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Sodium 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:

Potassium (K) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4lz4

Go back to Sodium Binding Sites List in 4lz4
Sodium 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 Sodium with other atoms in the Na 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
B:Na303

b:28.4
occ:1.00
O B:HOH446 2.2 18.9 1.0
O B:ARG221 2.3 41.3 1.0
O B:HOH452 2.3 14.8 1.0
O B:LYS224 2.3 28.2 1.0
O B:HOH482 2.6 29.1 1.0
O B:HOH443 3.0 25.1 1.0
C B:ARG221 3.3 37.7 1.0
C B:LYS224 3.5 31.7 1.0
O B:HOH444 3.8 31.5 1.0
O B:HOH445 3.8 22.2 1.0
N B:ARG221 3.8 33.8 1.0
N B:LYS224 3.9 31.5 1.0
O B:HOH486 3.9 23.7 1.0
O B:TYR184A 4.1 28.4 1.0
C B:ASP221A 4.1 31.3 1.0
N B:ASP222 4.2 38.3 1.0
N B:GLY223 4.2 31.6 1.0
CA B:ARG221 4.2 34.9 1.0
CA B:LYS224 4.3 31.1 1.0
CA B:ASP222 4.3 39.0 1.0
CA B:ASP221A 4.3 29.7 1.0
C B:ASP222 4.5 35.4 1.0
N B:TYR225 4.5 30.1 1.0
OD1 B:ASP221A 4.5 28.5 1.0
O B:HOH453 4.6 34.0 1.0
O B:ASP221A 4.7 29.6 1.0
CD1 B:TYR225 4.7 29.9 1.0
CB B:LYS224 4.8 31.3 1.0
CA B:TYR225 4.8 28.0 1.0
CE1 B:TYR225 4.9 32.9 1.0
C B:GLY223 4.9 30.4 1.0

Sodium binding site 2 out of 2 in 4lz4

Go back to Sodium Binding Sites List in 4lz4
Sodium 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 Sodium with other atoms in the Na 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
D:Na303

b:32.3
occ:1.00
O D:HOH459 2.3 18.0 1.0
O D:HOH461 2.3 24.2 1.0
O D:ARG221 2.4 30.3 1.0
O D:LYS224 2.4 31.2 1.0
O D:HOH460 2.8 30.1 1.0
C D:ARG221 3.4 29.6 1.0
C D:LYS224 3.5 28.8 1.0
O D:HOH476 3.9 22.4 1.0
N D:ARG221 3.9 25.9 1.0
N D:LYS224 4.0 30.2 1.0
O D:TYR184A 4.0 25.0 1.0
C D:ASP221A 4.1 25.8 1.0
O D:HOH458 4.1 25.4 1.0
CA D:ARG221 4.2 28.5 1.0
N D:ASP222 4.2 32.8 1.0
CA D:LYS224 4.3 29.3 1.0
CA D:ASP221A 4.3 24.9 1.0
N D:GLY223 4.3 30.6 1.0
CA D:ASP222 4.4 36.5 1.0
N D:TYR225 4.5 28.3 1.0
O D:HOH502 4.5 52.7 1.0
OD1 D:ASP221A 4.5 23.5 1.0
C D:ASP222 4.6 33.3 1.0
O D:ASP221A 4.6 25.5 1.0
CA D:TYR225 4.7 28.1 1.0
CD1 D:TYR225 4.8 30.1 1.0
CB D:LYS224 4.8 31.5 1.0
CE1 D:TYR225 4.9 30.6 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 Oct 7 16:53:18 2024

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