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Potassium in PDB 7zkm: X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta, PDB code: 7zkm was solved by R.Troisi, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.10 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.6, 76.6, 129.38, 90, 90, 120
R / Rfree (%) 22.6 / 25.2

Other elements in 7zkm:

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta 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 A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta (pdb code 7zkm). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta, PDB code: 7zkm:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 7zkm

Go back to Potassium Binding Sites List in 7zkm
Potassium binding site 1 out of 2 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta


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 A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K103

b:83.4
occ:1.00
O6 A:DG5 2.8 73.4 1.0
O6 A:DG15 2.8 94.6 1.0
O6 A:DG14 2.8 72.9 1.0
O6 A:DG11 2.9 72.4 1.0
O6 A:DG2 3.0 71.8 1.0
O6 A:DG1 3.0 75.6 1.0
N1 A:DG2 3.5 70.6 1.0
O6 A:DG10 3.5 80.9 1.0
C6 A:DG5 3.6 75.8 1.0
C6 A:DG2 3.6 71.0 1.0
C6 A:DG15 3.7 95.4 1.0
O A:HOH201 3.7 69.6 1.0
O6 A:DG6 3.7 89.3 1.0
N1 A:DG5 3.8 75.5 1.0
N1 A:DG15 3.8 95.6 1.0
N1 A:DG10 3.8 82.9 1.0
C6 A:DG1 3.8 79.4 1.0
C6 A:DG14 3.9 74.9 1.0
C6 A:DG11 4.0 73.5 1.0
C6 A:DG10 4.0 82.3 1.0
N1 A:DG1 4.1 80.0 1.0
N1 A:DG14 4.4 74.0 1.0
N1 A:DG6 4.5 88.7 1.0
C6 A:DG6 4.5 90.4 1.0
N1 A:DG11 4.5 74.9 1.0
C2 A:DG2 4.7 71.5 1.0
N3 A:DT4 4.9 80.0 1.0
C2 A:DG10 4.9 83.5 1.0
C5 A:DG5 4.9 77.6 1.0
C5 A:DG15 5.0 95.9 1.0
N2 A:DG2 5.0 71.6 1.0
C5 A:DG1 5.0 81.4 1.0

Potassium binding site 2 out of 2 in 7zkm

Go back to Potassium Binding Sites List in 7zkm
Potassium binding site 2 out of 2 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K103

b:63.8
occ:1.00
O6 B:DG14 2.7 59.8 1.0
O6 B:DG15 2.8 59.1 1.0
O6 B:DG10 2.8 66.1 1.0
O6 B:DG1 2.9 58.6 1.0
O6 B:DG5 2.9 54.7 1.0
O6 B:DG6 2.9 61.0 1.0
O6 B:DG11 2.9 58.7 1.0
O6 B:DG2 3.0 56.6 1.0
C6 B:DG14 3.5 59.9 1.0
C6 B:DG10 3.6 67.3 1.0
C6 B:DG6 3.7 62.3 1.0
C6 B:DG5 3.7 57.4 1.0
C6 B:DG15 3.7 60.8 1.0
C6 B:DG1 3.7 55.2 1.0
N1 B:DG6 3.7 62.7 1.0
N1 B:DG10 3.8 66.8 1.0
C6 B:DG11 3.8 61.2 1.0
N1 B:DG14 3.9 60.9 1.0
C6 B:DG2 3.9 56.4 1.0
N1 B:DG1 3.9 55.4 1.0
N1 B:DG5 3.9 56.2 1.0
N1 B:DG2 4.0 56.7 1.0
N1 B:DG15 4.1 61.6 1.0
N1 B:DG11 4.1 61.4 1.0
C36 B:JL0101 4.7 60.0 1.0
C5 B:DG14 4.8 61.2 1.0
C35 B:JL0101 4.8 61.2 1.0
C5 B:DG10 4.8 70.2 1.0
C5 B:DG15 4.9 63.8 1.0
C5 B:DG1 4.9 55.1 1.0
C5 B:DG5 4.9 58.7 1.0

Reference:

R.Troisi, C.Riccardi, K.Perez De Carvasal, M.Smietana, F.Morvan, P.Del Vecchio, D.Montesarchio, F.Sica. A Terminal Functionalization Strategy Reveals Unusual Binding Abilities of Anti-Thrombin Anticoagulant Aptamers. Mol Ther Nucleic Acids V. 30 585 2022.
ISSN: ISSN 2162-2531
PubMed: 36457701
DOI: 10.1016/J.OMTN.2022.11.007
Page generated: Sat Aug 9 15:25:53 2025

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