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Sodium in PDB 3qtv: 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: 3qtv 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) 35.65 / 1.63
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.900, 71.300, 72.400, 90.00, 100.40, 90.00
R / Rfree (%) 15.5 / 17.6

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 3qtv

Go back to Sodium Binding Sites List in 3qtv
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:13.3
occ:1.00
O H:THR172 2.3 14.3 1.0
O H:HOH3097 2.3 14.8 1.0
O H:LYS169 2.4 14.9 1.0
O H:HOH3141 2.4 24.6 1.0
O H:HOH3150 2.6 21.8 1.0
C H:LYS169 3.5 14.8 1.0
C H:THR172 3.6 14.1 1.0
CA H:ASP170 4.1 15.2 1.0
CG H:LYS169 4.2 23.4 1.0
N H:ASP170 4.2 11.6 1.0
N H:THR172 4.3 13.2 1.0
CA H:ARG173 4.4 13.5 1.0
O H:HOH3305 4.4 41.1 1.0
N H:ARG173 4.4 13.8 1.0
C H:ASP170 4.5 13.9 1.0
CA H:THR172 4.5 13.0 1.0
CA H:LYS169 4.5 12.0 1.0
NZ H:LYS169 4.6 39.1 1.0
OD1 H:ASP170 4.7 19.4 1.0
CG2 H:THR172 4.8 13.6 1.0
O H:ASP170 4.8 15.4 1.0
N H:SER171 4.9 13.7 1.0
CB H:LYS169 4.9 11.6 1.0
C H:ARG173 4.9 16.4 1.0

Sodium binding site 2 out of 2 in 3qtv

Go back to Sodium Binding Sites List in 3qtv
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:16.6
occ:1.00
O H:ARG221A 2.3 18.0 1.0
O H:HOH3221 2.4 17.8 1.0
O H:HOH3158 2.4 17.6 1.0
O H:LYS224 2.4 18.5 1.0
O H:HOH3146 2.5 14.0 1.0
O H:HOH3176 2.6 18.4 1.0
C H:ARG221A 3.4 18.1 1.0
C H:LYS224 3.4 13.6 1.0
N H:LYS224 3.8 16.4 1.0
O H:HOH3091 3.9 15.1 1.0
N H:ARG221A 4.0 17.8 1.0
O H:HOH3159 4.0 19.9 1.0
C H:ASP221 4.1 18.1 1.0
CA H:LYS224 4.1 15.3 1.0
O H:TYR184A 4.1 16.9 1.0
N H:GLY223 4.1 21.3 1.0
N H:ASP222 4.2 20.2 1.0
O H:HOH3113 4.2 14.7 1.0
CA H:ASP222 4.3 20.8 1.0
CA H:ARG221A 4.3 18.7 1.0
CA H:ASP221 4.4 19.0 1.0
C H:ASP222 4.4 19.3 1.0
N H:TYR225 4.4 13.1 1.0
CB H:LYS224 4.5 15.6 1.0
O H:ASP221 4.5 21.2 1.0
OD1 H:ASP221 4.6 17.3 1.0
CA H:TYR225 4.7 13.4 1.0
C H:GLY223 4.8 19.5 1.0
CA H:GLY223 5.0 19.5 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: Mon Oct 7 12:42:05 2024

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