Calcium in PDB 1obr: Carboxypeptidase T

All present enzymatic activity of Carboxypeptidase T:
3.4.17.18;

The structure of Carboxypeptidase T, PDB code: 1obr was solved by A.Teplyakov, K.Polyakov, G.Obmolova, A.Osterman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.30
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	159.420, 159.420, 106.860, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / n/a

The structure of Carboxypeptidase T also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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

Calcium binding site 1 out of 4 in the Carboxypeptidase T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Carboxypeptidase T within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:21.0 occ:1.00 OE1 A:GLU104 2.1 12.1 1.0 O A:HOH472 2.2 26.4 1.0 OE2 A:GLU61 2.3 15.1 1.0 O A:GLU57 2.3 26.7 1.0 O A:HOH481 2.5 29.8 1.0 OD1 A:ASP56 2.5 30.4 1.0 CD A:GLU104 3.2 23.3 1.0 CD A:GLU61 3.4 9.5 1.0 C A:GLU57 3.6 27.5 1.0 NH2 A:ARG189 3.6 20.9 1.0 CG A:ASP56 3.8 30.0 1.0 O A:GLU59 3.8 15.4 1.0 O A:HOH469 3.8 26.2 1.0 CG A:GLU61 3.9 12.4 1.0 OE2 A:GLU104 3.9 22.1 1.0 N A:GLU59 4.1 24.7 1.0 N A:GLU57 4.2 26.4 1.0 CG A:GLU104 4.2 18.6 1.0 C A:ASP56 4.3 25.4 1.0 CA A:ASN58 4.4 26.6 1.0 O A:HOH501 4.4 36.4 1.0 OD2 A:ASP56 4.4 40.7 1.0 OE1 A:GLU61 4.4 11.3 1.0 OE1 A:GLN196 4.4 23.8 1.0 N A:ASN58 4.5 27.4 1.0 CA A:GLU57 4.5 25.4 1.0 O A:ASP56 4.7 28.3 1.0 CG A:GLN196 4.7 16.0 1.0 CA A:ASP56 4.7 24.7 1.0 C A:ASN58 4.8 26.6 1.0 CB A:ASP56 4.8 24.8 1.0 CB A:GLU104 4.8 18.3 1.0 C A:GLU59 4.8 17.5 1.0 CB A:GLN196 4.9 17.2 1.0 CZ A:ARG189 4.9 25.2 1.0 CD A:GLN196 5.0 18.8 1.0

Calcium binding site 2 out of 4 in the Carboxypeptidase T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Carboxypeptidase T within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:24.6 occ:1.00 OD1 A:ASP51 2.1 22.7 1.0 OE1 A:GLU59 2.3 16.9 1.0 OE2 A:GLU57 2.3 31.8 1.0 OG A:SER50 2.4 17.6 1.0 O A:ASP51 2.5 18.3 1.0 O A:HOH426 2.6 12.9 1.0 CD A:GLU59 3.0 22.2 1.0 OE2 A:GLU59 3.1 25.1 1.0 CG A:ASP51 3.4 30.3 1.0 CD A:GLU57 3.4 31.4 1.0 C A:ASP51 3.4 17.9 1.0 N A:ASP51 3.5 15.9 1.0 CB A:SER50 3.7 9.8 1.0 CA A:CA403 3.8 44.0 1.0 CA A:ASP51 3.9 16.4 1.0 CG A:GLU57 4.0 25.9 1.0 CB A:ASP51 4.2 18.2 1.0 C A:SER50 4.2 15.5 1.0 OD2 A:ASP51 4.3 35.1 1.0 O A:ASN52 4.3 19.7 1.0 CB A:GLU57 4.3 20.9 1.0 OE1 A:GLU57 4.4 36.7 1.0 CB A:ASN52 4.4 25.0 1.0 OE2 A:GLU104 4.4 22.1 1.0 CG A:GLU59 4.5 14.4 1.0 CA A:SER50 4.5 14.8 1.0 N A:ASN52 4.5 18.2 1.0 CG A:GLU104 4.6 18.6 1.0 C A:ASN52 4.6 17.2 1.0 O A:ARG103 4.6 14.5 1.0 O A:VAL100 4.6 19.1 1.0 O A:ASN101 4.6 22.7 1.0 CA A:ASN52 4.8 16.2 1.0 OD1 A:ASN52 5.0 42.7 1.0 CD A:GLU104 5.0 23.3 1.0

