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Sodium in PDB 2zda: Exploring Thrombin S1 Pocket

Enzymatic activity of Exploring Thrombin S1 Pocket

All present enzymatic activity of Exploring Thrombin S1 Pocket:
3.4.21.5;

Protein crystallography data

The structure of Exploring Thrombin S1 Pocket, PDB code: 2zda was solved by B.Baum, 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 / 1.73
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.300, 71.500, 72.400, 90.00, 100.50, 90.00
R / Rfree (%) 18 / 22.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Exploring Thrombin S1 Pocket (pdb code 2zda). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Exploring Thrombin S1 Pocket, PDB code: 2zda:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2zda

Go back to Sodium Binding Sites List in 2zda
Sodium binding site 1 out of 2 in the Exploring Thrombin S1 Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Exploring Thrombin S1 Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1100

b:15.1
occ:1.00
O H:ARG221A 2.3 15.5 1.0
O H:HOH1333 2.3 12.9 1.0
O H:LYS224 2.4 12.2 1.0
O H:HOH1257 2.4 12.5 1.0
O H:HOH1231 2.5 10.3 1.0
O H:HOH1285 2.6 15.1 1.0
C H:ARG221A 3.4 11.6 1.0
C H:LYS224 3.5 10.8 1.0
N H:LYS224 3.8 8.4 1.0
O H:HOH1280 3.9 15.4 1.0
O H:HOH1230 4.0 14.4 1.0
O H:TYR184A 4.0 12.8 1.0
N H:ARG221A 4.1 16.0 1.0
CA H:LYS224 4.1 11.8 1.0
C H:ASP221 4.1 25.3 1.0
N H:GLY223 4.2 21.3 1.0
N H:ASP222 4.2 14.7 1.0
CA H:ASP222 4.2 20.3 1.0
O H:HOH1223 4.3 11.5 1.0
CA H:ARG221A 4.4 13.8 1.0
C H:ASP222 4.4 18.6 1.0
CA H:ASP221 4.5 15.9 1.0
O H:ASP221 4.5 17.1 1.0
CB H:LYS224 4.5 10.5 1.0
N H:TYR225 4.5 13.8 1.0
O H:HOH1327 4.7 19.4 1.0
C H:GLY223 4.8 19.0 1.0
OD1 H:ASP221 4.8 13.8 1.0
CA H:TYR225 4.8 10.3 1.0
CA H:GLY223 5.0 14.2 1.0

Sodium binding site 2 out of 2 in 2zda

Go back to Sodium Binding Sites List in 2zda
Sodium binding site 2 out of 2 in the Exploring Thrombin S1 Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Exploring Thrombin S1 Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1101

b:10.6
occ:1.00
O H:THR172 2.3 10.2 1.0
O H:HOH1246 2.3 9.6 1.0
O H:LYS169 2.4 15.8 1.0
O H:HOH1409 2.6 27.4 1.0
O H:HOH1224 2.7 16.8 1.0
C H:LYS169 3.5 15.0 1.0
C H:THR172 3.5 9.7 1.0
CA H:ASP170 4.1 9.9 1.0
N H:ASP170 4.2 12.6 1.0
N H:THR172 4.2 10.6 1.0
CA H:ARG173 4.4 15.8 1.0
C H:ASP170 4.4 13.3 1.0
O H:HOH1367 4.4 38.0 1.0
N H:ARG173 4.4 11.2 1.0
CA H:THR172 4.5 12.7 1.0
CA H:LYS169 4.6 8.3 1.0
CG2 H:THR172 4.8 11.9 1.0
O H:ASP170 4.8 13.1 1.0
N H:SER171 4.8 9.6 1.0
OD1 H:ASP170 4.8 13.9 1.0
C H:ARG173 5.0 16.0 1.0

Reference:

B.Baum, L.Muley, A.Heine, M.Smolinski, D.Hangauer, G.Klebe. Think Twice: Understanding the High Potency of Bis(Phenyl)Methane Inhibitors of Thrombin J.Mol.Biol. V. 391 552 2009.
ISSN: ISSN 0022-2836
PubMed: 19520086
DOI: 10.1016/J.JMB.2009.06.016
Page generated: Tue Dec 15 06:01:01 2020

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