Sodium in PDB 5ew2: Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12

All present enzymatic activity of Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12:
3.4.21.5;

The structure of Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12, PDB code: 5ew2 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 / 3.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.089, 41.296, 104.923, 90.00, 102.90, 90.00
R / Rfree (%)	20.8 / 26.8

The binding sites of Sodium atom in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12 (pdb code 5ew2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12, PDB code: 5ew2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12


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- DELTAT12 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:21.6 occ:1.00 O H:LYS224 2.6 68.4 1.0 O H:ARG221 3.3 73.5 1.0 O H:TYR184A 3.7 67.0 1.0 OD1 H:ASP221A 3.8 64.7 1.0 C H:LYS224 3.8 69.5 1.0 O H:HOH402 4.1 40.3 1.0 CA H:ASP221A 4.1 64.9 1.0 O H:GLY188 4.1 58.7 1.0 C H:ARG221 4.2 72.6 1.0 C H:ASP221A 4.2 67.8 1.0 N H:ARG221 4.3 68.0 1.0 CA H:TYR225 4.5 66.2 1.0 N H:TYR225 4.5 67.5 1.0 N H:TYR184A 4.6 57.6 1.0 OD2 H:ASP189 4.7 50.6 1.0 CB H:ASP189 4.7 50.8 1.0 N H:LYS224 4.7 74.9 1.0 O H:ASP221A 4.8 71.6 1.0 CG H:ASP221A 4.8 65.8 1.0 CA H:LYS224 4.8 73.2 1.0 CD2 H:TYR225 4.8 71.9 1.0 C H:TYR184A 4.9 66.0 1.0 N H:ASP221A 4.9 63.3 1.0 CA H:GLY184 4.9 54.1 1.0 CA H:ARG221 4.9 71.6 1.0 N H:ASP222 5.0 74.5 1.0

Sodium binding site 2 out of 3 in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12


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- DELTAT12 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:38.3 occ:1.00 O6 D:DG11 2.0 70.9 1.0 O6 D:DG20 2.1 60.8 1.0 O6 D:DG17 2.1 67.7 1.0 O6 D:DG8 2.3 60.6 1.0 C6 D:DG20 3.1 63.0 1.0 N2 D:DG5 3.1 77.4 1.0 C6 D:DG17 3.1 68.9 1.0 C6 D:DG11 3.2 72.5 1.0 C6 D:DG8 3.3 59.0 1.0 N1 D:DG20 3.4 64.8 1.0 O6 D:DG16 3.4 82.9 1.0 O6 D:DG7 3.4 72.0 1.0 N1 D:DG17 3.5 70.4 1.0 N2 D:DG12 3.6 82.7 1.0 N1 D:DG8 3.6 58.1 1.0 N1 D:DG11 3.7 72.8 1.0 O2 D:DT19 3.7 55.4 1.0 N3 D:DT19 3.8 56.8 1.0 N1 D:DA10 3.8 57.3 1.0 C6 D:DG16 4.0 81.1 1.0 C2 D:DT19 4.0 56.3 1.0 C6 D:DG7 4.0 70.9 1.0 C2 D:DG5 4.2 77.9 1.0 N6 D:DA10 4.4 57.1 1.0 C6 D:DA10 4.4 57.1 1.0 C5 D:DG20 4.4 64.4 1.0 C5 D:DG17 4.4 69.0 1.0 C5 D:DG11 4.4 74.2 1.0 N1 D:DG7 4.5 70.1 1.0 C2 D:DA10 4.5 59.4 1.0 C5 D:DG8 4.6 58.3 1.0 C5 D:DG16 4.6 80.1 1.0 C2 D:DG12 4.7 83.1 1.0 N3 D:DG5 4.7 76.6 1.0 C4 D:DT19 4.7 58.3 1.0 N1 D:DG16 4.7 82.1 1.0 C2 D:DG20 4.8 66.7 1.0 N7 D:DG16 4.8 80.7 1.0 C2 D:DG17 4.9 71.5 1.0 C5 D:DG7 4.9 71.0 1.0 C2 D:DG8 5.0 56.9 1.0 O4 D:DT19 5.0 60.0 1.0

Sodium binding site 3 out of 3 in the Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Thrombin Sandwiched Between Two Dna Aptamers: HD22 and HD1- DELTAT12 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:70.9 occ:1.00 O6 E:DG1 2.4 88.4 1.0 O6 E:DG10 2.5 93.9 1.0 O6 E:DG5 2.5 87.7 1.0 O6 E:DG14 2.6 84.2 1.0 O6 E:DG6 2.6 89.6 1.0 O6 E:DG11 2.9 91.6 1.0 O6 E:DG15 2.9 1.0 1.0 O6 E:DG2 2.9 83.4 1.0 C6 E:DG5 3.2 86.5 1.0 C6 E:DG10 3.4 95.0 1.0 C6 E:DG14 3.4 84.3 1.0 C6 E:DG1 3.4 89.9 1.0 N1 E:DG5 3.6 84.3 1.0 C6 E:DG6 3.7 92.2 1.0 C6 E:DG15 3.8 0.7 1.0 N2 E:DG8 3.8 0.2 1.0 N1 E:DG14 3.8 84.7 1.0 N1 E:DG10 3.8 94.8 1.0 C6 E:DG11 3.8 92.0 1.0 N1 E:DG15 3.9 0.7 1.0 N1 E:DG1 3.9 90.8 1.0 C6 E:DG2 3.9 81.7 1.0 N1 E:DG6 4.0 92.2 1.0 N1 E:DG11 4.1 92.3 1.0 N1 E:DG2 4.3 81.5 1.0 C5 E:DG5 4.4 87.8 1.0 C5 E:DG14 4.6 84.5 1.0 C2 E:DG8 4.6 1.0 1.0 C5 E:DG10 4.7 96.4 1.0 C5 E:DG1 4.7 89.3 1.0 C2 E:DG5 4.8 84.7 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