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Sodium in PDB 7ntu: X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER, PDB code: 7ntu was solved by R.Troisi, A.Santamaria, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.77 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.927, 77.616, 95.408, 90, 103.47, 90
R / Rfree (%) 20 / 25.7

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER (pdb code 7ntu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER, PDB code: 7ntu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7ntu

Go back to Sodium Binding Sites List in 7ntu
Sodium binding site 1 out of 4 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER


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 Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na101

b:26.3
occ:1.00
 O6 E:DG16 2.6 36.3 1.0
O6 E:DG7 2.7 29.5 1.0
O6 E:DG21 2.7 59.3 1.0
O6 E:DG12 2.7 25.3 1.0
O6 E:DG20 3.0 38.2 1.0
O6 E:DG11 3.1 34.7 1.0
O6 E:DG17 3.2 36.6 1.0
C6 E:DG16 3.4 38.7 1.0
O6 E:DG8 3.4 39.6 1.0
N1 E:DG16 3.5 39.1 1.0
C6 E:DG7 3.6 35.2 1.0
C6 E:DG12 3.6 25.3 1.0
C6 E:DG21 3.7 58.5 1.0
N1 E:DG12 3.7 25.3 1.0
N1 E:DG7 3.7 38.5 1.0
C6 E:DG20 3.8 39.7 1.0
N1 E:DG21 3.9 52.5 1.0
C6 E:DG17 3.9 34.9 1.0
C6 E:DG11 3.9 37.0 1.0
N6 E:DA6 4.0 41.5 1.0
N1 E:DA6 4.0 34.8 1.0
N1 E:DG20 4.0 37.3 1.0
C6 E:DA6 4.1 36.5 1.0
N1 E:DG17 4.2 30.1 1.0
N1 E:DG11 4.2 31.9 1.0
C6 E:DG8 4.2 32.5 1.0
O E:HOH201 4.3 73.7 1.0
N1 E:DG8 4.4 34.5 1.0
O4 E:DT22 4.7 59.2 1.0
C2 E:DG16 4.8 41.7 1.0
C2 E:DA6 4.8 33.9 1.0
C5 E:DG16 4.8 37.5 1.0
C5 E:DG7 4.9 39.8 1.0
C5 E:DG20 4.9 38.8 1.0
C5 E:DG12 5.0 29.1 1.0

Sodium binding site 2 out of 4 in 7ntu

Go back to Sodium Binding Sites List in 7ntu
Sodium binding site 2 out of 4 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER


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 Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na101

b:9.9
occ:1.00
 O6 F:DG11 2.3 40.3 1.0
O6 F:DG8 2.5 29.9 1.0
O6 F:DG20 2.6 23.7 1.0
O6 F:DG17 2.8 32.0 1.0
O6 F:DG7 2.9 30.7 1.0
O6 F:DG16 3.2 45.1 1.0
C6 F:DG11 3.3 39.1 1.0
C6 F:DG8 3.4 29.9 1.0
N2 F:DG5 3.5 36.9 1.0
C6 F:DG20 3.5 25.6 1.0
N1 F:DG8 3.5 28.3 1.0
C6 F:DG7 3.6 40.7 1.0
N1 F:DG11 3.6 34.2 1.0
N1 F:DG20 3.6 25.5 1.0
C6 F:DG17 3.7 28.4 1.0
N1 F:DG17 3.8 27.4 1.0
C6 F:DG16 3.9 45.9 1.0
N2 F:DG12 3.9 52.9 1.0
N1 F:DG7 4.0 46.9 1.0
N1 F:DA10 4.0 25.5 1.0
O2 F:DT19 4.2 33.7 1.0
N3 F:DT19 4.3 27.5 1.0
N6 F:DA10 4.3 35.2 1.0
C6 F:DA10 4.4 28.7 1.0
C5 F:DG7 4.5 44.0 1.0
C2 F:DT19 4.5 31.0 1.0
C2 F:DG5 4.5 32.3 1.0
N1 F:DG16 4.5 41.3 1.0
C5 F:DG16 4.6 44.7 1.0
C5 F:DG11 4.6 40.8 1.0
C2 F:DA10 4.7 27.1 1.0
C5 F:DG8 4.8 29.1 1.0
C2 F:DG8 4.8 28.0 1.0
C5 F:DG20 4.8 25.9 1.0
C2 F:DG20 4.9 29.1 1.0
C2 F:DG11 4.9 39.6 1.0
N7 F:DG16 4.9 41.7 1.0
N7 F:DG7 5.0 47.5 1.0

