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Zinc in PDB 5hvf: Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-I83)

Enzymatic activity of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-I83)

All present enzymatic activity of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-I83):
3.4.17.20;

Protein crystallography data

The structure of Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-I83), PDB code: 5hvf 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) 48.99 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.290, 69.978, 165.337, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-I83) (pdb code 5hvf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-I83), PDB code: 5hvf:

Zinc binding site 1 out of 1 in 5hvf

Go back to Zinc Binding Sites List in 5hvf
Zinc binding site 1 out of 1 in the Crystal Structure of Thrombin-Activatable Fibrinolysis Inhibitor in Complex with An Inhibitory Nanobody (Vhh-I83)


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-I83) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:52.2
occ:1.00
 ND1 A:HIS159 2.1 49.3 1.0
OA1 A:FLC509 2.1 62.5 1.0
CD2 A:HIS288 2.2 50.6 1.0
OE1 A:GLU162 2.3 53.1 1.0
OE2 A:GLU162 2.4 67.0 1.0
CAC A:FLC509 2.4 61.4 1.0
CD A:GLU162 2.7 59.3 1.0
OA2 A:FLC509 2.9 59.6 1.0
CE1 A:HIS159 3.0 49.0 1.0
CG A:HIS288 3.1 49.4 1.0
NE2 A:HIS288 3.2 51.0 1.0
CG A:HIS159 3.2 47.4 1.0
CA A:FLC509 3.3 64.7 1.0
CB A:HIS288 3.5 45.3 1.0
CB A:HIS159 3.7 43.6 1.0
CE1 A:HIS288 4.1 52.4 1.0
ND1 A:HIS288 4.1 53.3 1.0
CG A:GLU162 4.2 44.9 1.0
NE2 A:HIS159 4.2 48.7 1.0
O A:SER289 4.3 45.2 1.0
CD2 A:HIS159 4.3 48.8 1.0
NH1 A:ARG217 4.3 46.2 1.0
CA A:HIS288 4.4 44.8 1.0
OE2 A:GLU363 4.6 0.9 1.0
CB A:FLC509 4.6 71.0 1.0
OB1 A:FLC509 4.6 62.9 1.0
N A:SER289 4.6 39.0 1.0
CBC A:FLC509 4.7 68.1 1.0
CA A:HIS159 5.0 43.7 1.0

Reference:

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
Page generated: Sun Oct 27 17:40:11 2024

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