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

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

The structure of Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin B Complex, PDB code: 5lrg 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)	54.04 / 2.02
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	124.780, 124.780, 48.900, 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 B Complex (pdb code 5lrg). 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 B Complex, PDB code: 5lrg:
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 B 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 B Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:9.7 occ:1.00 ND1 A:HIS69 2.2 6.6 1.0 ND1 A:HIS196 2.2 4.2 1.0 OE2 A:GLU72 2.3 8.7 1.0 OE1 A:GLU72 2.3 10.4 1.0 CD A:GLU72 2.6 8.7 1.0 CE1 A:HIS69 3.1 6.4 1.0 CG A:HIS196 3.2 4.6 1.0 CE1 A:HIS196 3.2 5.1 1.0 CG A:HIS69 3.3 6.1 1.0 O26 F:73N1 3.4 12.6 1.0 CB A:HIS196 3.4 5.2 1.0 CB A:HIS69 3.6 5.9 1.0 C25 F:73N1 3.8 10.9 1.0 O A:HOH648 3.9 7.9 1.0 O A:SER197 3.9 9.5 1.0 C12 F:73N1 4.0 9.4 1.0 OE2 A:GLU270 4.1 14.1 1.0 CG A:GLU72 4.1 8.3 1.0 N23 F:73N1 4.2 10.7 1.0 NE2 A:HIS69 4.3 6.9 1.0 CD2 A:HIS196 4.3 4.1 1.0 NE2 A:HIS196 4.3 4.9 1.0 CA A:HIS196 4.3 6.6 1.0 CD2 A:HIS69 4.4 6.6 1.0 NH1 A:ARG127 4.4 6.1 1.0 N A:SER197 4.5 8.0 1.0 O A:HOH559 4.5 8.1 1.0 N F:DLY2 4.6 11.5 1.0 CA F:DLY2 4.6 11.7 1.0 C20 F:73N1 4.8 9.8 1.0 OE1 A:GLU270 4.8 12.8 1.0 O22 F:73N1 4.8 8.8 1.0 CD A:GLU270 4.9 12.6 1.0 CA A:HIS69 4.9 6.5 1.0 C A:SER197 4.9 8.9 1.0 CB A:GLU72 5.0 8.6 1.0 C A:HIS196 5.0 7.0 1.0 N A:HIS69 5.0 6.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin B 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 B Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:11.5 occ:1.00 ND1 B:HIS69 2.1 3.0 1.0 O B:HOH509 2.2 9.4 1.0 ND1 B:HIS196 2.2 6.1 1.0 OE2 B:GLU72 2.3 5.5 1.0 OE1 B:GLU72 2.4 7.0 1.0 CD B:GLU72 2.7 5.9 1.0 CE1 B:HIS69 3.0 2.9 1.0 CG B:HIS196 3.2 6.3 1.0 CG B:HIS69 3.2 3.3 1.0 CE1 B:HIS196 3.2 5.8 1.0 O26 G:73N1 3.4 8.7 1.0 CB B:HIS196 3.4 5.7 1.0 CB B:HIS69 3.6 3.7 1.0 C25 G:73N1 3.8 7.8 1.0 O B:SER197 3.8 6.8 1.0 O B:HOH590 4.0 4.9 1.0 OE2 B:GLU270 4.0 9.6 1.0 CG B:GLU72 4.2 6.5 1.0 NE2 B:HIS69 4.2 4.2 1.0 C12 G:73N1 4.2 6.5 1.0 N23 G:73N1 4.2 7.8 1.0 CD2 B:HIS69 4.3 3.2 1.0 NE2 B:HIS196 4.3 6.6 1.0 O B:HOH539 4.3 8.8 1.0 CD2 B:HIS196 4.3 6.5 1.0 CA B:HIS196 4.3 6.2 1.0 NH1 B:ARG127 4.4 4.8 1.0 N B:SER197 4.4 6.9 1.0 N G:DLY2 4.5 8.9 1.0 CA G:DLY2 4.6 9.2 1.0 OE1 B:GLU270 4.7 9.3 1.0 CD B:GLU270 4.8 8.8 1.0 O21 G:73N1 4.8 5.3 1.0 C20 G:73N1 4.8 5.9 1.0 C B:SER197 4.9 7.2 1.0 CA B:HIS69 4.9 4.8 1.0 C B:HIS196 4.9 6.9 1.0 N B:HIS69 5.0 5.6 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Porcine Carboxypeptidase B - Anabaenopeptin B 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 B Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:16.2 occ:1.00 ND1 C:HIS69 2.2 6.2 1.0 ND1 C:HIS196 2.2 12.0 1.0 O C:HOH503 2.3 19.2 1.0 OE2 C:GLU72 2.4 9.9 1.0 OE1 C:GLU72 2.4 8.7 1.0 CD C:GLU72 2.7 9.9 1.0 CE1 C:HIS69 3.1 7.2 1.0 CG C:HIS196 3.2 12.8 1.0 CE1 C:HIS196 3.2 12.7 1.0 CG C:HIS69 3.3 7.6 1.0 O C:HOH514 3.3 44.0 1.0 O26 H:73N1 3.3 14.2 1.0 CB C:HIS196 3.4 12.0 1.0 CB C:HIS69 3.7 8.4 1.0 C25 H:73N1 3.7 14.9 1.0 O C:SER197 3.9 13.4 1.0 O C:HOH620 4.1 9.7 1.0 N23 H:73N1 4.2 15.3 1.0 OE2 C:GLU270 4.2 15.5 1.0 CG C:GLU72 4.2 10.7 1.0 NE2 C:HIS69 4.2 6.2 1.0 CD2 C:HIS196 4.3 12.0 1.0 NE2 C:HIS196 4.3 12.7 1.0 CD2 C:HIS69 4.3 7.4 1.0 CA C:HIS196 4.3 12.4 1.0 O H:HOH703 4.4 10.3 1.0 N C:SER197 4.4 12.8 1.0 N H:DLY2 4.4 15.2 1.0 C12 H:73N1 4.4 14.8 1.0 NH1 C:ARG127 4.4 9.5 1.0 CA H:DLY2 4.5 16.3 1.0 OE1 C:GLU270 4.7 15.0 1.0 O21 H:73N1 4.8 14.3 1.0 C20 H:73N1 4.9 14.6 1.0 CD C:GLU270 4.9 15.3 1.0 C C:SER197 4.9 13.3 1.0 C C:HIS196 4.9 12.6 1.0 CA C:HIS69 5.0 9.2 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