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Potassium in PDB 4lz4: X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase

Enzymatic activity of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase

All present enzymatic activity of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase, PDB code: 4lz4 was solved by A.Pica, I.Russo Krauss, A.Merlino, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.62 / 2.56
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.736, 120.725, 67.233, 90.00, 94.22, 90.00
R / Rfree (%) 16.8 / 22.7

Other elements in 4lz4:

The structure of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase (pdb code 4lz4). 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 Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase, PDB code: 4lz4:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 4lz4

Go back to Potassium Binding Sites List in 4lz4
Potassium binding site 1 out of 2 in the X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase


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 Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K101

b:61.1
occ:1.00
O6 E:DG6 2.5 48.1 1.0
O6 E:DG10 2.6 41.5 1.0
O6 E:DG5 2.7 54.6 1.0
O6 E:DG1 2.7 38.9 1.0
O6 E:DG15 2.8 54.5 1.0
O6 E:DG14 2.9 45.8 1.0
O6 E:DG2 2.9 35.8 1.0
O6 E:DG11 3.1 37.9 1.0
C6 E:DG6 3.4 46.1 1.0
C6 E:DG5 3.5 51.6 1.0
C6 E:DG10 3.5 40.2 1.0
C6 E:DG1 3.5 34.9 1.0
N1 E:DG6 3.6 42.9 1.0
C6 E:DG15 3.6 61.7 1.0
C6 E:DG14 3.7 47.9 1.0
N1 E:DG1 3.8 36.0 1.0
N1 E:DG10 3.8 39.5 1.0
N1 E:DG15 3.8 59.5 1.0
N1 E:DG5 3.8 51.2 1.0
N1 E:DG14 3.9 45.4 1.0
C6 E:DG2 3.9 36.1 1.0
O E:HOH201 4.0 52.5 1.0
C6 E:DG11 4.0 44.0 1.0
N1 E:DG11 4.2 44.2 1.0
N1 E:DG2 4.2 34.0 1.0
C5 E:DG5 4.6 48.5 1.0
C5 E:DG6 4.7 49.8 1.0
C5 E:DG1 4.8 32.9 1.0
C5 E:DG10 4.8 43.2 1.0
C2 E:DG6 4.9 53.5 1.0
C5 E:DG14 4.9 49.0 1.0
C2 E:DG5 5.0 55.6 1.0

Potassium binding site 2 out of 2 in 4lz4

Go back to Potassium Binding Sites List in 4lz4
Potassium binding site 2 out of 2 in the X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase


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 Thrombin and the Tba Deletion Mutant Lacking Thymine 3 Nucleobase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K101

b:42.9
occ:1.00
O6 F:DG1 2.6 35.9 1.0
O6 F:DG10 2.6 47.3 1.0
O6 F:DG14 2.7 46.8 1.0
O6 F:DG6 2.8 40.9 1.0
O6 F:DG5 2.8 43.6 1.0
O6 F:DG15 2.9 38.5 1.0
O6 F:DG2 2.9 32.5 1.0
O6 F:DG11 3.0 42.6 1.0
C6 F:DG1 3.5 33.8 1.0
O F:HOH201 3.5 31.0 1.0
C6 F:DG14 3.5 44.3 1.0
C6 F:DG10 3.5 43.9 1.0
C6 F:DG5 3.6 43.6 1.0
C6 F:DG6 3.7 37.1 1.0
N1 F:DG14 3.7 40.2 1.0
C6 F:DG15 3.8 43.7 1.0
N1 F:DG10 3.8 41.7 1.0
N1 F:DG6 3.8 37.9 1.0
C6 F:DG2 3.8 34.0 1.0
N1 F:DG1 3.9 31.6 1.0
N1 F:DG15 3.9 44.9 1.0
C6 F:DG11 3.9 46.4 1.0
N1 F:DG5 3.9 43.6 1.0
N1 F:DG2 4.1 32.0 1.0
N1 F:DG11 4.2 49.4 1.0
C7 F:DT9 4.6 55.8 1.0
C5 F:DG1 4.7 33.6 1.0
C5 F:DG14 4.7 45.3 1.0
C5 F:DG5 4.8 46.2 1.0
C5 F:DG10 4.8 41.6 1.0
C5 F:DT9 4.9 53.2 1.0
C2 F:DG14 4.9 43.7 1.0

Reference:

A.Pica, I.Russo Krauss, A.Merlino, S.Nagatoishi, N.Sugimoto, F.Sica. Dissecting the Contribution of Thrombin Exosite I in the Recognition of Thrombin Binding Aptamer. Febs J. V. 280 6581 2013.
ISSN: ISSN 1742-464X
PubMed: 24128303
DOI: 10.1111/FEBS.12561
Page generated: Mon Aug 12 11:32:24 2024

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