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Sodium in PDB 1a46: Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor

Enzymatic activity of Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor

All present enzymatic activity of Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor:
3.4.21.5;

Protein crystallography data

The structure of Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor, PDB code: 1a46 was solved by R.St Charles, J.H.Matthews, E.Zhang, A.Tulinsky, M.Kahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.12
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.300, 73.090, 73.820, 90.00, 101.12, 90.00
R / Rfree (%) n/a / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor (pdb code 1a46). 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 Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor, PDB code: 1a46:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1a46

Go back to Sodium Binding Sites List in 1a46
Sodium binding site 1 out of 2 in the Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na548

b:24.4
occ:0.82
O H:HOH530 2.1 25.8 1.0
O H:ARG221A 2.4 24.0 1.0
O H:LYS224 2.5 20.7 1.0
O H:HOH531 2.5 25.1 0.9
O H:HOH416 2.7 22.0 1.0
O H:HOH443 2.9 24.5 1.0
C H:ARG221A 3.4 24.7 1.0
C H:LYS224 3.5 20.9 1.0
O H:HOH398 3.7 23.7 1.0
N H:ARG221A 3.8 23.1 1.0
O H:HOH460 4.0 28.4 0.8
N H:LYS224 4.0 21.9 1.0
C H:ASP221 4.0 22.4 1.0
N H:ASP222 4.2 24.9 1.0
O H:HOH453 4.2 21.1 1.0
CA H:ASP221 4.3 21.5 1.0
CA H:ARG221A 4.3 24.4 1.0
CA H:LYS224 4.3 20.7 1.0
CA H:ASP222 4.3 25.9 1.0
OD1 H:ASP221 4.3 23.1 1.0
O H:TYR184A 4.4 20.3 1.0
N H:GLY223 4.4 25.5 1.0
O H:ASP221 4.4 21.9 1.0
N H:TYR225 4.5 19.4 1.0
C H:ASP222 4.6 25.7 1.0
CB H:LYS224 4.7 21.7 1.0
CA H:TYR225 4.9 17.7 1.0
O H:HOH391 4.9 26.6 1.0
N H:ASP221 5.0 20.3 1.0

Sodium binding site 2 out of 2 in 1a46

Go back to Sodium Binding Sites List in 1a46
Sodium binding site 2 out of 2 in the Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Complexed with Hirugen and A Beta-Strand Mimetic Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na549

b:23.8
occ:1.00
O H:THR172 2.2 15.3 1.0
O H:HOH529 2.3 25.1 1.0
O H:LYS169 2.4 19.8 1.0
O H:HOH468 2.4 25.3 0.8
C H:THR172 3.5 15.7 1.0
C H:LYS169 3.5 19.0 1.0
CA H:ASP170 4.1 18.1 1.0
N H:THR172 4.2 15.9 1.0
N H:ASP170 4.2 17.8 1.0
C H:ASP170 4.4 18.4 1.0
N H:ARG173 4.4 15.7 1.0
CA H:ARG173 4.5 17.6 1.0
CA H:THR172 4.5 15.6 1.0
CA H:LYS169 4.5 20.0 1.0
N H:SER171 4.7 17.2 1.0
O H:HOH526 4.7 26.1 0.5
CB H:LYS169 4.8 23.7 1.0
OD1 H:ASP170 4.8 15.2 1.0
CG2 H:THR172 4.9 14.2 1.0
CE H:LYS169 4.9 34.0 1.0
O H:ASP170 5.0 18.7 1.0
C H:ARG173 5.0 17.6 1.0

Reference:

R.St Charles, J.H.Matthews, E.Zhang, A.Tulinsky. Bound Structures of Novel P3-P1' Beta-Strand Mimetic Inhibitors of Thrombin. J.Med.Chem. V. 42 1376 1999.
ISSN: ISSN 0022-2623
PubMed: 10212123
DOI: 10.1021/JM980052N
Page generated: Tue Dec 15 05:21:37 2020

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