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Sodium in PDB 3p17: Thrombin Inhibition By Pyridin Derivatives

Enzymatic activity of Thrombin Inhibition By Pyridin Derivatives

All present enzymatic activity of Thrombin Inhibition By Pyridin Derivatives:
3.4.21.5;

Protein crystallography data

The structure of Thrombin Inhibition By Pyridin Derivatives, PDB code: 3p17 was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.43
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.000, 71.400, 72.500, 90.00, 100.30, 90.00
R / Rfree (%) 14 / 17.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin Inhibition By Pyridin Derivatives (pdb code 3p17). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin Inhibition By Pyridin Derivatives, PDB code: 3p17:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3p17

Go back to Sodium Binding Sites List in 3p17
Sodium binding site 1 out of 2 in the Thrombin Inhibition By Pyridin Derivatives


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibition By Pyridin Derivatives within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1701

b:13.4
occ:1.00
O H:THR172 2.3 13.4 1.0
O H:HOH437 2.4 14.8 1.0
O H:LYS169 2.4 14.0 1.0
O H:HOH330 2.4 27.8 1.0
O H:HOH297 2.9 20.6 1.0
C H:LYS169 3.5 13.5 1.0
C H:THR172 3.5 12.8 1.0
CA H:ASP170 4.1 12.7 1.0
N H:ASP170 4.2 12.3 1.0
N H:THR172 4.2 12.8 1.0
CG H:LYS169 4.3 23.5 1.0
CA H:ARG173 4.4 13.3 1.0
N H:ARG173 4.4 12.3 1.0
C H:ASP170 4.4 12.2 1.0
O H:HOH445 4.4 39.9 1.0
CA H:THR172 4.5 12.3 1.0
CA H:LYS169 4.6 11.5 1.0
OD1 H:ASP170 4.7 17.6 1.0
O H:ASP170 4.8 15.4 1.0
CG2 H:THR172 4.8 13.8 1.0
N H:SER171 4.8 11.9 1.0
CB H:LYS169 4.9 13.8 1.0
C H:ARG173 5.0 15.3 1.0

Sodium binding site 2 out of 2 in 3p17

Go back to Sodium Binding Sites List in 3p17
Sodium binding site 2 out of 2 in the Thrombin Inhibition By Pyridin Derivatives


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibition By Pyridin Derivatives within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1702

b:17.5
occ:1.00
O H:HOH435 2.3 17.8 1.0
O H:LYS224 2.3 15.3 1.0
O H:ARG221A 2.3 20.0 1.0
O H:HOH281 2.4 16.5 1.0
O H:HOH257 2.5 15.9 1.0
O H:HOH294 2.9 20.7 1.0
C H:LYS224 3.4 14.3 1.0
C H:ARG221A 3.4 19.4 1.0
O H:HOH261 3.8 17.2 1.0
N H:ARG221A 3.8 17.1 1.0
N H:LYS224 3.8 16.4 1.0
C H:ASP221 4.0 16.8 1.0
O H:HOH305 4.1 20.9 1.0
CA H:LYS224 4.1 16.1 1.0
O H:TYR184A 4.2 15.8 1.0
CA H:ARG221A 4.2 18.6 1.0
N H:ASP222 4.3 21.0 1.0
CA H:ASP221 4.3 16.8 1.0
O H:HOH285 4.3 16.4 1.0
N H:GLY223 4.3 19.9 1.0
CA H:ASP222 4.4 21.0 1.0
N H:TYR225 4.4 13.7 1.0
CB H:LYS224 4.5 16.7 1.0
O H:ASP221 4.5 20.0 1.0
C H:ASP222 4.6 20.8 1.0
OD1 H:ASP221 4.7 17.9 1.0
CA H:TYR225 4.7 11.2 1.0
O H:HOH299 4.8 23.2 1.0
C H:GLY223 4.8 16.5 1.0
N H:ASP221 5.0 15.9 1.0

Reference:

A.Biela, M.Khayat, H.Tan, J.Kong, A.Heine, D.Hangauer, G.Klebe. Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin. J.Mol.Biol. V. 418 350 2012.
ISSN: ISSN 0022-2836
PubMed: 22366545
DOI: 10.1016/J.JMB.2012.01.054
Page generated: Tue Dec 15 06:20:39 2020

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