Zinc in PDB 5lyd: Crystal Structure of 1 in Complex with Tafcpb

All present enzymatic activity of Crystal Structure of 1 in Complex with Tafcpb:
3.4.17.2;

The structure of Crystal Structure of 1 in Complex with Tafcpb, PDB code: 5lyd was solved by H.Schreuder, A.Liesum, P.Loenze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.93 / 2.02
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.320, 82.320, 95.040, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.5

The binding sites of Zinc atom in the Crystal Structure of 1 in Complex with Tafcpb (pdb code 5lyd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of 1 in Complex with Tafcpb, PDB code: 5lyd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of 1 in Complex with Tafcpb


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 1 in Complex with Tafcpb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:33.0 occ:1.00 ND1 A:HIS69 2.0 32.9 1.0 N2 A:7B0406 2.0 34.7 0.9 ND1 A:HIS196 2.0 33.9 1.0 OE1 A:GLU72 2.1 34.5 1.0 OE2 A:GLU72 2.4 37.5 1.0 CD A:GLU72 2.6 45.1 1.0 CE1 A:HIS69 2.9 32.2 1.0 CE1 A:HIS196 3.1 33.2 1.0 CG A:HIS196 3.1 32.5 1.0 CG A:HIS69 3.1 31.5 1.0 O4 A:7B0406 3.1 35.1 0.9 S1 A:7B0406 3.2 36.0 0.9 CB A:HIS196 3.4 29.4 1.0 CB A:HIS69 3.6 28.7 1.0 O A:HOH670 3.9 34.0 1.0 N1 A:7B0406 4.1 35.9 0.9 CG A:GLU72 4.1 37.4 1.0 NE2 A:HIS69 4.1 32.6 1.0 O A:SER197 4.2 36.0 1.0 CD2 A:HIS69 4.2 32.9 1.0 NE2 A:HIS196 4.2 33.4 1.0 O2 A:7B0406 4.2 37.1 0.9 CD2 A:HIS196 4.2 33.8 1.0 CA A:HIS196 4.2 28.9 1.0 C4 A:7B0406 4.4 36.5 0.9 N A:SER197 4.5 31.3 1.0 OE1 A:GLU270 4.5 58.2 1.0 NH1 A:ARG127 4.6 32.7 1.0 O A:HOH510 4.6 40.5 1.0 N A:HIS69 4.7 29.0 1.0 CA A:HIS69 4.8 28.4 1.0 O1 A:7B0406 4.8 33.1 0.9 CB A:GLU72 4.9 32.3 1.0 C2 A:7B0406 4.9 35.6 0.9 C A:HIS196 4.9 33.5 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of 1 in Complex with Tafcpb


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 1 in Complex with Tafcpb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:35.5 occ:0.96 OE1 A:GLU291 2.1 34.8 1.0 OE2 A:GLU85 2.1 37.8 1.0 OE2 A:GLU291 2.2 37.9 1.0 CD A:GLU291 2.4 47.8 1.0 CD A:GLU85 3.0 49.6 1.0 OE1 A:GLU85 3.3 44.2 1.0 NH1 A:ARG84 3.9 39.2 1.0 CG A:GLU291 3.9 39.1 1.0 NE1 A:TRP81 4.3 34.2 1.0 CG A:GLU85 4.4 40.5 1.0 O A:HOH502 4.4 31.8 1.0 O A:HOH747 4.8 52.1 1.0 CB A:GLU291 4.9 30.9 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of 1 in Complex with Tafcpb


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 1 in Complex with Tafcpb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:54.0 occ:0.53 NE2 A:HIS307 2.0 43.3 1.0 CD2 A:HIS307 2.8 43.4 1.0 O A:HOH786 2.8 0.4 1.0 CE1 A:HIS307 3.1 42.9 1.0 O A:HOH736 3.8 55.9 1.0 CG A:HIS307 4.0 41.8 1.0 ND1 A:HIS307 4.2 43.5 1.0 OH A:TYR303 4.4 44.8 1.0 O A:HOH719 4.4 70.0 1.0 CZ A:TYR303 4.9 45.4 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of 1 in Complex with Tafcpb


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 1 in Complex with Tafcpb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:45.7 occ:0.38 O A:HOH658 1.9 54.4 1.0 O A:THR246 2.2 43.0 1.0 NE2 A:HIS201 2.3 41.8 1.0 CG2 A:THR246 2.7 46.1 1.0 C A:THR246 3.1 43.1 1.0 CD2 A:HIS201 3.2 42.0 1.0 CE1 A:HIS201 3.3 41.4 1.0 O A:HOH728 3.4 67.5 1.0 CB A:THR246 3.5 48.4 1.0 CA A:THR246 3.5 39.8 1.0 OG1 A:THR239 3.9 45.2 1.0 N A:LEU247 4.2 39.2 1.0 CD1 A:LEU247 4.3 43.9 1.0 CG A:HIS201 4.4 40.0 1.0 ND1 A:HIS201 4.4 42.0 1.0 CA A:LEU247 4.7 38.8 1.0 O A:HOH671 4.7 56.1 1.0 O A:HOH753 4.7 66.3 1.0 CB A:THR239 4.8 44.8 1.0 OG1 A:THR246 4.9 50.0 1.0 N A:THR246 5.0 40.0 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of 1 in Complex with Tafcpb


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of 1 in Complex with Tafcpb within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:99.1 occ:0.49 O A:HOH688 2.0 0.1 1.0 O A:HOH617 2.2 53.2 1.0 NE2 A:HIS95 2.2 46.5 1.0 O A:HOH754 2.4 62.1 1.0 CE1 A:HIS95 3.0 46.2 1.0 CD2 A:HIS95 3.3 46.5 1.0 ND1 A:HIS95 4.2 46.6 1.0 CG A:HIS95 4.3 44.4 1.0 O A:HOH598 4.4 50.8 1.0 O A:HOH570 4.7 55.5 1.0

N.Halland, J.Czech, W.Czechtizky, A.Evers, M.Follmann, M.Kohlmann, H.A.Schreuder, C.Kallus. Sulfamide As Zinc Binding Motif in Small Molecule Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (Tafia). J. Med. Chem. V. 59 9567 2016.
ISSN: ISSN 1520-4804
PubMed: 27749053
DOI: 10.1021/ACS.JMEDCHEM.6B01276