Zinc in PDB 5lrk: Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin F Complex

All present enzymatic activity of Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin F Complex:
3.4.17.2;

The structure of Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin F Complex, PDB code: 5lrk 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)	62.24 / 2.30
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	124.620, 124.620, 48.470, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin F Complex (pdb code 5lrk). 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 the Porcine Carboxypeptidase B - Anabaenopeptin F Complex, PDB code: 5lrk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin F Complex


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 the Porcine Carboxypeptidase B - Anabaenopeptin F Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:17.1 occ:1.00 ND1 A:HIS69 2.2 9.4 1.0 ND1 A:HIS196 2.2 11.5 1.0 OE2 A:GLU72 2.2 11.9 1.0 OE1 A:GLU72 2.4 11.8 1.0 CD A:GLU72 2.6 12.1 1.0 CE1 A:HIS69 3.1 9.4 1.0 CG A:HIS196 3.1 12.2 1.0 CE1 A:HIS196 3.2 12.5 1.0 CG A:HIS69 3.3 9.1 1.0 CB A:HIS196 3.4 12.0 1.0 O26 F:73N1 3.4 16.5 1.0 CB A:HIS69 3.6 9.6 1.0 C25 F:73N1 3.9 15.8 1.0 O A:SER197 3.9 13.5 1.0 O A:HOH640 4.0 8.1 1.0 OE2 A:GLU270 4.1 18.5 1.0 C12 F:73N1 4.2 14.1 1.0 CG A:GLU72 4.2 11.4 1.0 NE2 A:HIS69 4.2 9.3 1.0 NE2 A:HIS196 4.3 12.9 1.0 CD2 A:HIS196 4.3 12.6 1.0 CA A:HIS196 4.3 12.3 1.0 N23 F:73N1 4.3 15.5 1.0 CD2 A:HIS69 4.3 9.6 1.0 O A:HOH552 4.4 24.6 1.0 N F:DLY2 4.5 16.6 1.0 CA F:DLY2 4.5 16.9 1.0 N A:SER197 4.5 13.0 1.0 NH1 A:ARG127 4.6 11.0 1.0 OE1 A:GLU270 4.8 17.0 1.0 CD A:GLU270 4.8 17.6 1.0 C A:SER197 4.9 13.6 1.0 N A:HIS69 4.9 10.8 1.0 CA A:HIS69 4.9 10.1 1.0 C20 F:73N1 4.9 14.7 1.0 C A:HIS196 5.0 12.8 1.0 O22 F:73N1 5.0 14.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin F Complex


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 the Porcine Carboxypeptidase B - Anabaenopeptin F Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:14.0 occ:1.00 O B:HOH529 2.1 16.9 1.0 ND1 B:HIS196 2.2 12.2 1.0 OE2 B:GLU72 2.2 12.8 1.0 ND1 B:HIS69 2.2 5.4 1.0 OE1 B:GLU72 2.4 12.7 1.0 CD B:GLU72 2.6 12.4 1.0 CE1 B:HIS69 3.1 5.2 1.0 CG B:HIS196 3.1 12.7 1.0 CE1 B:HIS196 3.1 12.1 1.0 O26 G:73N1 3.2 12.9 1.0 CG B:HIS69 3.3 6.2 1.0 CB B:HIS196 3.4 12.7 1.0 C25 G:73N1 3.7 12.0 1.0 CB B:HIS69 3.7 6.6 1.0 O B:SER197 3.7 14.6 1.0 OE2 B:GLU270 4.0 14.3 1.0 O B:HOH556 4.0 16.2 1.0 N23 G:73N1 4.1 11.7 1.0 CG B:GLU72 4.1 12.5 1.0 C12 G:73N1 4.1 10.5 1.0 NE2 B:HIS69 4.2 6.6 1.0 NE2 B:HIS196 4.3 13.1 1.0 CD2 B:HIS196 4.3 13.1 1.0 CA B:HIS196 4.3 12.4 1.0 CD2 B:HIS69 4.4 6.4 1.0 O B:HOH596 4.4 18.3 1.0 N B:SER197 4.4 13.6 1.0 N G:DLY2 4.5 12.2 1.0 NH1 B:ARG127 4.5 7.7 1.0 CA G:DLY2 4.5 12.8 1.0 OE1 B:GLU270 4.6 15.0 1.0 CD B:GLU270 4.7 14.3 1.0 O21 G:73N1 4.8 10.4 1.0 C20 G:73N1 4.8 10.6 1.0 C B:SER197 4.8 14.2 1.0 C B:HIS196 4.9 13.1 1.0 CA B:HIS69 5.0 8.0 1.0 CB B:GLU72 5.0 12.1 1.0 N B:HIS69 5.0 8.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin F Complex


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 the Porcine Carboxypeptidase B - Anabaenopeptin F Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:20.1 occ:1.00 ND1 C:HIS69 2.3 13.7 1.0 ND1 C:HIS196 2.3 17.6 1.0 OE2 C:GLU72 2.3 16.0 1.0 O C:HOH552 2.4 40.4 1.0 OE1 C:GLU72 2.5 14.7 1.0 CD C:GLU72 2.7 15.8 1.0 CG C:HIS196 3.1 17.9 1.0 CE1 C:HIS69 3.2 13.0 1.0 CB C:HIS196 3.3 17.4 1.0 CG C:HIS69 3.3 14.1 1.0 CE1 C:HIS196 3.3 17.4 1.0 O26 H:73N1 3.5 23.0 1.0 CB C:HIS69 3.7 14.1 1.0 C25 H:73N1 3.8 22.5 1.0 O C:SER197 3.8 18.8 1.0 N23 H:73N1 4.1 21.6 1.0 O C:HOH659 4.1 24.6 1.0 OE2 C:GLU270 4.2 21.5 1.0 CA C:HIS196 4.2 17.5 1.0 CG C:GLU72 4.2 15.6 1.0 N C:SER197 4.3 18.0 1.0 CD2 C:HIS196 4.3 17.6 1.0 NE2 C:HIS69 4.3 13.5 1.0 O H:HOH103 4.4 7.6 1.0 NE2 C:HIS196 4.4 17.7 1.0 C12 H:73N1 4.4 20.7 1.0 CD2 C:HIS69 4.4 14.3 1.0 N H:DLY2 4.5 23.9 1.0 CA H:DLY2 4.6 24.2 1.0 NH1 C:ARG127 4.6 12.6 1.0 OE1 C:GLU270 4.6 20.9 1.0 O21 H:73N1 4.8 21.3 1.0 C C:HIS196 4.8 18.0 1.0 CD C:GLU270 4.8 21.9 1.0 C C:SER197 4.8 18.6 1.0 C20 H:73N1 4.9 21.0 1.0 CA C:HIS69 5.0 14.8 1.0 N C:HIS69 5.0 14.8 1.0

H.Schreuder, A.Liesum, P.Lonze, H.Stump, H.Hoffmann, M.Schiell, M.Kurz, L.Toti, A.Bauer, C.Kallus, C.Klemke-Jahn, J.Czech, D.Kramer, H.Enke, T.H.Niedermeyer, V.Morrison, V.Kumar, M.Bronstrup. Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins As Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (Tafia). Sci Rep V. 6 32958 2016.
ISSN: ESSN 2045-2322
PubMed: 27604544
DOI: 10.1038/SREP32958