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Fluorine in PDB 1ad8: Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety

Enzymatic activity of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety

All present enzymatic activity of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety:
3.4.21.5;

Protein crystallography data

The structure of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety, PDB code: 1ad8 was solved by H.Schreuder, C.Tardif, J.A.Malikayil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.550, 72.050, 73.000, 90.00, 101.00, 90.00
R / Rfree (%) 20.5 / n/a

Other elements in 1ad8:

The structure of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety (pdb code 1ad8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety, PDB code: 1ad8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 1ad8

Go back to Fluorine Binding Sites List in 1ad8
Fluorine binding site 1 out of 5 in the Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F250

b:35.6
occ:1.00
 F48 H:MDL250 0.0 35.6 1.0
C47 H:MDL250 1.3 33.3 1.0
F49 H:MDL250 2.1 28.9 1.0
C50 H:MDL250 2.3 36.9 1.0
C44 H:MDL250 2.4 28.1 1.0
F51 H:MDL250 2.5 35.1 1.0
F53 H:MDL250 2.8 43.4 1.0
C25 H:MDL250 2.8 22.8 1.0
O46 H:MDL250 2.9 24.9 1.0
O24 H:MDL250 3.2 28.3 1.0
N23 H:MDL250 3.4 30.8 1.0
F52 H:MDL250 3.5 40.2 1.0
C21 H:MDL250 3.5 28.8 1.0
OG H:SER195 3.7 24.9 1.0
CG H:GLU192 3.8 66.2 1.0
N H:GLY193 4.0 31.2 1.0
O H:HOH380 4.0 84.3 1.0
CA H:GLU192 4.1 33.6 1.0
C26 H:MDL250 4.2 20.8 1.0
CZ3 H:TRP60D 4.2 29.6 1.0
CH2 H:TRP60D 4.3 31.4 1.0
CB H:GLU192 4.4 43.8 1.0
C H:GLU192 4.6 32.3 1.0
OE1 H:GLU192 4.6 83.6 1.0
CB H:SER195 4.6 19.1 1.0
CD H:GLU192 4.6 80.6 1.0
C30 H:MDL250 4.7 25.6 1.0
C18 H:MDL250 4.8 23.3 1.0
C15 H:MDL250 4.9 25.0 1.0
C27 H:MDL250 4.9 19.7 1.0
CA H:GLY193 5.0 29.5 1.0

Fluorine binding site 2 out of 5 in 1ad8

Go back to Fluorine Binding Sites List in 1ad8
Fluorine binding site 2 out of 5 in the Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F250

b:28.9
occ:1.00
 F49 H:MDL250 0.0 28.9 1.0
C47 H:MDL250 1.3 33.3 1.0
F48 H:MDL250 2.1 35.6 1.0
C50 H:MDL250 2.2 36.9 1.0
C44 H:MDL250 2.3 28.1 1.0
F51 H:MDL250 2.6 35.1 1.0
F52 H:MDL250 2.6 40.2 1.0
N23 H:MDL250 2.7 30.8 1.0
OG H:SER195 2.8 24.9 1.0
C21 H:MDL250 2.8 28.8 1.0
C25 H:MDL250 2.9 22.8 1.0
NE2 H:HIS57 3.1 23.3 1.0
C15 H:MDL250 3.2 25.0 1.0
O24 H:MDL250 3.2 28.3 1.0
F53 H:MDL250 3.4 43.4 1.0
CD2 H:HIS57 3.4 22.7 1.0
C18 H:MDL250 3.5 23.3 1.0
O46 H:MDL250 3.6 24.9 1.0
CZ3 H:TRP60D 3.8 29.6 1.0
O H:HOH348 3.8 42.3 1.0
CB H:SER195 3.8 19.1 1.0
CH2 H:TRP60D 4.0 31.4 1.0
CE1 H:HIS57 4.2 22.5 1.0
C26 H:MDL250 4.3 20.8 1.0
C12 H:MDL250 4.5 25.3 1.0
CG H:HIS57 4.7 24.6 1.0
N8 H:MDL250 4.8 19.5 1.0
CE3 H:TRP60D 5.0 27.1 1.0
O H:HOH380 5.0 84.3 1.0

