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Sodium in PDB 3qto: 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: 3qto 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) 35.67 / 1.52
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.800, 71.400, 72.500, 90.00, 100.30, 90.00
R / Rfree (%) 15.5 / 16.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin Inhibition By Pyridin Derivatives (pdb code 3qto). 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: 3qto:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3qto

Go back to Sodium Binding Sites List in 3qto
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:Na2001

b:11.7
occ:1.00
O H:THR172 2.3 15.0 1.0
O H:LYS169 2.3 15.0 1.0
O H:HOH3268 2.4 15.8 1.0
O H:HOH3191 2.6 20.8 1.0
O H:HOH3123 2.7 21.8 1.0
C H:LYS169 3.5 12.6 1.0
C H:THR172 3.6 11.9 1.0
CA H:ASP170 4.0 15.1 1.0
N H:ASP170 4.2 12.2 1.0
CG H:LYS169 4.2 22.7 1.0
N H:THR172 4.3 13.0 1.0
O H:HOH3345 4.3 33.9 1.0
C H:ASP170 4.4 13.2 1.0
CA H:ARG173 4.4 12.8 1.0
N H:ARG173 4.4 12.2 1.0
CA H:LYS169 4.5 11.0 1.0
CA H:THR172 4.5 12.6 1.0
OD1 H:ASP170 4.7 19.9 1.0
O H:ASP170 4.8 14.2 1.0
N H:SER171 4.8 12.5 1.0
CG2 H:THR172 4.9 15.1 1.0
CB H:LYS169 4.9 13.0 1.0
C H:ARG173 5.0 15.7 1.0

Sodium binding site 2 out of 2 in 3qto

Go back to Sodium Binding Sites List in 3qto
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:Na2002

b:15.2
occ:1.00
O H:ARG221A 2.2 16.5 1.0
O H:LYS224 2.4 14.7 1.0
O H:HOH3312 2.4 17.7 1.0
O H:HOH3184 2.4 18.6 1.0
O H:HOH3129 2.6 14.1 1.0
O H:HOH3202 2.7 18.2 1.0
C H:ARG221A 3.3 16.4 1.0
C H:LYS224 3.4 11.9 1.0
N H:LYS224 3.8 14.2 1.0
N H:ARG221A 3.8 16.2 1.0
O H:HOH3101 3.9 13.8 1.0
O H:HOH3193 4.0 20.1 1.0
C H:ASP221 4.0 17.1 1.0
CA H:LYS224 4.1 15.1 1.0
N H:ASP222 4.1 19.4 1.0
N H:GLY223 4.2 19.8 1.0
CA H:ARG221A 4.2 17.6 1.0
O H:TYR184A 4.2 16.1 1.0
CA H:ASP222 4.2 21.4 1.0
O H:HOH3058 4.3 13.9 1.0
CA H:ASP221 4.3 17.1 1.0
N H:TYR225 4.4 11.2 1.0
CB H:LYS224 4.4 13.9 1.0
C H:ASP222 4.4 19.1 1.0
O H:ASP221 4.5 19.2 1.0
OD1 H:ASP221 4.6 15.4 1.0
CA H:TYR225 4.7 11.3 1.0
C H:GLY223 4.8 17.6 1.0
O H:HOH3189 5.0 17.6 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 06:23:07 2020

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