Zinc in PDB 3d66: Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi)

All present enzymatic activity of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi):
3.4.17.20;

The structure of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi), PDB code: 3d66 was solved by T.H.C.Brondijk, E.G.Huizinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.51 / 3.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.740, 161.740, 139.450, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24

The binding sites of Zinc atom in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) (pdb code 3d66). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi), PDB code: 3d66:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:99.3 occ:1.00 ND1 A:HIS159 2.2 89.8 1.0 ND1 A:HIS288 2.2 88.8 1.0 OE1 A:GLU162 2.3 84.9 1.0 OE2 A:GLU162 2.3 88.4 1.0 CD A:GLU162 2.6 85.8 1.0 CE1 A:HIS288 3.1 87.5 1.0 CE1 A:HIS159 3.1 89.8 1.0 CG A:HIS288 3.1 87.0 1.0 CG A:HIS159 3.2 88.4 1.0 CB A:HIS288 3.5 86.2 1.0 CB A:HIS159 3.6 86.6 1.0 O A:SER289 3.9 87.7 1.0 NE2 A:HIS288 4.1 86.7 1.0 CG A:GLU162 4.1 84.8 1.0 CD2 A:HIS288 4.2 86.2 1.0 NE2 A:HIS159 4.2 89.0 1.0 CD2 A:HIS159 4.3 90.7 1.0 NH1 A:ARG217 4.4 98.1 1.0 CA A:HIS288 4.4 86.0 1.0 N A:SER289 4.6 87.8 1.0 N A:HIS159 4.9 86.6 1.0 CA A:HIS159 4.9 86.3 1.0 CB A:GLU162 5.0 85.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:0.8 occ:1.00 OE2 B:GLU162 2.1 98.4 1.0 ND1 B:HIS159 2.2 87.7 1.0 OE1 B:GLU162 2.2 94.2 1.0 ND1 B:HIS288 2.2 97.4 1.0 CD B:GLU162 2.5 89.2 1.0 CE1 B:HIS159 3.0 86.5 1.0 CE1 B:HIS288 3.1 98.2 1.0 CG B:HIS288 3.2 94.5 1.0 CG B:HIS159 3.2 86.8 1.0 CB B:HIS288 3.5 93.6 1.0 CB B:HIS159 3.6 87.1 1.0 O B:SER289 3.8 99.5 1.0 CG B:GLU162 4.1 88.0 1.0 NE2 B:HIS288 4.2 96.9 1.0 NE2 B:HIS159 4.2 87.1 1.0 CD2 B:HIS288 4.2 95.0 1.0 CD2 B:HIS159 4.3 87.8 1.0 CA B:HIS288 4.4 92.6 1.0 NH1 B:ARG217 4.5 89.6 1.0 N B:SER289 4.6 96.2 1.0 N B:HIS159 4.9 87.5 1.0 CA B:HIS159 4.9 87.6 1.0 CB B:GLU162 4.9 87.6 1.0 C B:SER289 5.0 99.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor (Tafi) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:0.7 occ:1.00 ND1 C:HIS159 2.1 92.3 1.0 OE2 C:GLU162 2.1 98.4 1.0 OE1 C:GLU162 2.2 96.5 1.0 ND1 C:HIS288 2.2 95.0 1.0 CD C:GLU162 2.5 90.3 1.0 CE1 C:HIS159 3.0 92.9 1.0 CE1 C:HIS288 3.1 93.5 1.0 CG C:HIS159 3.1 90.9 1.0 CG C:HIS288 3.2 91.3 1.0 CB C:HIS159 3.5 91.3 1.0 CB C:HIS288 3.6 91.0 1.0 O C:SER289 4.0 93.9 1.0 CG C:GLU162 4.1 90.5 1.0 NE2 C:HIS159 4.1 92.7 1.0 NE2 C:HIS288 4.1 93.0 1.0 CD2 C:HIS288 4.2 92.5 1.0 CD2 C:HIS159 4.2 91.3 1.0 NH1 C:ARG217 4.4 97.4 1.0 CA C:HIS288 4.5 90.6 1.0 N C:SER289 4.7 92.0 1.0 CA C:HIS159 4.8 91.0 1.0 N C:HIS159 4.8 91.5 1.0 CB C:GLU162 4.9 89.0 1.0

P.F.Marx, T.H.Brondijk, T.Plug, R.A.Romijn, W.Hemrika, J.C.M.Meijers, E.G.Huizinga. Crystal Structures of Tafi Elucidate the Inactivation Mechanism of Activated Tafi: A Novel Mechanism For Enzyme Autoregulation Blood V. 112 2803 2008.
ISSN: ISSN 0006-4971
PubMed: 18559974
DOI: 10.1182/BLOOD-2008-03-146001