Calcium in PDB 4duk: Carboxypeptidase T with L-Benzylsuccinic Acid

All present enzymatic activity of Carboxypeptidase T with L-Benzylsuccinic Acid:
3.4.17.18;

The structure of Carboxypeptidase T with L-Benzylsuccinic Acid, PDB code: 4duk was solved by S.A.Kuznetsov, V.I.Timofeev, V.K.Akparov, I.P.Kuranova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.57
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.939, 157.939, 104.437, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 16.7

The structure of Carboxypeptidase T with L-Benzylsuccinic Acid also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Carboxypeptidase T with L-Benzylsuccinic Acid (pdb code 4duk). 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 with L-Benzylsuccinic Acid, PDB code: 4duk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Carboxypeptidase T with L-Benzylsuccinic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Carboxypeptidase T with L-Benzylsuccinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:30.3 occ:0.90 O A:HOH507 2.2 24.5 0.8 O A:SER7 2.4 17.9 1.0 O A:HOH748 2.4 35.6 1.0 O A:TYR9 2.4 13.2 1.0 OE1 A:GLU14 2.6 17.1 1.0 O A:HOH569 2.7 27.1 0.8 OE2 A:GLU14 2.9 24.5 1.0 CD A:GLU14 3.1 19.0 1.0 C A:SER7 3.5 16.5 1.0 C A:TYR9 3.6 12.3 1.0 O A:HOH675 4.1 29.6 0.8 CA A:SER7 4.2 16.9 1.0 O A:HOH569 4.2 11.2 0.1 CA A:HIS10 4.3 11.2 1.0 N A:TYR9 4.4 11.9 1.0 N A:HIS10 4.4 11.4 1.0 C A:GLY8 4.4 13.5 1.0 CG A:GLU14 4.5 15.7 1.0 O A:HOH613 4.5 26.1 1.0 N A:GLY8 4.5 15.4 1.0 O A:HOH736 4.6 28.2 0.5 CA A:TYR9 4.6 11.5 1.0 N A:ASN11 4.7 11.3 1.0 CB A:SER7 4.7 19.0 1.0 CA A:GLY8 4.7 15.9 1.0 O A:GLY8 4.7 14.6 1.0 CB A:GLU14 5.0 14.3 1.0 C A:HIS10 5.0 11.5 1.0

Calcium binding site 2 out of 4 in the Carboxypeptidase T with L-Benzylsuccinic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Carboxypeptidase T with L-Benzylsuccinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:35.7 occ:0.90 O A:ASP51 2.3 21.8 0.2 OE1 A:GLU57 2.3 38.0 1.0 O A:ASP51 2.4 21.0 0.8 O A:HOH595 2.4 24.4 1.0 OG A:SER50 2.4 18.8 1.0 O A:HOH685 2.5 22.7 0.5 OE1 A:GLU59 2.5 32.1 1.0 OD1 A:ASP51 2.6 26.7 0.8 CD A:GLU59 3.4 32.3 1.0 C A:ASP51 3.4 20.9 0.2 C A:ASP51 3.5 21.4 0.8 CD A:GLU57 3.5 37.1 1.0 OE2 A:GLU59 3.5 38.4 1.0 CB A:SER50 3.5 16.1 1.0 N A:ASP51 3.7 17.4 0.2 CG A:ASP51 3.7 27.0 0.8 N A:ASP51 3.8 18.3 0.8 O A:HOH653 3.9 32.3 1.0 CA A:ASP51 4.0 19.2 0.2 CG A:GLU57 4.0 37.2 1.0 CA A:ASP51 4.1 20.7 0.8 C A:SER50 4.2 17.0 1.0 CG A:GLU104 4.3 20.9 1.0 O A:ASN52 4.3 23.2 1.0 CB A:ASP51 4.3 19.0 0.2 CB A:GLU57 4.3 34.4 1.0 CA A:SER50 4.4 14.7 1.0 OE2 A:GLU104 4.4 25.9 1.0 O A:ARG103 4.5 16.5 1.0 OE2 A:GLU57 4.5 43.2 1.0 N A:ASN52 4.5 22.6 1.0 CB A:ASP51 4.5 23.4 0.8 C A:ASN52 4.6 22.1 1.0 OD2 A:ASP51 4.6 35.3 0.8 CB A:ASN52 4.6 25.8 1.0 O A:VAL100 4.7 17.2 1.0 CD A:GLU104 4.7 24.9 1.0 CG A:GLU59 4.7 28.3 1.0 CA A:ASN52 4.8 24.0 1.0 O A:SER50 4.9 16.9 1.0

