Calcium in PDB 3v7z: Carboxypeptidase T with Gemsa

All present enzymatic activity of Carboxypeptidase T with Gemsa:
3.4.17.18;

The structure of Carboxypeptidase T with Gemsa, PDB code: 3v7z 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 / 1.61
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.890, 157.890, 104.195, 90.00, 90.00, 120.00
R / Rfree (%)	13.3 / 15.2

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

Zinc	(Zn)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Carboxypeptidase T with Gemsa (pdb code 3v7z). 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 Gemsa, PDB code: 3v7z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Carboxypeptidase T with Gemsa


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 Gemsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:21.4 occ:1.00 O A:HOH535 2.2 21.1 1.0 OE1 A:GLU104 2.3 20.6 1.0 OD1 A:ASP56 2.4 20.7 1.0 O A:GLU57 2.4 22.8 1.0 OE2 A:GLU61 2.4 18.4 1.0 O A:HOH533 2.5 21.8 1.0 CD A:GLU104 3.4 17.8 1.0 CG A:ASP56 3.5 22.8 1.0 CD A:GLU61 3.5 16.5 1.0 C A:GLU57 3.6 22.4 1.0 NH2 A:ARG189 3.8 21.8 1.0 OE2 A:GLU104 3.8 18.9 1.0 O A:GLU59 3.9 18.0 1.0 CG A:GLU61 3.9 14.9 1.0 O A:HOH697 3.9 26.9 1.0 OD2 A:ASP56 3.9 24.2 1.0 N A:GLU57 4.0 21.4 1.0 N A:GLU59 4.3 22.3 1.0 C A:ASP56 4.4 22.6 1.0 CA A:GLU57 4.5 22.6 1.0 N A:ASN58 4.6 23.7 1.0 OE1 A:GLN196 4.6 20.4 1.0 OE1 A:GLU61 4.6 16.2 1.0 CG A:GLU104 4.6 16.1 1.0 O A:HOH529 4.7 34.4 1.0 CA A:ASN58 4.7 26.2 1.0 CB A:ASP56 4.7 23.0 1.0 CG A:GLN196 4.7 16.9 1.0 CA A:ASP56 4.7 22.0 1.0 CB A:GLN196 4.8 15.4 1.0 C A:GLU59 4.9 17.2 1.0 CB A:GLU104 4.9 14.8 1.0

Calcium binding site 2 out of 4 in the Carboxypeptidase T with Gemsa


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 Gemsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:20.8 occ:1.00 OE1 A:GLU57 2.3 25.1 1.0 O A:ASP51 2.3 19.0 1.0 OD1 A:ASP51 2.4 22.6 1.0 OG A:SER50 2.4 16.4 1.0 O A:HOH527 2.4 18.8 1.0 OE1 A:GLU59 2.4 22.8 1.0 CD A:GLU59 3.1 27.4 1.0 OE2 A:GLU59 3.2 34.4 1.0 C A:ASP51 3.4 19.1 1.0 CD A:GLU57 3.5 26.5 1.0 CB A:SER50 3.5 15.7 1.0 CG A:ASP51 3.5 21.9 1.0 N A:ASP51 3.7 17.0 1.0 CA A:CA427 4.0 34.2 1.0 CA A:ASP51 4.0 18.6 1.0 CG A:GLU57 4.0 24.6 1.0 C A:SER50 4.2 16.0 1.0 CG A:GLU104 4.3 16.1 1.0 CB A:GLU57 4.3 23.1 1.0 CA A:SER50 4.4 14.6 1.0 CB A:ASP51 4.4 20.9 1.0 OD2 A:ASP51 4.4 25.9 1.0 O A:ASN52 4.4 19.4 1.0 N A:ASN52 4.4 20.1 1.0 OE2 A:GLU104 4.4 18.9 1.0 O A:ARG103 4.5 15.1 1.0 OE2 A:GLU57 4.5 31.9 1.0 CB A:ASN52 4.5 22.6 1.0 CG A:GLU59 4.6 26.1 1.0 C A:ASN52 4.6 19.9 1.0 O A:VAL100 4.6 16.0 1.0 ND2 A:ASN52 4.7 30.8 1.0 CA A:ASN52 4.8 21.3 1.0 CD A:GLU104 4.8 17.8 1.0 O A:HOH538 4.8 32.2 0.6 O A:SER50 4.9 16.6 1.0 O A:ASN101 5.0 18.1 1.0

Calcium binding site 3 out of 4 in the Carboxypeptidase T with Gemsa


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 Gemsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:22.5 occ:1.00 O A:HOH541 2.3 19.7 1.0 O A:SER7 2.3 17.4 1.0 O A:HOH730 2.3 30.4 1.0 O A:TYR9 2.4 13.7 1.0 O A:HOH543 2.5 25.6 1.0 OE1 A:GLU14 2.5 15.8 1.0 OE2 A:GLU14 2.7 20.9 1.0 CD A:GLU14 3.0 16.5 1.0 C A:SER7 3.5 15.7 1.0 C A:TYR9 3.6 12.9 1.0 CA A:SER7 4.2 16.6 1.0 O A:HOH715 4.3 29.1 1.0 C A:GLY8 4.3 14.4 1.0 CA A:HIS10 4.3 12.6 1.0 N A:TYR9 4.3 12.7 1.0 N A:HIS10 4.4 12.7 1.0 CG A:GLU14 4.4 14.8 1.0 N A:GLY8 4.5 14.8 1.0 O A:GLY8 4.6 16.1 1.0 CA A:TYR9 4.6 12.2 1.0 O A:HOH594 4.6 24.5 1.0 O A:HOH632 4.6 33.8 1.0 N A:ASN11 4.7 12.5 1.0 CA A:GLY8 4.7 15.4 1.0 CB A:SER7 4.7 19.3 1.0 O A:HOH789 4.8 36.8 1.0 CB A:GLU14 4.9 14.9 1.0 C A:HIS10 5.0 12.7 1.0

Calcium binding site 4 out of 4 in the Carboxypeptidase T with Gemsa


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 Gemsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca427 b:34.2 occ:1.00 O A:HOH538 2.3 32.2 0.6 OE2 A:GLU59 2.3 34.4 1.0 O A:HOH540 2.4 34.7 0.6 O A:ASN101 2.5 18.1 1.0 OD2 A:ASP51 2.7 25.9 1.0 OD1 A:ASP51 2.8 22.6 1.0 CG A:ASP51 3.1 21.9 1.0 CD A:GLU59 3.5 27.4 1.0 C A:ASN101 3.6 17.6 1.0 OE1 A:GLU57 3.6 25.1 1.0 CA A:CA402 4.0 20.8 1.0 OE1 A:GLU59 4.2 22.8 1.0 CD A:GLU57 4.3 26.5 1.0 O A:HOH800 4.3 34.8 1.0 CA A:ASN101 4.4 17.1 1.0 OE2 A:GLU57 4.4 31.9 1.0 CG A:GLU59 4.4 26.1 1.0 N A:ASN102 4.5 16.4 1.0 ND2 A:ASN52 4.5 30.8 1.0 CA A:ASN102 4.6 16.7 1.0 CB A:ASP51 4.7 20.9 1.0 OD1 A:ASN102 4.7 20.9 1.0 CB A:ASN101 4.9 18.8 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