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Sodium in PDB 6gn7: X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions.

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions.

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions.:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions., PDB code: 6gn7 was solved by R.Troisi, I.Russo Krauss, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.51 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 67.330, 120.690, 208.940, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.3

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions. (pdb code 6gn7). 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 NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions., PDB code: 6gn7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6gn7

Go back to Sodium Binding Sites List in 6gn7
Sodium binding site 1 out of 2 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions.


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 NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:48.5
occ:1.00
O H:ARG221 2.1 47.5 1.0
O H:HOH461 2.2 44.7 1.0
O H:LYS224 2.2 32.6 1.0
O H:HOH468 2.2 51.5 1.0
O H:HOH428 2.7 37.5 1.0
O H:HOH451 2.7 46.4 1.0
C H:ARG221 3.2 45.3 1.0
C H:LYS224 3.3 34.0 1.0
N H:LYS224 3.6 35.8 1.0
N H:ARG221 3.8 32.2 1.0
CA H:LYS224 3.9 32.5 1.0
N H:ASP222 4.0 53.1 1.0
C H:ASP221A 4.1 31.9 1.0
CA H:ARG221 4.1 36.6 1.0
CA H:ASP222 4.1 54.6 1.0
N H:GLY223 4.1 37.0 1.0
O H:TYR184A 4.2 41.1 1.0
CB H:LYS224 4.2 36.5 1.0
C H:ASP222 4.3 37.3 1.0
O H:HOH449 4.3 37.3 1.0
N H:TYR225 4.4 28.6 1.0
O H:HOH427 4.4 33.6 1.0
CA H:ASP221A 4.5 34.5 1.0
O H:ASP221A 4.5 32.2 1.0
O H:HOH404 4.6 52.8 1.0
C H:GLY223 4.7 39.6 1.0
CA H:TYR225 4.7 36.0 1.0
OD1 H:ASP221A 4.7 33.0 1.0
CD1 H:TYR225 4.9 39.3 1.0
CA H:GLY223 5.0 37.0 1.0
CE1 H:TYR225 5.0 44.9 1.0

Sodium binding site 2 out of 2 in 6gn7

Go back to Sodium Binding Sites List in 6gn7
Sodium binding site 2 out of 2 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions.


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 NU172, A Duplex/Quadruplex 26-Mer Dna Aptamer, in the Presence of Sodium Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na101

b:35.4
occ:0.60
O6 E:DG12 2.3 48.6 1.0
O6 E:DG16 2.4 41.5 1.0
O6 E:DG7 2.5 70.1 1.0
O6 E:DG11 2.5 54.8 1.0
O6 E:DG21 2.5 75.2 1.0
O6 E:DG20 2.7 59.8 1.0
O6 E:DG8 2.7 42.4 1.0
O6 E:DG17 2.8 50.1 1.0
C6 E:DG12 3.2 46.8 1.0
C6 E:DG11 3.3 55.9 1.0
C6 E:DG7 3.3 48.8 1.0
C6 E:DG16 3.4 50.0 1.0
C6 E:DG20 3.5 62.2 1.0
C6 E:DG21 3.6 83.6 1.0
C6 E:DG17 3.6 48.3 1.0
N1 E:DG12 3.6 35.6 1.0
N1 E:DG7 3.7 49.5 1.0
N1 E:DG11 3.7 49.0 1.0
C6 E:DG8 3.7 52.1 1.0
N1 E:DG16 3.8 52.3 1.0
N1 E:DG20 3.8 58.1 1.0
N1 E:DG17 3.9 44.2 1.0
N1 E:DG21 3.9 79.0 1.0
O E:HOH202 4.0 43.6 1.0
N1 E:DG8 4.2 51.1 1.0
C5 E:DG11 4.4 38.5 1.0
N1 E:DA6 4.4 45.8 1.0
N6 E:DA6 4.4 53.4 1.0
C6 E:DA6 4.5 60.4 1.0
C5 E:DG12 4.5 36.0 1.0
C5 E:DG7 4.6 47.8 1.0
C5 E:DG16 4.6 39.5 1.0
C5 E:DG20 4.7 66.4 1.0
C5 E:DG17 4.8 38.4 1.0
C5 E:DG21 4.8 75.8 1.0
C2 E:DG11 4.9 56.1 1.0
C5 E:DG8 4.9 42.7 1.0
C2 E:DG7 5.0 57.8 1.0
C2 E:DG12 5.0 43.2 1.0
N7 E:DG11 5.0 45.2 1.0

Reference:

R.Troisi, V.Napolitano, V.Spiridonova, I.Russo Krauss, F.Sica. Several Structural Motifs Cooperate in Determining the Highly Effective Anti-Thrombin Activity of NU172 Aptamer. Nucleic Acids Res. V. 46 12177 2018.
ISSN: ESSN 1362-4962
PubMed: 30357392
DOI: 10.1093/NAR/GKY990
Page generated: Tue Oct 8 09:02:44 2024

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