Zinc in PDB 5hvg: Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-A204)

All present enzymatic activity of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-A204):
3.4.17.20;

The structure of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-A204), PDB code: 5hvg was solved by X.Zhou, S.D.Weeks, S.V.Strelkov, P.J.Declerck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.38 / 3.05
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	193.266, 193.266, 111.767, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21.2

The binding sites of Zinc atom in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-A204) (pdb code 5hvg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-A204), PDB code: 5hvg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-A204)


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 in Complex with An Inhibitory Nanobody (Vhh-A204) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:71.6 occ:1.00 ND1 A:HIS159 1.9 69.5 1.0 ND1 A:HIS288 2.0 68.0 1.0 OE1 A:GLU162 2.3 64.4 1.0 OE2 A:GLU162 2.5 75.8 1.0 OXT A:ACT510 2.5 90.0 1.0 CD A:GLU162 2.7 79.2 1.0 CE1 A:HIS159 2.8 69.7 1.0 C A:ACT510 2.9 91.4 1.0 CE1 A:HIS288 3.0 67.8 1.0 CG A:HIS159 3.0 68.4 1.0 CG A:HIS288 3.1 66.9 1.0 O A:ACT510 3.2 93.2 1.0 CB A:HIS159 3.5 65.6 1.0 CB A:HIS288 3.5 63.7 1.0 NE2 A:HIS159 4.0 70.6 1.0 CH3 A:ACT510 4.0 90.6 1.0 CD2 A:HIS159 4.1 70.8 1.0 NE2 A:HIS288 4.1 69.2 1.0 CG A:GLU162 4.2 67.5 1.0 CD2 A:HIS288 4.2 69.3 1.0 CA A:HIS288 4.4 63.4 1.0 O A:SER289 4.4 71.2 1.0 NH1 A:ARG217 4.5 62.4 1.0 OE1 A:GLU363 4.6 79.1 1.0 N A:SER289 4.7 68.6 1.0 OE2 A:GLU363 4.7 95.6 1.0 CA A:HIS159 4.8 66.7 1.0 N A:HIS159 4.9 67.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-A204)


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 in Complex with An Inhibitory Nanobody (Vhh-A204) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn504 b:61.9 occ:1.00 ND1 C:HIS288 2.1 50.1 1.0 ND1 C:HIS159 2.2 65.5 1.0 OE2 C:GLU162 2.2 63.3 1.0 OE1 C:GLU162 2.3 50.0 1.0 CD C:GLU162 2.6 77.9 1.0 CE1 C:HIS159 3.0 65.8 1.0 CG C:HIS288 3.1 48.9 1.0 CE1 C:HIS288 3.2 48.9 1.0 OXT C:ACT505 3.2 87.5 1.0 CG C:HIS159 3.4 63.2 1.0 CB C:HIS288 3.4 46.3 1.0 OE2 C:GLU363 3.5 81.7 1.0 CB C:HIS159 3.8 59.2 1.0 CG C:GLU162 4.1 61.3 1.0 C C:ACT505 4.1 83.1 1.0 O C:SER289 4.2 56.1 1.0 NE2 C:HIS159 4.2 66.0 1.0 CD2 C:HIS288 4.2 50.0 1.0 NE2 C:HIS288 4.3 49.4 1.0 CA C:HIS288 4.4 44.9 1.0 CD2 C:HIS159 4.4 65.8 1.0 NH1 C:ARG217 4.4 75.3 1.0 CD C:GLU363 4.4 92.5 1.0 N C:SER289 4.5 52.0 1.0 OE1 C:GLU363 4.8 96.0 1.0 O C:ACT505 4.8 81.4 1.0 CH3 C:ACT505 5.0 79.8 1.0 C C:HIS288 5.0 52.4 1.0

X.Zhou, S.D.Weeks, P.Ameloot, N.Callewaert, S.V.Strelkov, P.J.Declerck. Elucidation of the Molecular Mechanisms of Two Nanobodies That Inhibit Thrombin-Activatable Fibrinolysis Inhibitor Activation and Activated Thrombin-Activatable Fibrinolysis Inhibitor Activity. J.Thromb.Haemost. V. 14 1629 2016.
ISSN: ESSN 1538-7836
PubMed: 27279497
DOI: 10.1111/JTH.13381