Sodium in PDB 8bw5: X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER:
3.4.21.5;

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER, PDB code: 8bw5 was solved by R.Troisi, V.Napolitano, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.27 / 2.80
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.06, 75.49, 114.31, 90, 90, 90
R / Rfree (%)	20.6 / 25.2

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER (pdb code 8bw5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER, PDB code: 8bw5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:61.0 occ:1.00 O H:HOH402 2.4 69.4 1.0 O H:LYS224 2.6 53.5 1.0 O H:ARG221 2.7 56.0 1.0 C H:ARG221 3.7 54.6 1.0 C H:LYS224 3.7 53.5 1.0 C H:ASP221A 3.8 53.0 1.0 N H:ARG221 3.9 52.6 1.0 CA H:ASP221A 4.0 53.7 1.0 N H:LYS224 4.2 54.1 1.0 O H:ASP221A 4.3 54.1 1.0 CA H:LYS224 4.3 52.2 1.0 OD1 H:ASP221A 4.3 58.4 1.0 O H:TYR184A 4.4 51.6 1.0 CA H:ARG221 4.4 54.0 1.0 CB H:LYS224 4.4 49.9 1.0 N H:ASP222 4.5 54.6 1.0 CA H:ASP222 4.6 56.2 1.0 N H:ASP221A 4.7 55.1 1.0 N H:TYR225 4.7 54.5 1.0 O H:HOH414 4.7 45.7 1.0 N H:GLY223 4.8 56.2 1.0 O H:GLY188 4.8 51.0 1.0 OD2 H:ASP189 4.9 53.0 1.0 CA H:TYR225 5.0 54.8 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Complex Between Human Alpha Thrombin and the Duplex/Quadruplex Aptamer M08S-1_41MER within 5.0Å range: probe atom residue distance (Å) B Occ F:Na101 b:71.2 occ:1.00 O6 F:DG22 2.2 77.9 1.0 O6 F:DG19 2.3 60.9 1.0 O6 F:DG18 2.6 57.4 1.0 O6 F:DG14 2.6 62.3 1.0 O6 F:DG15 2.6 58.1 1.0 O6 F:DG27 2.8 83.5 1.0 O6 F:DG26 2.8 79.8 1.0 O6 F:DG23 3.0 71.3 1.0 C6 F:DG19 3.2 65.4 1.0 C6 F:DG18 3.2 57.5 1.0 N1 F:DG19 3.3 62.4 1.0 C6 F:DG22 3.3 76.1 1.0 N2 F:DG20 3.5 74.1 1.0 C6 F:DG14 3.5 60.2 1.0 C6 F:DG26 3.6 83.0 1.0 N1 F:DG18 3.6 57.1 1.0 C6 F:DG15 3.7 60.4 1.0 C6 F:DG23 3.9 70.9 1.0 N1 F:DG14 3.9 57.2 1.0 C6 F:DG27 3.9 83.9 1.0 N1 F:DG26 3.9 79.6 1.0 O F:HOH201 4.0 67.2 1.0 N1 F:DG22 4.0 74.8 1.0 C2 F:DG20 4.1 70.9 1.0 N1 F:DG23 4.2 68.2 1.0 N1 F:DG15 4.2 58.0 1.0 C5 F:DG18 4.2 57.5 1.0 N1 F:DG27 4.3 80.2 1.0 C5 F:DG22 4.5 77.0 1.0 C5 F:DG19 4.5 65.9 1.0 N3 F:DG20 4.6 69.0 1.0 C2 F:DG19 4.6 62.8 1.0 C5 F:DG14 4.7 60.9 1.0 C5 F:DG26 4.7 84.1 1.0 C2 F:DG18 4.8 56.9 1.0 N7 F:DG18 4.8 58.4 1.0 C5 F:DG15 4.9 61.2 1.0 N1 F:DG20 4.9 69.3 1.0 N7 F:DG22 5.0 78.8 1.0

R.Troisi, V.Napolitano, F.Sica. Steric Hindrance and Structural Flexibility Shape the Functional Properties of A Guanine-Rich Oligonucleotide To Be Published 2023.