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Potassium in PDB 6eo7: X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(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-(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-(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-(Acetamide-N-Yl)-1- Propen-1-Yl)-2'-Deoxyuridine Residue, PDB code: 6eo7 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) 81.91 / 2.24
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.579, 94.579, 125.566, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 20.8

Other elements in 6eo7:

The structure of X-Ray Structure of the Complex Between Human Alpha-Thrombin and Modified 15-Mer Dna Aptamer Containing 5-(3-(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-(Acetamide-N-Yl)-1- Propen-1-Yl)-2'-Deoxyuridine Residue (pdb code 6eo7). 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-(Acetamide-N-Yl)-1- Propen-1-Yl)-2'-Deoxyuridine Residue, PDB code: 6eo7:

Potassium binding site 1 out of 1 in 6eo7

Go back to Potassium Binding Sites List in 6eo7
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-(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-(Acetamide-N-Yl)-1- Propen-1-Yl)-2'-Deoxyuridine Residue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K501

b:35.1
occ:1.00
 O6 D:DG410 2.6 36.2 1.0
O6 D:DG402 2.7 33.5 1.0
O6 D:DG414 2.7 36.5 1.0
O6 D:DG405 2.8 38.5 1.0
O6 D:DG401 2.8 32.6 1.0
O6 D:DG415 2.8 33.3 1.0
O6 D:DG406 2.8 37.4 1.0
O6 D:DG411 2.9 33.0 1.0
C6 D:DG410 3.5 38.8 1.0
C6 D:DG405 3.5 35.9 1.0
C6 D:DG414 3.5 33.4 1.0
O D:HOH608 3.6 30.7 1.0
C6 D:DG401 3.7 31.7 1.0
C6 D:DG402 3.7 28.7 1.0
C6 D:DG415 3.7 35.8 1.0
C6 D:DG406 3.7 36.0 1.0
N1 D:DG405 3.8 36.8 1.0
N1 D:DG414 3.8 32.4 1.0
O D:HOH606 3.8 35.7 1.0
C6 D:DG411 3.8 32.2 1.0
N1 D:DG415 3.9 28.5 1.0
N1 D:DG410 3.9 37.0 1.0
N1 D:DG406 3.9 36.1 1.0
N1 D:DG402 4.0 29.3 1.0
N1 D:DG401 4.0 32.1 1.0
N1 D:DG411 4.2 33.1 1.0
C5 D:DG410 4.7 33.4 1.0
C5 D:DG414 4.7 33.3 1.0
C5 D:DG405 4.7 32.3 1.0
C5 D:DG401 4.8 29.2 1.0
C2 D:DG405 5.0 34.2 1.0
C5 D:DG402 5.0 23.9 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 Aug 12 16:01:15 2024

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