Fluorine binding site 3 out of 5 in 1ad8

Go back to Fluorine Binding Sites List in 1ad8
Fluorine binding site 3 out of 5 in the Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F250

b:35.1
occ:1.00
 F51 H:MDL250 0.0 35.1 1.0
C50 H:MDL250 1.3 36.9 1.0
F53 H:MDL250 2.1 43.4 1.0
F52 H:MDL250 2.1 40.2 1.0
C47 H:MDL250 2.2 33.3 1.0
F48 H:MDL250 2.5 35.6 1.0
F49 H:MDL250 2.6 28.9 1.0
NZ H:LYS60F 3.5 44.5 1.0
C44 H:MDL250 3.7 28.1 1.0
CZ3 H:TRP60D 3.7 29.6 1.0
O H:HOH348 4.1 42.3 1.0
O46 H:MDL250 4.2 24.9 1.0
OG H:SER195 4.3 24.9 1.0
O H:LEU41 4.4 31.7 1.0
CH2 H:TRP60D 4.6 31.4 1.0
O H:HOH321 4.6 31.7 1.0
CE3 H:TRP60D 4.6 27.1 1.0
CB H:SER195 4.7 19.1 1.0
C25 H:MDL250 4.7 22.8 1.0
SG H:CYS42 4.8 24.5 1.0
CD2 H:HIS57 4.8 22.7 1.0
NE2 H:HIS57 4.9 23.3 1.0

Fluorine binding site 4 out of 5 in 1ad8

Go back to Fluorine Binding Sites List in 1ad8
Fluorine binding site 4 out of 5 in the Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F250

b:40.2
occ:1.00
 F52 H:MDL250 0.0 40.2 1.0
C50 H:MDL250 1.3 36.9 1.0
F51 H:MDL250 2.1 35.1 1.0
F53 H:MDL250 2.2 43.4 1.0
C47 H:MDL250 2.3 33.3 1.0
F49 H:MDL250 2.6 28.9 1.0
CB H:SER195 3.0 19.1 1.0
OG H:SER195 3.0 24.9 1.0
C44 H:MDL250 3.0 28.1 1.0
SG H:CYS42 3.0 24.5 1.0
NE2 H:HIS57 3.4 23.3 1.0
F48 H:MDL250 3.5 35.6 1.0
CD2 H:HIS57 3.6 22.7 1.0
O46 H:MDL250 3.7 24.9 1.0
SG H:CYS58 4.0 22.6 1.0
O H:LEU41 4.1 31.7 1.0
O H:HOH321 4.2 31.7 1.0
NZ H:LYS60F 4.3 44.5 1.0
O H:HOH348 4.3 42.3 1.0
C25 H:MDL250 4.4 22.8 1.0
CA H:SER195 4.4 19.6 1.0
CA H:CYS58 4.6 25.0 1.0
CE1 H:HIS57 4.6 22.5 1.0
N23 H:MDL250 4.7 30.8 1.0
CB H:CYS42 4.7 27.6 1.0
O H:HIS57 4.8 22.0 1.0
CG H:HIS57 4.9 24.6 1.0
CB H:CYS58 4.9 19.4 1.0
C H:SER195 4.9 21.9 1.0
N H:SER195 4.9 22.0 1.0
O H:SER195 5.0 21.7 1.0

Fluorine binding site 5 out of 5 in 1ad8

Go back to Fluorine Binding Sites List in 1ad8
Fluorine binding site 5 out of 5 in the Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F250

b:43.4
occ:1.00
 F53 H:MDL250 0.0 43.4 1.0
C50 H:MDL250 1.3 36.9 1.0
F51 H:MDL250 2.1 35.1 1.0
F52 H:MDL250 2.2 40.2 1.0
C47 H:MDL250 2.3 33.3 1.0
O46 H:MDL250 2.7 24.9 1.0
F48 H:MDL250 2.8 35.6 1.0
C44 H:MDL250 2.9 28.1 1.0
F49 H:MDL250 3.4 28.9 1.0
O H:LEU41 3.4 31.7 1.0
N H:GLY193 3.5 31.2 1.0
CB H:SER195 3.6 19.1 1.0
OG H:SER195 3.6 24.9 1.0
CA H:GLY193 3.7 29.5 1.0
SG H:CYS42 3.9 24.5 1.0
C H:GLY193 4.2 27.1 1.0
C25 H:MDL250 4.3 22.8 1.0
N H:SER195 4.5 22.0 1.0
C H:LEU41 4.6 33.9 1.0
CA H:SER195 4.6 19.6 1.0
O H:GLY193 4.7 30.4 1.0
C H:GLU192 4.7 32.3 1.0
N H:ASP194 4.8 23.8 1.0
CA H:CYS42 4.9 27.0 1.0

Reference:

J.A.Malikayil, J.P.Burkhart, H.A.Schreuder, R.J.Broersma Jr., C.Tardif, L.W.Kutcher 3Rd., S.Mehdi, G.L.Schatzman, B.Neises, N.P.Peet. Molecular Design and Characterization of An Alpha-Thrombin Inhibitor Containing A Novel P1 Moiety. Biochemistry V. 36 1034 1997.
ISSN: ISSN 0006-2960
PubMed: 9033393
DOI: 10.1021/BI9622231
Page generated: Wed Jul 31 10:46:21 2024

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