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Sodium in PDB 2c8x: Thrombin Inhibitors

Enzymatic activity of Thrombin Inhibitors

All present enzymatic activity of Thrombin Inhibitors:
3.4.21.5;

Protein crystallography data

The structure of Thrombin Inhibitors, PDB code: 2c8x was solved by N.Howard, C.Abell, W.Blakemore, R.Carr, G.Chessari, M.Congreve, S.Howard, H.Jhoti, C.W.Murray, L.C.A.Seavers, R.L.M.Van Montfort, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.12 / 2.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.966, 71.571, 71.682, 90.00, 100.37, 90.00
R / Rfree (%) 15.3 / 22.9

Other elements in 2c8x:

The structure of Thrombin Inhibitors also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin Inhibitors (pdb code 2c8x). 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 Thrombin Inhibitors, PDB code: 2c8x:

Sodium binding site 1 out of 1 in 2c8x

Go back to Sodium Binding Sites List in 2c8x
Sodium binding site 1 out of 1 in the Thrombin Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1250

b:29.6
occ:1.00
O B:HOH2246 2.2 11.2 1.0
O B:HOH2222 2.8 19.7 1.0
O B:LYS224 2.9 18.9 1.0
OD2 B:ASP189 3.3 14.2 1.0
O B:ARG221A 3.3 22.9 1.0
O B:HOH2206 3.5 13.4 1.0
CA B:ASP221 3.5 22.4 1.0
C B:LYS224 3.5 19.4 1.0
O B:HOH2240 3.5 16.5 1.0
N B:ARG221A 3.5 24.0 1.0
O B:HOH2251 3.6 15.0 1.0
N B:ASP221 3.7 18.2 1.0
O B:HOH2224 3.7 24.1 1.0
CG B:ASP189 3.7 17.1 1.0
C B:ASP221 3.8 23.1 1.0
N B:TYR225 4.0 16.4 1.0
CA B:TYR225 4.0 16.3 1.0
CB B:ASP189 4.1 16.0 1.0
C B:ARG221A 4.3 25.5 1.0
CB B:LYS224 4.3 24.7 1.0
OD1 B:ASP189 4.4 14.0 1.0
CA B:LYS224 4.5 21.0 1.0
CA B:ARG221A 4.5 26.4 1.0
C B:TYR225 4.5 17.9 1.0
OD1 B:ASP221 4.6 19.5 1.0
N B:GLY226 4.6 15.3 1.0
O B:GLY188 4.7 15.7 1.0
O B:ASP221 4.7 22.9 1.0
C B:CYS220 4.8 16.2 1.0
O B:HOH2221 4.8 16.5 1.0
CB B:ASP221 4.8 19.1 1.0
N B:LYS224 4.9 21.5 1.0

Reference:

N.Howard, C.Abell, W.Blakemore, G.Chessari, M.Congreve, S.Howard, H.Jhoti, C.W.Murray, L.C.A.Seavers, R.L.M.Van Montfort. Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors J.Med.Chem. V. 49 1346 2006.
ISSN: ISSN 0022-2623
PubMed: 16480269
DOI: 10.1021/JM050850V
Page generated: Tue Dec 15 05:46:35 2020

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