 59.3 1.0 O6 A:DG16 2.8 56.6 1.0 O6 A:DG22 2.8 58.0 1.0 O6 A:DG9 2.8 58.4 1.0 O6 A:DG4 2.8 56.0 1.0 NA A:NA101 3.2 48.0 1.0 NA A:NA103 3.4 54.7 1.0 C6 A:DG3 3.5 51.7 1.0 C6 A:DG10 3.5 55.4 1.0 C6 A:DG15 3.5 55.5 1.0 C6 A:DG21 3.5 50.4 1.0 C6 A:DG9 3.6 52.7 1.0 C6 A:DG4 3.6 56.4 1.0 C6 A:DG22 3.7 55.3 1.0 C6 A:DG16 3.7 56.5 1.0 N1 A:DG3 3.7 49.7 1.0 N1 A:DG21 3.7 50.2 1.0 N1 A:DG10 3.7 64.3 1.0 N1 A:DG4 3.8 53.8 1.0 N1 A:DG15 3.8 50.9 1.0 N1 A:DG9 3.8 61.9 1.0 N1 A:DG22 3.9 52.8 1.0 N1 A:DG16 4.1 56.9 1.0 C5 A:DG3 4.7 57.3 1.0 C5 A:DG10 4.8 58.1 1.0 C5 A:DG15 4.8 60.1 1.0 C5 A:DG21 4.8 50.7 1.0 C5 A:DG9 4.8 53.1 1.0 O6 A:DG11 4.9 62.9 1.0 C5 A:DG4 4.9 58.5 1.0 C5 A:DG16 4.9 65.2 1.0 C5 A:DG22 4.9 56.2 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX


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 A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:54.7 occ:1.00 O6 A:DG23 2.5 60.3 1.0 O6 A:DG17 2.5 70.4 1.0 O6 A:DG11 2.5 62.9 1.0 O6 A:DG5 2.7 66.1 1.0 O6 A:DG22 2.8 58.0 1.0 O6 A:DG16 2.9 56.6 1.0 O6 A:DG4 2.9 56.0 1.0 O6 A:DG10 3.1 56.9 1.0 NA A:NA102 3.4 50.4 1.0 C6 A:DG23 3.5 58.7 1.0 C6 A:DG11 3.5 64.4 1.0 C6 A:DG17 3.5 67.2 1.0 C6 A:DG22 3.6 55.3 1.0 C6 A:DG4 3.7 56.4 1.0 C6 A:DG5 3.7 63.3 1.0 N1 A:DG11 3.7 61.9 1.0 C6 A:DG16 3.7 56.5 1.0 C6 A:DG10 3.8 55.4 1.0 N1 A:DG22 3.8 52.8 1.0 N1 A:DG23 3.8 56.7 1.0 N1 A:DG17 3.8 64.7 1.0 N1 A:DG4 3.9 53.8 1.0 C1 A:MMP106 3.9 77.3 1.0 N1 A:DG10 4.0 64.3 1.0 N1 A:DG5 4.0 66.3 1.0 N1 A:DG16 4.1 56.9 1.0 C5 A:DG23 4.8 58.1 1.0 C5 A:DG22 4.8 56.2 1.0 C5 A:DG17 4.8 66.3 1.0 C5 A:DG11 4.8 68.1 1.0 C5 A:DG4 4.9 58.5 1.0 C5 A:DG10 4.9 58.1 1.0 C5 A:DG16 4.9 65.2 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX


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 A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:47.0 occ:0.50 O6 A:DG14 2.6 48.2 1.0 O6 A:DG2 2.6 47.8 1.0 O6 A:DG20 2.6 53.1 1.0 O6 A:DG8 2.7 47.9 1.0 NA A:NA101 3.2 48.0 1.0 C6 A:DG14 3.5 52.8 1.0 C6 A:DG20 3.5 50.8 1.0 C6 A:DG2 3.5 54.5 1.0 C6 A:DG8 3.6 48.6 1.0 N1 A:DG20 3.8 51.2 1.0 N1 A:DG14 3.8 49.3 1.0 N1 A:DG2 3.8 48.6 1.0 N1 A:DG8 4.0 49.1 1.0 C5 A:DG14 4.7 53.4 1.0 C5 A:DG20 4.7 56.5 1.0 C5 A:DG2 4.8 54.1 1.0 C5 A:DG8 4.9 52.5 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of A Four-Tetrad, Parallel, and Na+ Stabilized Tetrahymena Thermophila Telomeric G-Quadruplex in Complex with N- Methyl Mesoporphyrin IX within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:98.5 occ:0.50 O2 A:MPD107 2.5 144.8 0.5 C3 A:MPD107 2.6 141.1 0.5 C2 A:MPD107 3.1 142.3 0.5 O2 A:DT19 3.8 99.8 1.0 C4 A:MPD107 4.0 139.6 0.5 C1 A:MPD107 4.0 141.8 0.5 CM A:MPD107 4.2 141.9 0.5 C5 A:MPD107 4.4 139.1 0.5 C1' A:DT19 4.6 111.4 1.0 O4 A:MPD107 4.6 139.0 0.5 C2 A:DT19 4.9 91.8 1.0

D.Beseiso, E.V.Chen, L.A.Yatsunyk. Biophysical and Structural Characterization of Telomeric G-Quadruplexes From Tetrahymena Thermophila in Complex with N-Methyl Mesoporphyrin IX To Be Published.