Atomistry » Sodium » PDB 4lh6-4lzw » 4lz1
Atomistry »
  Sodium »
    PDB 4lh6-4lzw »
      4lz1 »

Sodium in PDB 4lz1: X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase

Enzymatic activity of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase

All present enzymatic activity of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 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 12 Nucleobase, PDB code: 4lz1 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) 25.20 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.892, 44.484, 52.643, 65.24, 82.53, 63.72
R / Rfree (%) 15.5 / 19

Other elements in 4lz1:

The structure of X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase also contains other interesting chemical elements:

Potassium (K) 1 atom

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 12 Nucleobase (pdb code 4lz1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 Nucleobase, PDB code: 4lz1:

Sodium binding site 1 out of 1 in 4lz1

Go back to Sodium Binding Sites List in 4lz1
Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Human Thrombin and the Tba Deletion Mutant Lacking Thymine 12 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 12 Nucleobase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:26.2
occ:1.00
O H:HOH431 2.2 26.5 1.0
O H:LYS224 2.2 22.4 1.0
O H:HOH449 2.3 16.5 1.0
O H:ARG221 2.3 18.8 1.0
O H:HOH432 2.4 21.4 1.0
O H:HOH434 2.8 22.6 1.0
C H:ARG221 3.4 19.5 1.0
C H:LYS224 3.4 18.1 1.0
O H:HOH451 3.8 22.5 1.0
N H:LYS224 3.8 21.8 1.0
N H:ARG221 3.9 17.6 1.0
O H:HOH450 4.0 26.4 1.0
O H:TYR184A 4.0 21.0 1.0
C H:ASP221A 4.1 19.0 1.0
O H:HOH429 4.2 31.8 1.0
CA H:LYS224 4.2 20.8 1.0
O H:HOH433 4.2 17.9 1.0
N H:GLY223 4.3 18.9 1.0
CA H:ARG221 4.3 21.0 1.0
N H:ASP222 4.3 21.1 1.0
CA H:ASP222 4.4 22.8 1.0
N H:TYR225 4.4 19.4 1.0
CA H:ASP221A 4.5 16.7 1.0
CB H:LYS224 4.5 20.9 1.0
O H:ASP221A 4.6 21.9 1.0
C H:ASP222 4.6 21.2 1.0
CA H:TYR225 4.7 17.6 1.0
OD1 H:ASP221A 4.7 20.7 1.0
C H:GLY223 4.9 20.9 1.0
CD1 H:TYR225 4.9 18.4 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: Tue Dec 15 06:52:55 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy