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Potassium 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:

Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total only one binding site of Potassium 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:

Potassium binding site 1 out of 1 in 6eo6

Go back to Potassium Binding Sites List in 6eo6
Potassium 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 Potassium with other atoms in the K 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
D:K501

b:23.6
occ:1.00
O6 D:DG410 2.7 26.6 1.0
O6 D:DG401 2.7 24.2 1.0
O6 D:DG405 2.8 23.3 1.0
O6 D:DG402 2.8 22.8 1.0
O6 D:DG406 2.8 24.5 1.0
O6 D:DG414 2.8 23.2 1.0
O6 D:DG411 2.8 23.8 1.0
O6 D:DG415 2.8 24.5 1.0
C6 D:DG414 3.5 21.9 1.0
C6 D:DG405 3.5 21.1 1.0
C6 D:DG401 3.6 21.4 1.0
C6 D:DG410 3.6 25.7 1.0
O D:HOH622 3.6 22.5 1.0
C6 D:DG406 3.7 24.7 1.0
C6 D:DG415 3.7 24.4 1.0
C6 D:DG402 3.8 20.8 1.0
C6 D:DG411 3.8 24.5 1.0
N1 D:DG414 3.8 24.2 1.0
N1 D:DG405 3.8 21.4 1.0
N1 D:DG406 3.8 24.7 1.0
N1 D:DG415 3.9 26.6 1.0
N1 D:DG401 4.0 23.9 1.0
N1 D:DG410 4.0 28.1 1.0
O D:HOH619 4.1 27.4 1.0
N1 D:DG411 4.1 23.9 1.0
N1 D:DG402 4.1 23.6 1.0
C5 D:DG414 4.7 23.4 1.0
C5 D:DG405 4.7 21.4 1.0
C5 D:DG401 4.8 23.5 1.0
C5 D:DG410 4.8 26.3 1.0
C5 D:DG406 5.0 25.1 1.0
C2 D:DG414 5.0 23.6 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: Mon Dec 14 00:35:52 2020

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