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Sodium in PDB 1tbz: Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen

Enzymatic activity of Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen

All present enzymatic activity of Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen:
3.4.21.5;

Protein crystallography data

The structure of Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen, PDB code: 1tbz was solved by J.H.Matthews, R.Krishnan, M.J.Costanzo, B.E.Maryanoff, A.Tulinsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.790, 72.530, 73.120, 90.00, 101.00, 90.00
R / Rfree (%) 15.8 / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen (pdb code 1tbz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen, PDB code: 1tbz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1tbz

Go back to Sodium Binding Sites List in 1tbz
Sodium binding site 1 out of 2 in the Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1

b:23.5
occ:0.86
 O H:LYS224 2.1 24.1 1.0
O H:ARG221A 2.1 27.4 1.0
O H:HOH731 3.0 15.6 0.5
C H:LYS224 3.0 22.7 1.0
O H:HOH406 3.2 10.0 1.0
C H:ARG221A 3.3 26.9 1.0
N H:ARG221A 3.5 27.1 1.0
O H:HOH502 3.5 24.9 0.8
CA H:LYS224 3.7 23.7 1.0
N H:LYS224 3.7 24.6 1.0
C H:ASP221 3.9 27.0 1.0
N H:TYR225 3.9 20.9 1.0
CB H:LYS224 3.9 27.0 1.0
CA H:ARG221A 4.0 27.6 1.0
O H:HOH603 4.1 23.5 0.7
CA H:ASP221 4.1 25.6 1.0
O H:HOH422 4.2 28.3 1.0
N H:ASP222 4.3 27.7 1.0
O H:ASP221 4.4 27.3 1.0
CA H:TYR225 4.4 17.6 1.0
CA H:ASP222 4.5 28.6 1.0
N H:ASP221 4.6 23.9 1.0
C H:ASP222 4.7 28.1 1.0
CB H:ARG221A 4.7 29.5 1.0
O H:HOH420 4.7 12.7 1.0
N H:GLY223 4.8 27.8 1.0
OD2 H:ASP189 4.8 24.2 1.0
O H:TYR184A 4.9 24.2 1.0
OD1 H:ASP221 4.9 22.6 1.0
C H:GLY223 5.0 25.9 1.0

Sodium binding site 2 out of 2 in 1tbz

Go back to Sodium Binding Sites List in 1tbz
Sodium binding site 2 out of 2 in the Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin with Active Site N-Methyl-D Phenylalanyl-N-[5- (Aminoiminomethyl)Amino]-1-{{Benzothiazolyl)Carbonyl] Butyl]-L- Prolinamide Trifluroacetate and Exosite-Hirugen within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na2

b:24.8
occ:0.87
 O H:THR172 2.3 21.8 1.0
O H:LYS169 2.6 23.6 1.0
O H:HOH627 2.9 10.1 0.6
C H:THR172 3.5 19.6 1.0
C H:LYS169 3.7 22.0 1.0
CA H:ASP170 4.3 22.8 1.0
N H:ASP170 4.3 21.4 1.0
N H:ARG173 4.3 19.6 1.0
N H:THR172 4.4 20.0 1.0
CA H:ARG173 4.4 22.0 1.0
CA H:THR172 4.6 19.8 1.0
CA H:LYS169 4.7 22.6 1.0
C H:ASP170 4.7 22.9 1.0
OD1 H:ASP170 4.7 21.2 1.0
O H:ILE174 5.0 16.9 1.0
C H:ARG173 5.0 22.1 1.0

Reference:

J.H.Matthews, R.Krishnan, M.J.Costanzo, B.E.Maryanoff, A.Tulinsky. Crystal Structures of Thrombin with Thiazole-Containing Inhibitors: Probes of the S1' Binding Site. Biophys.J. V. 71 2830 1996.
ISSN: ISSN 0006-3495
PubMed: 8913620
Page generated: Tue Dec 15 05:36:23 2020

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