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Sodium in PDB 2xby: Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor

Enzymatic activity of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor

All present enzymatic activity of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor:
3.4.21.6;

Protein crystallography data

The structure of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor, PDB code: 2xby was solved by D.W.Banner, J.Benz, D.Schlatter, S.Thomi, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.85 / 2.02
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.640, 106.640, 50.900, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.6

Other elements in 2xby:

The structure of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor (pdb code 2xby). 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 Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor, PDB code: 2xby:

Sodium binding site 1 out of 1 in 2xby

Go back to Sodium Binding Sites List in 2xby
Sodium binding site 1 out of 1 in the Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Factor Xa in Complex with A Pyrrolidine-3,4-Dicarboxylic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1247

b:27.0
occ:1.00
 O A:ARG222 2.2 24.9 1.0
O A:TYR185 2.4 22.6 1.0
O A:LYS224 2.5 24.1 1.0
O A:HOH2170 2.5 26.9 1.0
O A:ASP185A 2.7 29.6 1.0
O A:HOH2192 2.8 28.8 1.0
C A:ASP185A 3.3 28.3 1.0
C A:ARG222 3.3 25.8 1.0
C A:TYR185 3.5 25.3 1.0
C A:LYS224 3.6 22.3 1.0
N A:LYS224 3.7 22.4 1.0
CA A:ASP185A 3.8 27.8 1.0
N A:ARG222 4.1 24.9 1.0
C A:ALA221 4.1 25.7 1.0
N A:ASP185A 4.1 25.5 1.0
N A:LYS223 4.1 25.7 1.0
CA A:LYS223 4.1 27.7 1.0
N A:GLY223A 4.1 25.5 1.0
N A:THR185B 4.1 29.8 1.0
CA A:LYS224 4.2 21.5 1.0
O A:ALA221 4.2 24.4 1.0
CA A:ARG222 4.3 26.0 1.0
C A:LYS223 4.4 26.6 1.0
O A:HOH2163 4.4 24.6 1.0
CA A:THR185B 4.6 33.1 1.0
CA A:ALA221 4.6 25.1 1.0
O A:LYS186 4.7 35.9 1.0
N A:TYR225 4.7 19.6 1.0
CA A:TYR185 4.7 25.4 1.0
C A:GLY223A 4.8 23.5 1.0
CB A:LYS224 4.8 21.7 1.0
CA A:TYR225 5.0 18.6 1.0

Reference:

L.Anselm, D.W.Banner, J.Benz, K.Groebke Zbinden, J.Himber, H.Hilpert, W.Huber, B.Kuhn, J.L.Mary, M.B.Otteneder, N.Panday, F.Ricklin, M.Stahl, S.Thomi, W.Haap. Discovery of A Factor Xa Inhibitor (3R,4R)-1-(2,2-Difluoro-Ethyl)-Pyrrolidine-3,4-Dicarboxylic Acid 3-[(5-Chloro-Pyridin-2-Yl)-Amide] 4-{[2-Fluoro-4-(2-Oxo-2H-Pyridin-1-Yl)-Phenyl]-Amide} As A Clinical Candidate. Bioorg.Med.Chem. V. 20 5313 2010.
ISSN: ISSN 0968-0896
PubMed: 20650636
DOI: 10.1016/J.BMCL.2010.06.126
Page generated: Mon Oct 7 05:08:48 2024

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