Calcium binding site 3 out of 4 in the Carboxypeptidase T with L-Benzylsuccinic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Carboxypeptidase T with L-Benzylsuccinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:41.0 occ:0.90 O A:TYR5 2.3 20.4 1.0 O A:HOH673 2.3 20.3 0.3 O A:HOH577 2.5 22.6 1.0 OD1 A:ASP291 2.6 15.3 1.0 OE2 A:GLU292 2.6 26.0 0.7 OE1 A:GLU292 2.7 16.7 0.7 CD A:GLU292 3.0 20.7 0.7 C A:TYR5 3.4 19.8 1.0 CG A:ASP291 3.5 14.8 1.0 O A:HOH659 3.6 30.3 0.8 OD2 A:ASP291 3.9 15.7 1.0 CA A:TYR5 4.2 20.3 1.0 CB A:TYR5 4.4 22.7 1.0 OD1 A:ASP6 4.4 18.1 1.0 N A:ASP291 4.5 12.3 1.0 N A:ASP6 4.5 16.6 1.0 CG A:GLU292 4.5 18.4 0.7 N A:GLU292 4.8 13.1 0.7 CB A:ASP291 4.8 12.8 1.0 CA A:ASP6 4.8 15.7 1.0 N A:GLU292 4.8 12.4 0.3 OE2 A:GLU292 4.9 15.9 0.3

Calcium binding site 4 out of 4 in the Carboxypeptidase T with L-Benzylsuccinic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Carboxypeptidase T with L-Benzylsuccinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca427 b:42.3 occ:0.90 O A:HOH678 2.0 25.7 0.8 OE1 A:GLU104 2.3 28.4 1.0 OD1 A:ASP56 2.5 37.1 1.0 O A:HOH679 2.5 32.7 1.0 OE2 A:GLU61 2.5 19.1 1.0 O A:GLU57 2.6 30.5 1.0 CD A:GLU104 3.4 24.9 1.0 CG A:ASP56 3.6 42.4 1.0 CD A:GLU61 3.6 17.3 1.0 O A:HOH729 3.7 26.7 0.5 O A:GLU59 3.7 19.0 1.0 NH2 A:ARG189 3.7 23.9 1.0 C A:GLU57 3.8 30.4 1.0 OE2 A:GLU104 3.9 25.9 1.0 CG A:GLU61 4.0 14.6 1.0 OD2 A:ASP56 4.0 47.3 1.0 N A:GLU59 4.1 28.2 1.0 N A:GLU57 4.2 31.9 1.0 OE1 A:GLN196 4.5 24.4 1.0 CG A:GLN196 4.6 18.1 1.0 CG A:GLU104 4.7 20.9 1.0 C A:ASP56 4.7 34.4 1.0 CA A:GLU57 4.7 32.0 1.0 C A:GLU59 4.7 18.4 1.0 OE1 A:GLU61 4.7 16.9 1.0 N A:ASN58 4.7 33.3 1.0 CB A:GLN196 4.7 15.7 1.0 CA A:ASN58 4.7 36.4 1.0 CB A:ASP56 4.8 39.7 1.0 CA A:GLU59 4.8 23.4 1.0 CA A:ASP56 4.9 33.6 1.0 C A:ASN58 4.9 35.9 1.0 CB A:GLU104 4.9 17.7 1.0

V.K.H.Akparov, V.I.Timofeev, I.G.Khaliullin, V.Svedas, G.G.Chestukhina, I.P.Kuranova. Structural Insights Into the Broad Substrate Specificity of Carboxypeptidase T From Thermoactinomyces Vulgaris. Febs J. V. 282 1214 2015.
ISSN: ISSN 1742-464X
PubMed: 25619204
DOI: 10.1111/FEBS.13210