Sodium binding site 3 out of 4 in 7ntu

Go back to Sodium Binding Sites List in 7ntu
Sodium binding site 3 out of 4 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na101

b:52.5
occ:1.00
 O6 G:DG12 2.5 23.8 1.0
O6 G:DG16 2.6 37.3 1.0
O6 G:DG7 2.9 44.7 1.0
O6 G:DG21 2.9 50.0 1.0
O6 G:DG11 2.9 47.3 1.0
O6 G:DG20 3.1 61.0 1.0
O6 G:DG17 3.1 64.3 1.0
O6 G:DG8 3.4 48.7 1.0
C6 G:DG12 3.4 27.7 1.0
C6 G:DG16 3.5 38.6 1.0
N1 G:DG12 3.5 30.1 1.0
N1 G:DG16 3.6 38.0 1.0
C6 G:DG11 3.7 51.5 1.0
C6 G:DG7 3.7 42.8 1.0
N1 G:DG7 3.8 38.5 1.0
C6 G:DG17 3.9 48.8 1.0
C6 G:DG21 3.9 51.8 1.0
C6 G:DG20 3.9 52.3 1.0
N6 G:DA6 4.0 44.3 1.0
N1 G:DG17 4.0 40.4 1.0
N1 G:DG11 4.0 44.4 1.0
N1 G:DG21 4.1 53.6 1.0
N1 G:DG20 4.1 46.3 1.0
N1 G:DA6 4.1 44.4 1.0
C6 G:DA6 4.2 43.3 1.0
C6 G:DG8 4.3 42.9 1.0
N1 G:DG8 4.5 45.5 1.0
C5 G:DG12 4.8 29.6 1.0
C5 G:DG16 4.8 37.8 1.0
O4 G:DT22 4.8 59.0 1.0
C2 G:DG12 4.8 35.6 1.0
C2 G:DA6 4.9 51.7 1.0
C5 G:DG11 4.9 57.1 1.0
O G:HOH202 4.9 66.7 1.0
C2 G:DG16 4.9 36.3 1.0

Sodium binding site 4 out of 4 in 7ntu

Go back to Sodium Binding Sites List in 7ntu
Sodium binding site 4 out of 4 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the Complex Between Human Alpha Thrombin and Two Duplex/Quadruplex Aptamers: NU172 and HD22_27MER within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na101

b:19.6
occ:1.00
 O6 I:DG20 2.1 20.7 1.0
O6 I:DG11 2.5 32.0 1.0
O6 I:DG8 2.6 18.9 1.0
O6 I:DG17 2.8 24.2 1.0
C6 I:DG20 3.0 24.8 1.0
O6 I:DG7 3.0 20.4 1.0
N1 I:DG20 3.2 27.7 1.0
N1 I:DG8 3.4 21.4 1.0
O6 I:DG16 3.4 50.1 1.0
N2 I:DG5 3.4 42.1 1.0
C6 I:DG8 3.4 21.7 1.0
C6 I:DG7 3.5 27.1 1.0
C6 I:DG11 3.6 33.6 1.0
C6 I:DG17 3.8 24.9 1.0
N1 I:DG7 3.8 30.8 1.0
O2 I:DT19 3.9 22.8 1.0
N1 I:DG11 3.9 32.8 1.0
C6 I:DG16 4.0 44.6 1.0
N1 I:DG17 4.1 26.1 1.0
N1 I:DA10 4.2 35.0 1.0
N3 I:DT19 4.2 17.5 1.0
C2 I:DG5 4.3 39.1 1.0
N2 I:DG12 4.3 61.2 1.0
C2 I:DT19 4.3 19.4 1.0
N6 I:DA10 4.3 31.4 1.0
C5 I:DG20 4.4 26.5 1.0
C6 I:DA10 4.5 32.0 1.0
C2 I:DG20 4.5 30.5 1.0
C5 I:DG7 4.6 31.2 1.0
C5 I:DG16 4.6 36.5 1.0
C2 I:DG8 4.6 18.7 1.0
N1 I:DG16 4.8 41.2 1.0
N3 I:DG5 4.8 35.5 1.0
C5 I:DG8 4.8 23.3 1.0
N7 I:DG16 4.8 33.6 1.0
C2 I:DG7 4.9 33.1 1.0
C5 I:DG11 4.9 34.4 1.0
C2 I:DA10 5.0 30.7 1.0

Reference:

R.Troisi, N.Balasco, A.Santamaria, L.Vitagliano, F.Sica. Structural and Functional Analysis of the Simultaneous Binding of Two Duplex/Quadruplex Aptamers to Human Alpha-Thrombin. Int.J.Biol.Macromol. 2021.
ISSN: ISSN 0141-8130
PubMed: 33864869
DOI: 10.1016/J.IJBIOMAC.2021.04.076
Page generated: Tue Oct 8 18:12:08 2024

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