Calcium 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:

Zinc

(Zn)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Procarboxypeptidase Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca996 b:20.9 occ:1.00 O A:HOH1085 2.2 18.9 1.0 O A:GLY171 2.3 18.2 1.0 O A:ASP137 2.3 20.4 1.0 O A:GLY169 2.4 21.4 1.0 OD1 A:ASP173 2.4 17.9 1.0 O A:HOH1078 2.6 19.2 1.0 CG A:ASP173 3.4 17.7 1.0 C A:ASP137 3.5 22.1 1.0 C A:GLY171 3.5 17.6 1.0 C A:GLY169 3.6 22.0 1.0 OD2 A:ASP173 3.8 18.3 1.0 N A:GLY171 4.0 18.4 1.0 C A:ILE170 4.0 18.6 1.0 ND2 A:ASN139 4.1 25.1 1.0 N A:ASP173 4.2 15.9 1.0 O A:ALA136 4.2 28.1 1.0 O A:ILE170 4.2 17.2 1.0 CA A:GLY171 4.3 18.0 1.0 CA A:ASP137 4.3 22.6 1.0 N A:ILE138 4.4 19.9 1.0 N A:GLY169 4.4 23.5 1.0 CA A:ILE138 4.5 20.0 1.0 CA A:GLY169 4.5 22.5 1.0 O A:GLY167 4.5 24.9 1.0 N A:ILE170 4.5 21.3 1.0 N A:GLY172 4.5 17.9 1.0 CA A:ILE170 4.5 20.4 1.0 N A:ASN139 4.6 18.9 1.0 CB A:ASP173 4.6 15.9 1.0 C A:GLY172 4.6 16.4 1.0 CA A:GLY172 4.7 17.4 1.0 O A:HOH1079 4.7 39.1 1.0 CA A:ASP173 4.8 15.6 1.0 O A:HOH1077 4.8 27.8 1.0 C A:GLN168 4.8 25.1 1.0 CH2 A:TRP88 4.9 24.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Procarboxypeptidase Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca997 b:12.9 occ:1.00 O A:ILE159 2.2 12.1 1.0 O A:ASN157 2.3 14.3 1.0 OE2 A:GLU180 2.3 13.5 1.0 OD2 A:ASP177 2.3 12.2 1.0 OD1 A:ASP154 2.4 11.8 1.0 O A:GLY155 2.4 15.2 1.0 CG A:ASP177 3.4 11.8 1.0 C A:ILE159 3.4 13.9 1.0 C A:ASN157 3.5 14.1 1.0 CD A:GLU180 3.5 14.6 1.0 CG A:ASP154 3.6 13.1 1.0 C A:GLY155 3.6 14.4 1.0 N A:ILE159 3.9 13.7 1.0 CB A:ASP177 3.9 11.5 1.0 N A:ASN157 4.0 14.7 1.0 OD2 A:ASP154 4.1 13.1 1.0 N A:GLY155 4.1 13.5 1.0 C A:PRO156 4.2 15.6 1.0 OE1 A:GLU180 4.2 14.0 1.0 C A:GLY158 4.2 13.9 1.0 CA A:ILE159 4.2 14.8 1.0 C A:ASP154 4.3 14.3 1.0 CA A:ASN157 4.3 14.9 1.0 OD1 A:ASP177 4.3 13.2 1.0 N A:ASP154 4.4 14.1 1.0 N A:LEU160 4.4 13.2 1.0 N A:GLY158 4.5 14.0 1.0 CA A:GLY155 4.5 14.3 1.0 CG A:GLU180 4.5 13.6 1.0 N A:PRO156 4.5 15.2 1.0 O A:HOH1031 4.5 23.8 1.0 CA A:GLY158 4.5 13.5 1.0 CA A:PRO156 4.6 14.6 1.0 CA A:LEU160 4.6 12.3 1.0 O A:PRO156 4.6 15.2 1.0 CA A:ASP154 4.6 12.6 1.0 O A:ASP154 4.7 14.9 1.0 CB A:ASP154 4.7 11.6 1.0 CG2 A:ILE159 4.7 21.4 1.0 O A:GLY158 4.8 13.5 1.0 CD1 A:LEU160 5.0 14.