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Sodium in PDB 3da9: Crystal Structure of Thrombin in Complex with Inhibitor

Enzymatic activity of Crystal Structure of Thrombin in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Thrombin in Complex with Inhibitor:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Thrombin in Complex with Inhibitor, PDB code: 3da9 was solved by Y.Xue, S.K.Hansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.830, 71.455, 71.905, 90.00, 100.35, 90.00
R / Rfree (%) 18.2 / 21.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Thrombin in Complex with Inhibitor (pdb code 3da9). 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 Thrombin in Complex with Inhibitor, PDB code: 3da9:

Sodium binding site 1 out of 1 in 3da9

Go back to Sodium Binding Sites List in 3da9
Sodium binding site 1 out of 1 in the Crystal Structure of Thrombin in Complex with Inhibitor


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 Thrombin in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:35.4
occ:1.00
O B:HOH628 2.3 30.4 1.0
O B:ARG263 2.4 35.0 1.0
O B:HOH629 2.4 31.2 1.0
O B:LYS266 2.4 29.8 1.0
O B:HOH414 2.5 28.3 1.0
O B:HOH429 2.6 33.6 1.0
C B:ARG263 3.4 35.6 1.0
C B:LYS266 3.5 30.2 1.0
O B:HOH446 3.9 33.9 1.0
N B:LYS266 3.9 32.1 1.0
N B:ARG263 3.9 34.9 1.0
O B:HOH462 4.0 32.5 1.0
O B:TYR220 4.1 34.0 1.0
C B:ASP262 4.1 34.5 1.0
O B:HOH406 4.2 28.7 1.0
CA B:LYS266 4.2 30.6 1.0
N B:ASP264 4.2 35.5 1.0
CA B:ARG263 4.3 35.4 1.0
N B:GLY265 4.3 34.7 1.0
CA B:ASP264 4.3 36.2 1.0
CA B:ASP262 4.3 34.0 1.0
N B:TYR267 4.5 29.7 1.0
C B:ASP264 4.5 35.5 1.0
CB B:LYS266 4.6 30.8 1.0
OD1 B:ASP262 4.6 34.9 1.0
O B:ASP262 4.6 34.7 1.0
CA B:TYR267 4.7 29.6 1.0
O B:HOH411 4.8 34.7 1.0
C B:GLY265 4.9 33.2 1.0

Reference:

M.Nilsson, M.Hamalainen, M.Ivarsson, J.Gottfries, Y.Xue, S.Hansson, R.Isaksson, T.Fex. Compounds Binding to the S2-S3 Pockets of Thrombin. J.Med.Chem. V. 52 2708 2009.
ISSN: ISSN 0022-2623
PubMed: 19371038
DOI: 10.1021/JM8011849
Page generated: Tue Dec 15 06:08:37 2020

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