Zinc in PDB 1kbc: Procarboxypeptidase Ternary Complex

All present enzymatic activity of Procarboxypeptidase Ternary Complex:
3.4.24.34;

The structure of Procarboxypeptidase Ternary Complex, PDB code: 1kbc was solved by M.Betz, F.X.Gomis-Rueth, W.Bode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.700, 80.800, 108.100, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / n/a

The structure of Procarboxypeptidase Ternary Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

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

Zinc binding site 1 out of 4 in the Procarboxypeptidase Ternary Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Procarboxypeptidase Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:16.9 occ:1.00 NE2 A:HIS162 1.9 12.0 1.0 OD2 A:ASP149 1.9 15.6 1.0 NE2 A:HIS147 2.0 12.8 1.0 ND1 A:HIS175 2.1 15.0 1.0 CE1 A:HIS162 2.7 13.9 1.0 CG A:ASP149 2.8 15.7 1.0 CD2 A:HIS147 3.0 11.8 1.0 CE1 A:HIS147 3.0 12.7 1.0 CE1 A:HIS175 3.1 16.4 1.0 CD2 A:HIS162 3.1 12.9 1.0 OD1 A:ASP149 3.2 13.7 1.0 CG A:HIS175 3.2 15.2 1.0 CB A:HIS175 3.5 13.1 1.0 ND1 A:HIS162 3.9 13.2 1.0 CG A:HIS147 4.1 13.1 1.0 ND1 A:HIS147 4.1 13.6 1.0 CG A:HIS162 4.2 13.2 1.0 CB A:ASP149 4.2 15.5 1.0 NE2 A:HIS175 4.2 17.5 1.0 CE1 A:PHE164 4.3 22.2 1.0 O A:SER151 4.3 16.3 1.0 CD2 A:HIS175 4.3 17.2 1.0 CZ A:PHE164 4.3 23.0 1.0 CE2 A:PHE153 4.6 13.6 1.0 CD2 A:TYR143 4.7 22.0 1.0 CZ A:PHE153 4.8 13.7 1.0

Zinc binding site 2 out of 4 in the Procarboxypeptidase Ternary Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Procarboxypeptidase Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:16.6 occ:1.00 NE2 A:HIS207 2.1 17.4 1.0 NE2 A:HIS201 2.1 15.1 1.0 O2 A:HLE1 2.1 15.2 1.0 NE2 A:HIS197 2.1 14.5 1.0 OH A:HLE1 2.1 16.9 1.0 C2 A:HLE1 2.8 14.6 1.0 N A:HLE1 2.9 14.9 1.0 CE1 A:HIS207 3.1 16.9 1.0 CE1 A:HIS201 3.1 14.8 1.0 CD2 A:HIS207 3.1 16.7 1.0 CD2 A:HIS201 3.1 13.3 1.0 CE1 A:HIS197 3.1 13.5 1.0 CD2 A:HIS197 3.1 12.0 1.0 ND1 A:HIS207 4.2 16.5 1.0 O A:HOH1033 4.2 15.7 1.0 ND1 A:HIS201 4.2 15.1 1.0 CG A:HIS207 4.2 17.0 1.0 C1 A:HLE1 4.2 14.8 1.0 CG A:HIS201 4.3 14.4 1.0 ND1 A:HIS197 4.3 12.5 1.0 CG A:HIS197 4.3 10.7 1.0 CA A:HLE1 4.6 12.8 1.0 OE2 A:GLU198 4.7 14.8 1.0 OE1 A:GLU198 4.7 13.6 1.0 CB A:HLE1 4.7 13.0 1.0 CE A:MET215 4.8 15.8 1.0 O3 A:HLE1 4.9 14.9 1.0

Zinc binding site 3 out of 4 in the Procarboxypeptidase Ternary Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Procarboxypeptidase Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn998 b:22.1 occ:1.00 OD2 B:ASP149 1.9 21.2 1.0 NE2 B:HIS162 2.0 19.0 1.0 NE2 B:HIS147 2.0 20.0 1.0 ND1 B:HIS175 2.1 21.4 1.0 CE1 B:HIS162 2.8 18.3 1.0 CG B:ASP149 2.8 21.8 1.0 CD2 B:HIS147 3.0 19.4 1.0 CE1 B:HIS147 3.1 19.8 1.0 CE1 B:HIS175 3.1 21.0 1.0 OD1 B:ASP149 3.1 19.8 1.0 CG B:HIS175 3.2 21.6 1.0 CD2 B:HIS162 3.2 17.3 1.0 CB B:HIS175 3.5 19.4 1.0 ND1 B:HIS162 4.0 17.2 1.0 CG B:HIS147 4.1 20.3 1.0 ND1 B:HIS147 4.2 20.0 1.0 CE1 B:PHE164 4.2 22.8 1.0 CG B:HIS162 4.2 18.1 1.0 CB B:ASP149 4.2 22.5 1.0 CZ B:PHE164 4.3 22.7 1.0 NE2 B:HIS175 4.3 20.9 1.0 O B:SER151 4.3 21.6 1.0 CD2 B:HIS175 4.3 21.1 1.0 CE2 B:PHE153 4.5 18.9 1.0 CZ B:PHE153 4.7 18.9 1.0 CD2 B:TYR143 4.8 27.5 1.0 CA B:HIS175 5.0 20.2 1.0

Zinc binding site 4 out of 4 in the Procarboxypeptidase Ternary Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Procarboxypeptidase Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn999 b:18.8 occ:1.00 NE2 B:HIS197 2.0 17.7 1.0 OH B:HLE1 2.0 18.5 1.0 NE2 B:HIS207 2.1 19.0 1.0 O2 B:HLE1 2.1 18.2 1.0 NE2 B:HIS201 2.1 17.0 1.0 C2 B:HLE1 2.8 18.2 1.0 N B:HLE1 2.8 17.7 1.0 CE1 B:HIS197 3.0 17.1 1.0 CD2 B:HIS197 3.0 15.8 1.0 CE1 B:HIS207 3.1 17.9 1.0 CD2 B:HIS207 3.1 18.4 1.0 CD2 B:HIS201 3.1 15.7 1.0 CE1 B:HIS201 3.1 17.8 1.0 ND1 B:HIS197 4.1 16.8 1.0 CG B:HIS197 4.2 17.4 1.0 C1 B:HLE1 4.2 18.4 1.0 ND1 B:HIS207 4.2 17.9 1.0 CG B:HIS207 4.2 19.4 1.0 CG B:HIS201 4.3 15.9 1.0 ND1 B:HIS201 4.3 17.9 1.0 O B:HOH1015 4.3 18.4 1.0 OE2 B:GLU198 4.6 19.7 1.0 CA B:HLE1 4.6 18.7 1.0 OE1 B:GLU198 4.7 19.2 1.0 CB B:HLE1 4.7 18.6 1.0 CE B:MET215 4.8 19.1 1.0 O3 B:HLE1 4.9 18.0 1.0

M.Betz, P.Huxley, S.J.Davies, Y.Mushtaq, M.Pieper, H.Tschesche, W.Bode, F.X.Gomis-Ruth. 1.8-A Crystal Structure of the Catalytic Domain of Human Neutrophil Collagenase (Matrix Metalloproteinase-8) Complexed with A Peptidomimetic Hydroxamate Primed-Side Inhibitor with A Distinct Selectivity Profile. Eur.J.Biochem. V. 247 356 1997.
ISSN: ISSN 0014-2956
PubMed: 9249047
DOI: 10.1111/J.1432-1033.1997.00356.X