Zinc in PDB 3dgv: 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: 3dgv was solved by K.Anand, I.Pallares, Z.Valnickova, T.Christensen, H.Schreuder, J.Enghild, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	146.470, 146.470, 231.690, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.3

The binding sites of Zinc atom in the Crystal Structure of Thrombin Activatable Fibrinolysis Inhibitor (Tafi) (pdb code 3dgv). 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: 3dgv:
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:Zn318 b:39.2 occ:1.00 ND1 A:HIS69 2.1 35.1 1.0 ND1 A:HIS196 2.2 39.1 1.0 OE1 A:GLU72 2.2 38.0 1.0 O6 A:MLI328 2.3 72.1 1.0 OE2 A:GLU72 2.5 40.6 1.0 CD A:GLU72 2.7 39.1 1.0 CE1 A:HIS69 3.0 34.8 1.0 CG A:HIS196 3.1 38.2 1.0 C2 A:MLI328 3.2 73.4 1.0 CG A:HIS69 3.2 34.9 1.0 CE1 A:HIS196 3.2 39.1 1.0 CB A:HIS196 3.3 36.1 1.0 CB A:HIS69 3.6 35.7 1.0 O7 A:MLI328 3.7 73.8 1.0 O A:HOH337 4.1 31.0 1.0 O A:SER197 4.1 40.3 1.0 NE2 A:HIS69 4.2 35.2 1.0 C1 A:MLI328 4.2 72.9 1.0 CG A:GLU72 4.2 39.1 1.0 CA A:HIS196 4.2 36.8 1.0 CD2 A:HIS69 4.3 35.2 1.0 CD2 A:HIS196 4.3 38.3 1.0 NE2 A:HIS196 4.3 39.4 1.0 N A:SER197 4.4 37.7 1.0 O A:HOH369 4.6 28.3 1.0 NH1 A:ARG127 4.6 41.0 1.0 CA A:HIS69 4.9 36.2 1.0 C A:HIS196 4.9 37.3 1.0 OE1 A:GLU270 4.9 50.0 1.0 N A:HIS69 4.9 35.9 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:Zn317 b:39.5 occ:1.00 ND1 B:HIS69 2.1 39.3 1.0 ND1 B:HIS196 2.2 34.5 1.0 OE2 B:GLU72 2.2 36.8 1.0 OE1 B:GLU72 2.4 34.1 1.0 O6 B:MLI329 2.5 67.4 1.0 CD B:GLU72 2.7 35.6 1.0 C2 B:MLI329 3.0 68.3 1.0 CE1 B:HIS69 3.0 39.7 1.0 CE1 B:HIS196 3.1 34.5 1.0 CG B:HIS196 3.2 33.7 1.0 CG B:HIS69 3.2 38.7 1.0 O7 B:MLI329 3.4 68.2 1.0 CB B:HIS196 3.5 35.2 1.0 CB B:HIS69 3.5 38.4 1.0 C1 B:MLI329 3.8 67.8 1.0 O B:HOH398 3.9 47.5 1.0 CG B:GLU72 4.2 35.6 1.0 NE2 B:HIS69 4.2 40.2 1.0 NE2 B:HIS196 4.3 33.5 1.0 CD2 B:HIS69 4.3 40.0 1.0 CD2 B:HIS196 4.3 33.7 1.0 O B:SER197 4.3 38.8 1.0 CA B:HIS196 4.3 37.6 1.0 O B:HOH336 4.6 20.6 1.0 N B:SER197 4.6 38.2 1.0 O B:HOH478 4.8 50.5 1.0 CA B:HIS69 4.8 38.7 1.0 NH1 B:ARG127 4.8 36.8 1.0 N B:HIS69 4.9 39.2 1.0 C3 B:MLI329 5.0 67.4 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:Zn310 b:0.7 occ:1.00 ND1 C:HIS69 2.1 99.9 1.0 ND1 C:HIS196 2.3 0.3 1.0 OE2 C:GLU72 2.4 99.2 1.0 OE1 C:GLU72 2.6 99.5 1.0 CG C:HIS196 2.7 0.4 1.0 CD C:GLU72 2.8 99.6 1.0 CE1 C:HIS69 2.9 100.0 1.0 CE1 C:HIS196 2.9 0.6 1.0 CB C:HIS196 3.2 0.6 1.0 CG C:HIS69 3.3 99.9 1.0 O7 C:MLI313 3.3 0.8 1.0 CD2 C:HIS196 3.4 0.5 1.0 NE2 C:HIS196 3.5 0.6 1.0 CB C:HIS69 3.8 99.7 1.0 NE2 C:HIS69 4.1 99.8 1.0 CA C:HIS196 4.2 0.0 1.0 C2 C:MLI313 4.2 0.7 1.0 CD2 C:HIS69 4.3 99.9 1.0 CG C:GLU72 4.3 99.6 1.0 O6 C:MLI313 4.4 0.6 1.0 O C:SER197 4.4 0.7 1.0 N C:SER197 4.6 0.0 1.0 NH1 C:ARG127 4.7 95.3 1.0 O9 C:MLI313 4.8 0.5 1.0 N C:HIS69 4.9 99.0 1.0 O C:MET195 4.9 0.6 1.0 C C:HIS196 5.0 0.9 1.0 CA C:HIS69 5.0 99.5 1.0

K.Anand, I.Pallares, Z.Valnickova, T.Christensen, J.Vendrell, K.U.Wendt, H.A.Schreuder, J.J.Enghild, F.X.Avil S. The Crystal Structure of Tafi Provides the Structural Basis For the Intrinsic Activity of the Proenzyme and Short Half-Life of Tafia To Be Published.