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Sodium in PDB 6tkg: Tsetse Thrombin Inhibitor in Complex with Human Alpha-Thrombin - Orthorhombic Form at 12KEV

Enzymatic activity of Tsetse Thrombin Inhibitor in Complex with Human Alpha-Thrombin - Orthorhombic Form at 12KEV

All present enzymatic activity of Tsetse Thrombin Inhibitor in Complex with Human Alpha-Thrombin - Orthorhombic Form at 12KEV:
3.4.21.5;

Protein crystallography data

The structure of Tsetse Thrombin Inhibitor in Complex with Human Alpha-Thrombin - Orthorhombic Form at 12KEV, PDB code: 6tkg was solved by B.M.Calisto, J.Ripoll-Rozada, D.De Sanctis, P.J.B.Pereira, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.77 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.438, 81.124, 85.544, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 19.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Tsetse Thrombin Inhibitor in Complex with Human Alpha-Thrombin - Orthorhombic Form at 12KEV (pdb code 6tkg). 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 Tsetse Thrombin Inhibitor in Complex with Human Alpha-Thrombin - Orthorhombic Form at 12KEV, PDB code: 6tkg:

Sodium binding site 1 out of 1 in 6tkg

Go back to Sodium Binding Sites List in 6tkg
Sodium binding site 1 out of 1 in the Tsetse Thrombin Inhibitor in Complex with Human Alpha-Thrombin - Orthorhombic Form at 12KEV


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tsetse Thrombin Inhibitor in Complex with Human Alpha-Thrombin - Orthorhombic Form at 12KEV within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na603

b:18.4
occ:1.00
 O H:ARG553 2.2 17.6 1.0
O H:HOH790 2.3 18.9 1.0
O H:LYS556 2.4 16.3 1.0
O H:HOH890 2.4 17.2 1.0
O H:HOH810 2.5 16.1 1.0
O H:HOH771 2.6 18.1 1.0
C H:ARG553 3.3 18.0 1.0
C H:LYS556 3.5 14.7 1.0
N H:ARG553 3.8 16.8 1.0
N H:LYS556 3.9 16.0 1.0
O H:HOH842 3.9 16.8 1.0
O H:HOH732 4.0 20.8 1.0
C H:ASP552 4.0 16.1 1.0
O H:TYR510 4.0 18.6 1.0
N H:ASP554 4.1 20.7 1.0
CA H:ARG553 4.1 17.8 1.0
O H:HOH815 4.2 16.6 1.0
CA H:LYS556 4.2 14.7 1.0
N H:GLY555 4.3 19.1 1.0
CA H:ASP554 4.3 21.1 1.0
CA H:ASP552 4.4 17.1 1.0
C H:ASP554 4.5 20.4 1.0
N H:TYR557 4.5 14.4 1.0
O H:ASP552 4.6 18.4 1.0
CB H:LYS556 4.7 15.8 1.0
OD1 H:ASP552 4.7 20.7 1.0
O H:HOH806 4.8 19.8 1.0
CA H:TYR557 4.8 13.8 1.0
O H:HOH717 4.9 38.7 1.0
C H:GLY555 4.9 18.8 1.0

Reference:

B.M.Calisto, J.Ripoll-Rozada, L.J.Dowman, C.Franck, S.M.Agten, B.L.Parker, R.C.Veloso, N.Vale, P.Gomes, D.De Sanctis, R.J.Payne, P.J.B.Pereira. Sulfotyrosine-Mediated Recognition of Human Thrombin By A Tsetse Fly Anticoagulant Mimics Physiological Substrates. Cell Chem Biol 2020.
ISSN: ESSN 2451-9456
PubMed: 33096052
DOI: 10.1016/J.CHEMBIOL.2020.10.002
Page generated: Tue Dec 15 14:24:42 2020

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