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Calcium in PDB 7q87: Carboxypeptidase T with (S)-3-Phenyllactic Acid

Enzymatic activity of Carboxypeptidase T with (S)-3-Phenyllactic Acid

All present enzymatic activity of Carboxypeptidase T with (S)-3-Phenyllactic Acid:
3.4.17.18;

Protein crystallography data

The structure of Carboxypeptidase T with (S)-3-Phenyllactic Acid, PDB code: 7q87 was solved by V.I.Timofeev, V.K.Akparov, M.B.Shevtsov, I.P.Kuranova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 1.73
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 157.328, 157.328, 104.132, 90, 90, 120
R / Rfree (%) 13.1 / 14.5

Other elements in 7q87:

The structure of Carboxypeptidase T with (S)-3-Phenyllactic Acid also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Carboxypeptidase T with (S)-3-Phenyllactic Acid (pdb code 7q87). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Carboxypeptidase T with (S)-3-Phenyllactic Acid, PDB code: 7q87:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7q87

Go back to Calcium Binding Sites List in 7q87
Calcium binding site 1 out of 6 in the Carboxypeptidase T with (S)-3-Phenyllactic 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 (S)-3-Phenyllactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:19.2
occ:1.00
 OD1 A:ASP51 2.2 21.6 1.0
OE1 A:GLU57 2.3 22.6 1.0
O A:ASP51 2.3 16.0 1.0
OG A:SER50 2.4 15.0 1.0
OE1 A:GLU59 2.4 20.8 1.0
O A:HOH581 2.4 18.8 1.0
OE2 A:GLU59 2.9 31.6 1.0
CD A:GLU59 3.0 24.3 1.0
C A:ASP51 3.3 16.7 1.0
CD A:GLU57 3.4 29.9 1.0
CB A:SER50 3.4 14.8 1.0
CG A:ASP51 3.5 21.2 1.0
N A:ASP51 3.7 16.4 1.0
CA A:CA408 3.9 30.1 1.0
CA A:ASP51 3.9 17.3 1.0
CG A:GLU57 4.0 23.2 1.0
C A:SER50 4.2 15.2 1.0
CB A:GLU57 4.3 20.2 1.0
CB A:ASP51 4.3 18.1 1.0
CA A:SER50 4.3 13.0 1.0
CG A:GLU104 4.4 16.3 1.0
OE2 A:GLU104 4.4 18.1 1.0
N A:ASN52 4.4 18.5 1.0
OD2 A:ASP51 4.4 24.7 1.0
CB A:ASN52 4.4 22.2 1.0
CG A:GLU59 4.4 23.3 1.0
O A:ASN52 4.4 18.7 1.0
OE2 A:GLU57 4.5 34.1 1.0
O A:ARG103 4.5 14.6 1.0
C A:ASN52 4.6 17.8 1.0
O A:HOH551 4.6 41.6 1.0
OD1 A:ASN52 4.6 38.4 1.0
O A:VAL100 4.7 14.1 1.0
CA A:ASN52 4.7 19.0 1.0
CD A:GLU104 4.8 20.1 1.0
O A:SER50 4.8 13.9 1.0
O A:ASN101 4.9 17.0 1.0
CG A:ASN52 5.0 30.2 1.0

Calcium binding site 2 out of 6 in 7q87

Go back to Calcium Binding Sites List in 7q87
Calcium binding site 2 out of 6 in the Carboxypeptidase T with (S)-3-Phenyllactic 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 (S)-3-Phenyllactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:21.3
occ:1.00
 OE1 A:GLU104 2.2 20.9 1.0
O A:HOH534 2.3 18.9 1.0
OD1 A:ASP56 2.3 20.8 1.0
OE2 A:GLU61 2.4 16.3 1.0
O A:GLU57 2.4 21.3 1.0
O A:HOH675 2.4 20.5 1.0
CD A:GLU104 3.3 20.1 1.0
CG A:ASP56 3.4 23.5 1.0
CD A:GLU61 3.5 17.7 1.0
C A:GLU57 3.6 23.6 1.0
NH2 A:ARG189 3.8 24.9 1.0
OD2 A:ASP56 3.9 23.9 1.0
OE2 A:GLU104 3.9 18.1 1.0
O A:GLU59 3.9 16.3 1.0
O A:HOH513 3.9 30.1 1.0
CG A:GLU61 4.0 15.5 1.0
N A:GLU57 4.0 19.4 1.0
N A:GLU59 4.2 20.0 1.0
C A:ASP56 4.3 22.3 1.0
O A:HOH779 4.4 34.2 1.0
CA A:GLU57 4.5 20.1 1.0
OE1 A:GLN196 4.5 17.4 1.0
OE1 A:GLU61 4.6 16.1 1.0
CG A:GLU104 4.6 16.3 1.0
N A:ASN58 4.6 22.9 1.0
CA A:ASP56 4.6 20.6 1.0
CA A:ASN58 4.6 27.9 1.0
CB A:ASP56 4.6 20.9 1.0
CG A:GLN196 4.7 15.2 1.0
CB A:GLN196 4.7 13.9 1.0
C A:GLU59 4.9 15.6 1.0
CB A:GLU104 5.0 14.4 1.0
C A:ASN58 5.0 26.1 1.0

