Sodium in PDB 5ew1: Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3

All present enzymatic activity of Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3:
3.4.21.5;

The structure of Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3, PDB code: 5ew1 was solved by A.Pica, I.Russo Krauss, V.Parente, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.95
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	145.548, 145.548, 145.548, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 20.8

The binding sites of Sodium atom in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3 (pdb code 5ew1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3, PDB code: 5ew1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:42.1 occ:0.69 O6 D:DG11 2.1 51.8 1.0 O6 D:DG20 2.1 50.6 1.0 O6 D:DG8 2.2 50.0 1.0 O6 D:DG17 2.2 53.6 1.0 O6 D:DG7 3.0 59.2 1.0 C6 D:DG11 3.1 57.4 1.0 C6 D:DG20 3.2 51.2 1.0 O6 D:DG16 3.2 61.0 1.0 N2 D:DG5 3.2 55.2 1.0 C6 D:DG8 3.3 52.1 1.0 N2 D:DG12 3.3 80.8 1.0 C6 D:DG17 3.3 49.6 1.0 N1 D:DG20 3.6 49.9 1.0 N1 D:DG11 3.6 58.7 1.0 N1 D:DG8 3.6 51.2 1.0 N1 D:DG17 3.7 50.7 1.0 C6 D:DG7 3.7 59.7 1.0 C6 D:DG16 3.8 59.7 1.0 N1 D:DG7 4.2 60.3 1.0 N1 D:DA10 4.2 51.8 1.0 C2 D:DG5 4.2 56.0 1.0 O2 D:DT19 4.4 49.3 1.0 C5 D:DG11 4.4 60.9 1.0 N3 D:DT19 4.4 48.2 1.0 C2 D:DG12 4.4 80.8 1.0 C5 D:DG16 4.5 60.7 1.0 C5 D:DG20 4.5 50.7 1.0 C5 D:DG8 4.6 53.3 1.0 C6 D:DA10 4.6 50.1 1.0 C5 D:DG17 4.6 49.0 1.0 N6 D:DA10 4.6 49.6 1.0 N1 D:DG16 4.6 58.1 1.0 C2 D:DT19 4.7 49.6 1.0 N7 D:DG16 4.7 61.9 1.0 C5 D:DG7 4.7 59.0 1.0 C2 D:DA10 4.7 51.2 1.0 N3 D:DG5 4.8 56.0 1.0 N1 D:DG12 4.9 82.0 1.0 C2 D:DG20 4.9 48.0 1.0 C2 D:DG11 5.0 61.5 1.0

Sodium binding site 2 out of 2 in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:35.9 occ:1.00 O6 E:DG14 2.4 42.2 1.0 O6 E:DG6 2.5 45.3 1.0 O6 E:DG15 2.6 57.5 1.0 O6 E:DG1 2.6 48.6 1.0 O6 E:DG10 2.6 57.8 1.0 O6 E:DG2 2.6 47.5 1.0 O6 E:DG5 2.7 41.1 1.0 O6 E:DG11 2.8 44.4 1.0 C6 E:DG14 3.3 45.2 1.0 C6 E:DG5 3.5 43.1 1.0 C6 E:DG1 3.5 48.9 1.0 C6 E:DG6 3.5 47.8 1.0 C6 E:DG10 3.5 57.0 1.0 C6 E:DG15 3.6 53.4 1.0 C6 E:DG2 3.7 45.8 1.0 N1 E:DG14 3.7 50.0 1.0 N1 E:DG5 3.7 42.5 1.0 C6 E:DG11 3.8 43.2 1.0 N1 E:DG6 3.8 47.9 1.0 N2 E:DG8 3.9 86.8 1.0 N1 E:DG15 3.9 57.3 1.0 N1 E:DG10 3.9 57.0 1.0 N1 E:DG1 4.0 48.7 1.0 N1 E:DG2 4.0 45.5 1.0 N1 E:DG11 4.2 42.3 1.0 C5 E:DG14 4.5 48.3 1.0 C5 E:DG5 4.7 44.7 1.0 C5 E:DG1 4.7 47.2 1.0 C2 E:DG8 4.7 88.7 1.0 C5 E:DG10 4.8 55.5 1.0 C5 E:DG15 4.8 50.4 1.0 C5 E:DG6 4.8 50.0 1.0 C2 E:DG14 4.9 54.1 1.0 C5 E:DG2 5.0 47.2 1.0 C2 E:DG5 5.0 43.9 1.0

A.Pica, I.Russo Krauss, V.Parente, H.Tateishi-Karimata, S.Nagatoishi, K.Tsumoto, N.Sugimoto, F.Sica. Through-Bond Effects in the Ternary Complexes of Thrombin Sandwiched By Two Dna Aptamers. Nucleic Acids Res. V. 45 461 2017.
ISSN: ESSN 1362-4962
PubMed: 27899589
DOI: 10.1093/NAR/GKW1113