Atomistry » Calcium » PDB 4elg-4fa1 » 4f8z
Atomistry »
  Calcium »
    PDB 4elg-4fa1 »
      4f8z »

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

Enzymatic activity of Carboxypeptidase T with Boc-Leu

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

Protein crystallography data

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

Other elements in 4f8z:

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

Zinc (Zn) 1 atom

Calcium Binding Sites:

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 4f8z

Go back to Calcium Binding Sites List in 4f8z
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 4f8z

Go back to Calcium Binding Sites List in 4f8z
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 4f8z

Go back to Calcium Binding Sites List in 4f8z
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 4f8z

Go back to Calcium Binding Sites List in 4f8z
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

Reference:

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
Page generated: Sat Dec 12 04:45:52 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy