Calcium in PDB 4f8z: Carboxypeptidase T with Boc-Leu

All present enzymatic activity of Carboxypeptidase T with Boc-Leu:
3.4.17.18;

The structure of Carboxypeptidase T with Boc-Leu, PDB code: 4f8z was solved by V.I.Timofeev, S.A.Kuznetsov, 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)	14.00 / 1.38
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.914, 157.914, 104.068, 90.00, 90.00, 120.00
R / Rfree (%)	13.9 / 15.2

The structure of Carboxypeptidase T with Boc-Leu also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Carboxypeptidase T with Boc-Leu (pdb code 4f8z). 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 Boc-Leu, PDB code: 4f8z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Carboxypeptidase T with Boc-Leu


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 Boc-Leu within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:22.3 occ:0.90 OE1 A:GLU57 2.3 27.6 1.0 O A:ASP51 2.3 21.4 1.0 OG A:SER50 2.4 19.3 1.0 O A:HOH506 2.4 21.5 1.0 OD1 A:ASP51 2.4 24.4 1.0 OE1 A:GLU59 2.5 28.1 1.0 CD A:GLU59 3.4 30.9 1.0 C A:ASP51 3.4 20.5 1.0 CD A:GLU57 3.4 28.6 1.0 CB A:SER50 3.5 16.7 1.0 CG A:ASP51 3.6 23.9 1.0 OE2 A:GLU59 3.6 37.9 1.0 N A:ASP51 3.7 17.4 1.0 CA A:CA408 3.9 45.2 1.0 CA A:ASP51 4.0 19.8 1.0 CG A:GLU57 4.0 26.8 1.0 C A:SER50 4.2 16.4 1.0 CG A:GLU104 4.3 17.5 1.0 CA A:SER50 4.3 15.1 1.0 CB A:GLU57 4.3 25.2 1.0 OD2 A:ASP51 4.4 31.0 1.0 CB A:ASP51 4.4 22.3 1.0 OE2 A:GLU104 4.4 21.5 1.0 O A:ASN52 4.4 22.2 1.0 O A:ARG103 4.4 15.7 1.0 OE2 A:GLU57 4.5 34.3 1.0 N A:ASN52 4.5 22.6 1.0 CB A:ASN52 4.5 24.3 1.0 O A:VAL100 4.6 16.1 1.0 C A:ASN52 4.6 22.1 1.0 CG A:GLU59 4.7 28.8 1.0 OD1 A:ASN52 4.7 36.0 1.0 CD A:GLU104 4.8 21.0 1.0 CA A:ASN52 4.8 23.3 1.0 O A:SER50 4.9 17.1 1.0 O A:ASN101 4.9 18.9 1.0

Calcium binding site 2 out of 4 in the Carboxypeptidase T with Boc-Leu


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 Boc-Leu within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:24.9 occ:1.00 O A:HOH800 2.1 25.9 1.0 OE1 A:GLU104 2.3 23.7 1.0 OD1 A:ASP56 2.4 25.3 1.0 O A:HOH646 2.4 25.7 1.0 O A:GLU57 2.4 25.0 1.0 OE2 A:GLU61 2.5 18.6 1.0 CD A:GLU104 3.4 21.0 1.0 CG A:ASP56 3.5 26.7 1.0 CD A:GLU61 3.6 15.7 1.0 C A:GLU57 3.6 25.1 1.0 NH2 A:ARG189 3.8 22.5 1.0 O A:GLU59 3.8 18.7 1.0 O A:HOH709 3.8 28.7 1.0 OE2 A:GLU104 3.9 21.5 1.0 OD2 A:ASP56 3.9 30.4 1.0 CG A:GLU61 4.0 14.8 1.0 N A:GLU57 4.1 25.3 1.0 N A:GLU59 4.2 24.7 1.0 OE1 A:GLN196 4.5 21.8 1.0 C A:ASP56 4.5 25.5 1.0 CA A:GLU57 4.5 25.2 1.0 N A:ASN58 4.6 26.3 1.0 O A:HOH777 4.6 36.5 1.0 CA A:ASN58 4.6 28.1 1.0 OE1 A:GLU61 4.6 16.2 1.0 CG A:GLU104 4.7 17.5 1.0 CG A:GLN196 4.7 16.7 1.0 CB A:ASP56 4.7 25.7 1.0 CA A:ASP56 4.7 24.6 1.0 CB A:GLN196 4.8 14.8 1.0 C A:GLU59 4.8 17.9 1.0 CB A:GLU104 4.9 15.8 1.0 C A:ASN58 4.9 28.3 1.0 CA A:GLU59 5.0 22.3 1.0

Calcium binding site 3 out of 4 in the Carboxypeptidase T with Boc-Leu


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 Boc-Leu within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:45.2 occ:1.00 OE2 A:GLU59 2.4 37.9 1.0 O A:ASN101 2.5 18.9 1.0 OD2 A:ASP51 2.9 31.0 1.0 OD1 A:ASP51 2.9 24.4 1.0 CG A:ASP51 3.3 23.9 1.0 OE1 A:GLU57 3.4 27.6 1.0 CD A:GLU59 3.5 30.9 1.0 C A:ASN101 3.7 17.0 1.0 CA A:CA406 3.9 22.3 0.9 OE1 A:GLU59 4.0 28.1 1.0 CD A:GLU57 4.1 28.6 1.0 OE2 A:GLU57 4.1 34.3 1.0 O A:HOH687 4.3 34.3 1.0 OD1 A:ASN52 4.5 36.0 1.0 CG A:GLU59 4.5 28.8 1.0 N A:ASN102 4.5 15.4 1.0 CA A:ASN101 4.5 16.8 1.0 CA A:ASN102 4.6 16.1 1.0 O A:HOH877 4.6 49.1 1.0 OD1 A:ASN102 4.8 22.0 1.0 CB A:ASP51 4.8 22.3 1.0

Calcium binding site 4 out of 4 in the Carboxypeptidase T with Boc-Leu


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 Boc-Leu within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:26.8 occ:1.00 O A:HOH501 2.3 22.5 1.0 O A:HOH866 2.3 35.3 1.0 O A:SER7 2.4 18.1 1.0 O A:TYR9 2.4 13.7 1.0 O A:HOH555 2.5 29.0 1.0 OE1 A:GLU14 2.5 15.1 1.0 OE2 A:GLU14 2.9 21.4 1.0 CD A:GLU14 3.0 16.6 1.0 C A:SER7 3.5 15.9 1.0 C A:TYR9 3.6 12.4 1.0 CA A:SER7 4.3 16.0 1.0 CA A:HIS10 4.3 11.9 1.0 C A:GLY8 4.3 13.2 1.0 N A:TYR9 4.3 12.4 1.0 O A:HOH666 4.3 32.0 1.0 N A:HIS10 4.3 11.9 1.0 CG A:GLU14 4.4 14.5 1.0 O A:HOH679 4.5 38.2 1.0 N A:GLY8 4.5 14.4 1.0 CA A:TYR9 4.6 11.5 1.0 N A:ASN11 4.6 12.3 1.0 O A:GLY8 4.6 15.1 1.0 CA A:GLY8 4.7 14.3 1.0 O A:HOH654 4.7 26.3 1.0 CB A:SER7 4.8 18.5 1.0 CB A:GLU14 4.9 13.4 1.0 C A:HIS10 4.9 12.0 1.0

V.I.Timofeev, S.A.Kuznetsov, V.K.H.Akparov, G.G.Chestukhina, I.P.Kuranova. Three-Dimensional Structure of Carboxypeptidase T From Thermoactinomyces Vulgaris in Complex with N-Boc-L-Leucine. Biochemistry Mosc. V. 78 252 2013.
ISSN: ISSN 0006-2979
PubMed: 23586718
DOI: 10.1134/S0006297913030061