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Sodium in PDB 4i7y: Crystal Structure of Human Alpha Thrombin in Complex with A 27-Mer Aptamer Bound to Exosite II

Enzymatic activity of Crystal Structure of Human Alpha Thrombin in Complex with A 27-Mer Aptamer Bound to Exosite II

All present enzymatic activity of Crystal Structure of Human Alpha Thrombin in Complex with A 27-Mer Aptamer Bound to Exosite II:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Human Alpha Thrombin in Complex with A 27-Mer Aptamer Bound to Exosite II, PDB code: 4i7y was solved by A.Pica, I.Russo Krauss, A.Merlino, L.Mazzarella, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.144, 81.904, 53.720, 90.00, 99.66, 90.00
R / Rfree (%) 18.1 / 24.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Alpha Thrombin in Complex with A 27-Mer Aptamer Bound to Exosite II (pdb code 4i7y). 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 Crystal Structure of Human Alpha Thrombin in Complex with A 27-Mer Aptamer Bound to Exosite II, PDB code: 4i7y:

Sodium binding site 1 out of 1 in 4i7y

Go back to Sodium Binding Sites List in 4i7y
Sodium binding site 1 out of 1 in the Crystal Structure of Human Alpha Thrombin in Complex with A 27-Mer Aptamer Bound to Exosite II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Alpha Thrombin in Complex with A 27-Mer Aptamer Bound to Exosite II within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:46.8
occ:1.00
 O H:HOH416 2.2 37.3 1.0
O H:HOH453 2.3 37.1 1.0
O H:LYS224 2.3 51.4 1.0
O H:HOH411 2.3 50.6 1.0
O H:ARG221 2.4 51.0 1.0
O H:HOH429 2.5 49.5 1.0
C H:LYS224 3.4 46.3 1.0
C H:ARG221 3.5 47.5 1.0
O H:HOH462 3.7 60.7 1.0
O H:TYR184A 3.8 49.7 1.0
N H:LYS224 3.9 45.7 1.0
O H:HOH450 4.0 39.1 1.0
CA H:LYS224 4.1 48.7 1.0
N H:ARG221 4.1 43.2 1.0
O H:HOH427 4.2 38.9 1.0
N H:GLY223 4.2 47.5 1.0
C H:ASP221A 4.3 47.3 1.0
N H:ASP222 4.4 50.0 1.0
CA H:ASP222 4.4 46.4 1.0
CB H:LYS224 4.4 50.9 1.0
CA H:ARG221 4.4 45.4 1.0
N H:TYR225 4.5 44.4 1.0
C H:ASP222 4.6 45.1 1.0
CA H:ASP221A 4.6 50.8 1.0
O H:HOH433 4.7 66.6 1.0
CA H:TYR225 4.7 40.8 1.0
CD1 H:TYR225 4.7 43.2 1.0
O H:ASP221A 4.7 46.3 1.0
CE1 H:TYR225 4.8 39.8 1.0
C H:GLY223 4.8 43.2 1.0
OD1 H:ASP221A 4.8 58.1 1.0
CA H:GLY223 5.0 43.7 1.0

Reference:

I.Russo Krauss, A.Pica, A.Merlino, L.Mazzarella, F.Sica. Duplex-Quadruplex Motifs in A Peculiar Structural Organization Cooperatively Contribute to Thrombin Binding of A Dna Aptamer. Acta Crystallogr.,Sect.D V. 69 2403 2013.
ISSN: ISSN 0907-4449
PubMed: 24311581
DOI: 10.1107/S0907444913022269
Page generated: Mon Oct 7 15:58:14 2024

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