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Sodium 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:

Fluorine (F) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Complex of Thrombin with and Inhibitor Containing A Novel P1 Moiety, PDB code: 1ad8:

Sodium binding site 1 out of 1 in 1ad8

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na1

b:-3.1
occ:1.00
O H:THR172 2.2 27.9 1.0
O H:HOH313 2.2 62.9 1.0
O H:HOH358 2.2 41.8 1.0
O H:HOH296 2.2 43.2 1.0
O H:LYS169 2.4 29.6 1.0
C H:THR172 3.4 24.7 1.0
C H:LYS169 3.5 26.4 1.0
CA H:ASP170 4.1 28.3 1.0
N H:ASP170 4.2 25.8 1.0
N H:THR172 4.2 23.1 1.0
N H:ARG173 4.3 24.0 1.0
CA H:ARG173 4.3 29.4 1.0
C H:ASP170 4.4 28.2 1.0
CA H:THR172 4.4 21.8 1.0
CA H:LYS169 4.6 29.6 1.0
O H:ASP170 4.8 30.4 1.0
N H:SER171 4.8 26.5 1.0
CG2 H:THR172 4.8 17.1 1.0
C H:ARG173 4.8 28.6 1.0
OD1 H:ASP170 4.8 23.7 1.0
CB H:LYS169 5.0 29.1 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: Tue Dec 15 05:21:46 2020

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