Calcium binding site 3 out of 4 in the Carboxypeptidase T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Carboxypeptidase T within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:44.0 occ:1.00 O A:ASN101 2.3 22.7 1.0 OD2 A:ASP51 2.5 35.1 1.0 OE2 A:GLU59 2.5 25.1 1.0 OD1 A:ASP51 2.8 22.7 1.0 O A:HOH516 2.8 46.7 1.0 CG A:ASP51 3.0 30.3 1.0 C A:ASN101 3.4 21.5 1.0 CD A:GLU59 3.5 22.2 1.0 OE2 A:GLU57 3.7 31.8 1.0 CA A:CA402 3.8 24.6 1.0 OE1 A:GLU59 4.1 16.9 1.0 CA A:ASN101 4.2 19.8 1.0 OE1 A:GLU57 4.3 36.7 1.0 CD A:GLU57 4.4 31.4 1.0 N A:ASN102 4.4 19.3 1.0 CG A:GLU59 4.5 14.4 1.0 CB A:ASP51 4.5 18.2 1.0 CA A:ASN102 4.5 17.5 1.0 OD1 A:ASN102 4.6 26.1 1.0 CB A:ASN101 4.7 17.4 1.0 OD1 A:ASN52 4.8 42.7 1.0

Calcium binding site 4 out of 4 in the Carboxypeptidase T


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Carboxypeptidase T within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:43.7 occ:1.00 O A:SER7 2.3 25.8 1.0 O A:HOH466 2.3 25.5 1.0 O A:TYR9 2.5 15.9 1.0 OE2 A:GLU14 2.7 32.2 1.0 OE1 A:GLU14 2.7 26.8 1.0 O A:HOH455 2.7 22.6 1.0 CD A:GLU14 3.0 26.4 1.0 C A:SER7 3.4 22.0 1.0 C A:TYR9 3.7 11.8 1.0 CA A:SER7 3.9 22.0 1.0 O A:HOH505 4.3 39.1 1.0 CB A:SER7 4.3 23.8 1.0 N A:TYR9 4.3 10.9 1.0 CA A:HIS10 4.4 8.3 1.0 O A:HOH480 4.4 29.6 1.0 C A:GLY8 4.5 12.3 1.0 N A:GLY8 4.5 18.0 1.0 CG A:GLU14 4.5 18.1 1.0 N A:HIS10 4.5 11.5 1.0 CA A:TYR9 4.6 11.3 1.0 OD2 A:ASP1 4.7 37.5 1.0 O A:GLY8 4.8 10.1 1.0 N A:ASN11 4.8 7.8 1.0 CA A:GLY8 4.8 12.4 1.0 O A:HOH489 4.9 32.9 1.0 CD1 A:PHE2 4.9 20.7 1.0 OD1 A:ASP1 5.0 33.0 1.0

A.Teplyakov, K.Polyakov, G.Obmolova, B.Strokopytov, I.Kuranova, A.Osterman, N.Grishin, S.Smulevitch, O.Zagnitko, O.Galperina, M.Matz, V.Stepanov. Crystal Structure of Carboxypeptidase T From Thermoactinomyces Vulgaris. Eur.J.Biochem. V. 208 281 1992.
ISSN: ISSN 0014-2956
PubMed: 1521526
DOI: 10.1111/J.1432-1033.1992.TB17184.X