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Fluorine in PDB 1z71: Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure

Enzymatic activity of Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure

All present enzymatic activity of Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure:
3.4.21.5;

Protein crystallography data

The structure of Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure, PDB code: 1z71 was solved by P.G.Nantermet, C.S.Burgey, K.A.Robinson, J.M.Pellicore, C.L.Newton, J.Z.Deng, T.A.Lyle, H.G.Selnick, S.D.Lewis, B.J.Lucas, J.A.Krueger, C.Miller-Stein, R.B.White, B.Wong, D.R.Mcmasters, A.A.Wallace, J.J.Lynchjr., Y.Yan, Z.Chen, L.Kuo, S.J.Gardell, J.A.Shafer, J.P.Vacca, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.970, 71.490, 72.260, 90.00, 100.50, 90.00
R / Rfree (%) 22.3 / 25.4

Other elements in 1z71:

The structure of Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure (pdb code 1z71). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure, PDB code: 1z71:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 1z71

Go back to Fluorine Binding Sites List in 1z71
Fluorine binding site 1 out of 2 in the Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:22.3
occ:1.00
F1 A:L171001 0.0 22.3 1.0
C11 A:L171001 1.4 22.5 1.0
F2 A:L171001 2.2 22.0 1.0
C1 A:L171001 2.3 20.0 1.0
C2 A:L171001 2.4 22.8 1.0
O1 A:L171001 2.6 29.2 1.0
N1 A:L171001 2.8 23.2 1.0
CD1 A:ILE174 3.5 18.9 1.0
C8 A:L171001 3.6 19.1 1.0
N18 A:L171001 3.6 16.8 1.0
CG1 A:ILE174 3.8 17.0 1.0
O A:HOH1190 4.1 31.3 1.0
CG A:GLU217 4.2 23.3 1.0
C4 A:L171001 4.2 23.4 1.0
OE1 A:GLU217 4.2 25.9 1.0
CD A:GLU217 4.5 24.9 1.0
C21 A:L171001 4.6 16.3 1.0
C3 A:L171001 4.7 17.0 1.0
C6 A:L171001 4.8 21.5 1.0

Fluorine binding site 2 out of 2 in 1z71

Go back to Fluorine Binding Sites List in 1z71
Fluorine binding site 2 out of 2 in the Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thrombin and P2 Pyridine N-Oxide Inhibitor Complex Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:22.0
occ:1.00
F2 A:L171001 0.0 22.0 1.0
C11 A:L171001 1.4 22.5 1.0
F1 A:L171001 2.2 22.3 1.0
C1 A:L171001 2.3 20.0 1.0
C2 A:L171001 2.4 22.8 1.0
C8 A:L171001 2.8 19.1 1.0
N18 A:L171001 2.9 16.8 1.0
CG A:GLU217 3.2 23.3 1.0
CE3 A:TRP215 3.3 16.3 1.0
CZ3 A:TRP215 3.6 16.7 1.0
N1 A:L171001 3.7 23.2 1.0
O A:GLY216 3.7 16.2 1.0
CG1 A:ILE174 3.8 17.0 1.0
CD A:GLU217 3.9 24.9 1.0
C A:GLY216 4.0 16.8 1.0
C21 A:L171001 4.1 16.3 1.0
CD1 A:ILE174 4.1 18.9 1.0
O1 A:L171001 4.1 29.2 1.0
C6 A:L171001 4.3 21.5 1.0
OE1 A:GLU217 4.3 25.9 1.0
CD2 A:TRP215 4.3 15.2 1.0
N A:GLU217 4.4 17.3 1.0
CB A:GLU217 4.4 20.6 1.0
OE2 A:GLU217 4.5 23.3 1.0
CA A:GLU217 4.6 18.2 1.0
N A:GLY216 4.7 15.2 1.0
CA A:GLY216 4.7 16.1 1.0
C3 A:L171001 4.7 17.0 1.0
CH2 A:TRP215 4.7 16.1 1.0
O28 A:L171001 4.8 14.7 1.0
O A:HOH1067 4.9 21.0 1.0
N2 A:L171001 4.9 15.7 1.0
C4 A:L171001 4.9 23.4 1.0
CB A:ILE174 4.9 16.6 1.0
CB A:TRP215 5.0 13.3 1.0

Reference:

P.G.Nantermet, C.S.Burgey, K.A.Robinson, J.M.Pellicore, C.L.Newton, J.Z.Deng, H.G.Selnick, S.D.Lewis, B.J.Lucas, J.A.Krueger, C.Miller-Stein, R.B.White, B.Wong, D.R.Mcmasters, A.A.Wallace, J.J.Lynch Jr., Y.Yan, Z.Chen, L.Kuo, S.J.Gardell, J.A.Shafer, J.P.Vacca, T.A.Lyle. P(2) Pyridine N-Oxide Thrombin Inhibitors: A Novel Peptidomimetic Scaffold Bioorg.Med.Chem.Lett. V. 15 2771 2005.
ISSN: ISSN 0960-894X
PubMed: 15911253
DOI: 10.1016/J.BMCL.2005.03.110
Page generated: Sun Dec 13 11:34:26 2020

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