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Sodium in PDB 6eo6: X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue, PDB code: 6eo6 was solved by R.M.Dolot, B.Nawrot, X.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.49 / 1.69
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.095, 94.095, 124.710, 90.00, 90.00, 120.00
R / Rfree (%) 14.5 / 16.8

Other elements in 6eo6:

The structure of X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue also contains other interesting chemical elements:

Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue (pdb code 6eo6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue, PDB code: 6eo6:

Sodium binding site 1 out of 1 in 6eo6

Go back to Sodium Binding Sites List in 6eo6
Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue


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 Modified 15-Mer Dna Aptamer Containing 5-(3-(2-(1H-Indol-3-Yl) Acetamide-N-Yl)-1-Propen-1-Yl)-2'-Deoxyuridine Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na702

b:19.3
occ:1.00
 O H:LYS599 2.3 21.0 1.0
O H:HOH1001 2.3 19.3 1.0
O H:ARG596 2.3 19.5 1.0
O H:HOH894 2.4 20.5 1.0
O H:HOH879 2.4 19.8 1.0
O H:HOH903 2.6 21.5 1.0
C H:LYS599 3.4 17.3 1.0
C H:ARG596 3.5 20.0 1.0
N H:LYS599 3.9 19.2 1.0
O H:HOH939 3.9 20.8 1.0
O H:HOH842 3.9 22.1 1.0
N H:ARG596 4.0 19.6 1.0
O H:TYR553 4.0 21.2 1.0
C H:ASP595 4.1 20.8 1.0
CA H:LYS599 4.1 18.7 1.0
O H:HOH887 4.2 19.2 1.0
N H:GLY598 4.2 20.2 1.0
CA H:ASP597 4.3 20.9 1.0
N H:ASP597 4.3 19.6 1.0
CA H:ARG596 4.3 20.2 1.0
CA H:ASP595 4.4 19.3 1.0
N H:TYR600 4.4 19.6 1.0
O H:ASP595 4.5 19.8 1.0
CB H:LYS599 4.5 20.9 1.0
C H:ASP597 4.6 24.3 1.0
O H:HOH849 4.6 24.2 1.0
OD1 H:ASP595 4.6 20.4 1.0
CA H:TYR600 4.7 17.7 1.0
C H:GLY598 4.9 20.7 1.0

Reference:

R.Dolot, C.H.Lam, M.Sierant, Q.Zhao, F.W.Liu, B.Nawrot, M.Egli, X.Yang. Crystal Structures of Thrombin in Complex with Chemically Modified Thrombin Dna Aptamers Reveal the Origins of Enhanced Affinity. Nucleic Acids Res. V. 46 4819 2018.
ISSN: ESSN 1362-4962
PubMed: 29684204
DOI: 10.1093/NAR/GKY268
Page generated: Tue Oct 8 08:27:30 2024

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