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Procarboxypeptidase Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca996 b:24.0 occ:1.00 O B:ASP137 2.3 23.0 1.0 O B:HOH1024 2.4 19.6 1.0 OD1 B:ASP173 2.4 20.7 1.0 O B:GLY171 2.4 19.1 1.0 O B:GLY169 2.4 20.5 1.0 O B:HOH1023 2.5 22.3 1.0 CG B:ASP173 3.3 20.2 1.0 C B:ASP137 3.5 25.1 1.0 C B:GLY171 3.6 18.7 1.0 C B:GLY169 3.6 21.8 1.0 OD2 B:ASP173 3.8 20.2 1.0 C B:ILE170 3.9 17.2 1.0 N B:GLY171 4.0 16.9 1.0 ND2 B:ASN139 4.1 28.7 1.0 O B:ILE170 4.1 18.1 1.0 N B:ASP173 4.2 17.8 1.0 O B:ALA136 4.3 30.4 1.0 CA B:ASP137 4.3 26.5 1.0 CA B:GLY171 4.3 17.4 1.0 CA B:ILE170 4.4 19.0 1.0 O B:GLY167 4.4 22.8 1.0 N B:ILE138 4.4 23.1 1.0 N B:ILE170 4.5 19.9 1.0 N B:GLY172 4.5 18.5 1.0 CB B:ASP173 4.5 19.6 1.0 CA B:ILE138 4.6 22.6 1.0 CA B:GLY169 4.6 21.7 1.0 C B:GLY172 4.6 17.9 1.0 N B:GLY169 4.7 22.5 1.0 CA B:GLY172 4.7 18.3 1.0 O B:HOH1016 4.7 27.1 1.0 O B:HOH1062 4.7 34.2 1.0 N B:ASN139 4.7 23.6 1.0 CA B:ASP173 4.8 18.9 1.0 CH2 B:TRP88 4.8 22.8 1.0 C B:GLN168 4.9 24.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Procarboxypeptidase Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca997 b:20.3 occ:1.00 O B:GLY155 2.3 26.1 1.0 O B:ASN157 2.3 23.0 1.0 OE2 B:GLU180 2.3 26.4 1.0 OD2 B:ASP177 2.3 24.2 1.0 OD1 B:ASP154 2.3 21.5 1.0 O B:ILE159 2.4 18.2 1.0 CG B:ASP177 3.4 23.2 1.0 C B:GLY155 3.5 26.2 1.0 C B:ILE159 3.5 20.5 1.0 CD B:GLU180 3.5 26.9 1.0 C B:ASN157 3.5 23.5 1.0 CG B:ASP154 3.5 21.1 1.0 N B:ILE159 3.9 21.1 1.0 CB B:ASP177 4.0 21.2 1.0 N B:GLY155 4.0 26.0 1.0 N B:ASN157 4.0 24.5 1.0 C B:PRO156 4.2 25.5 1.0 OD2 B:ASP154 4.2 20.6 1.0 C B:ASP154 4.2 24.1 1.0 OE1 B:GLU180 4.2 26.5 1.0 C B:GLY158 4.3 21.2 1.0 N B:ASP154 4.3 22.7 1.0 CA B:ILE159 4.3 21.6 1.0 CA B:ASN157 4.3 24.3 1.0 CA B:GLY155 4.4 26.0 1.0 N B:LEU160 4.4 21.8 1.0 OD1 B:ASP177 4.4 21.6 1.0 N B:PRO156 4.4 26.2 1.0 N B:GLY158 4.5 22.7 1.0 CG B:GLU180 4.5 27.8 1.0 CA B:GLY158 4.5 22.7 1.0 CA B:PRO156 4.6 26.4 1.0 CA B:ASP154 4.6 23.4 1.0 CA B:LEU160 4.6 20.9 1.0 O B:ASP154 4.6 22.8 1.0 O B:PRO156 4.6 25.6 1.0 CB B:ASP154 4.6 22.2 1.0 O B:GLY158 4.9 21.2 1.0 CD1 B:LEU160 4.9 21.6 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