Calcium binding site 3 out of 6 in 7q87

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Calcium binding site 3 out of 6 in the Carboxypeptidase T with (S)-3-Phenyllactic 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 (S)-3-Phenyllactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:19.2
occ:1.00
 O A:HOH722 2.2 20.6 1.0
O A:SER7 2.3 17.0 1.0
O A:HOH672 2.3 25.3 1.0
O A:TYR9 2.4 11.9 1.0
O A:HOH775 2.5 22.6 1.0
OE1 A:GLU14 2.5 14.9 1.0
OE2 A:GLU14 2.6 20.0 1.0
CD A:GLU14 2.9 19.3 1.0
C A:SER7 3.5 15.6 1.0
C A:TYR9 3.6 13.0 1.0
CA A:SER7 4.2 15.8 1.0
O A:HOH571 4.2 28.1 1.0
CA A:HIS10 4.3 11.9 1.0
N A:TYR9 4.3 12.2 1.0
N A:HIS10 4.4 11.9 1.0
C A:GLY8 4.4 13.4 1.0
CG A:GLU14 4.4 14.7 1.0
N A:GLY8 4.5 14.8 1.0
O A:HOH802 4.5 31.8 1.0
CA A:TYR9 4.6 11.2 1.0
N A:ASN11 4.6 12.3 1.0
O A:GLY8 4.6 14.3 1.0
O A:HOH633 4.6 20.9 1.0
CB A:SER7 4.7 16.5 1.0
CA A:GLY8 4.7 15.0 1.0
O A:HOH524 4.8 41.2 1.0
O A:HOH748 4.9 40.9 1.0
OD1 A:ASP1 4.9 16.6 1.0
CB A:GLU14 5.0 13.1 1.0
C A:HIS10 5.0 13.7 1.0

Calcium binding site 4 out of 6 in 7q87

Go back to Calcium Binding Sites List in 7q87
Calcium binding site 4 out of 6 in the Carboxypeptidase T with (S)-3-Phenyllactic 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 (S)-3-Phenyllactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:29.9
occ:1.00
 O A:TYR5 2.4 19.6 1.0
OE1 A:GLU292 2.4 30.1 1.0
OD1 A:ASP291 2.4 14.3 1.0
O A:HOH788 2.4 29.3 1.0
O A:HOH770 2.5 35.8 1.0
O A:HOH632 2.5 20.4 1.0
OE2 A:GLU292 2.6 19.7 1.0
CD A:GLU292 2.8 25.6 1.0
O A:HOH601 3.1 42.0 1.0
CG A:ASP291 3.4 18.7 1.0
C A:TYR5 3.6 18.7 1.0
OD2 A:ASP291 3.9 15.1 1.0
CA A:TYR5 4.3 18.7 1.0
CG A:GLU292 4.3 22.9 1.0
OD1 A:ASP6 4.4 14.9 1.0
N A:ASP291 4.4 12.5 1.0
N A:GLU292 4.5 13.2 1.0
O A:HOH855 4.6 36.5 1.0
CB A:TYR5 4.6 19.1 1.0
O A:HOH516 4.6 36.1 1.0
N A:ASP6 4.6 15.7 1.0
CB A:ASP291 4.6 14.8 1.0
O A:HOH792 4.7 47.1 1.0
CA A:ASP6 4.8 14.9 1.0
CA A:ASP291 4.9 13.1 1.0

Calcium binding site 5 out of 6 in 7q87

Go back to Calcium Binding Sites List in 7q87
Calcium binding site 5 out of 6 in the Carboxypeptidase T with (S)-3-Phenyllactic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Carboxypeptidase T with (S)-3-Phenyllactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:30.1
occ:1.00
 OE2 A:GLU59 2.4 31.6 1.0
O A:HOH749 2.4 46.4 1.0
O A:ASN101 2.4 17.0 1.0
O A:HOH695 2.4 35.9 1.0
O A:HOH551 2.4 41.6 1.0
OD2 A:ASP51 2.5 24.7 1.0
OD1 A:ASP51 2.7 21.6 1.0
CG A:ASP51 2.9 21.2 1.0
C A:ASN101 3.5 17.8 1.0
CD A:GLU59 3.5 24.3 1.0
OE1 A:GLU57 3.6 22.6 1.0
CA A:CA404 3.9 19.2 1.0
CA A:ASN101 4.3 17.5 1.0
OE1 A:GLU59 4.4 20.8 1.0
CD A:GLU57 4.4 29.9 1.0
N A:ASN102 4.4 15.7 1.0
CG A:GLU59 4.4 23.3 1.0
OD1 A:ASN52 4.4 38.4 1.0
CB A:ASP51 4.4 18.1 1.0
OE2 A:GLU57 4.5 34.1 1.0
CA A:ASN102 4.5 16.7 1.0
O A:HOH639 4.6 42.8 1.0
OD1 A:ASN102 4.7 21.0 1.0
CB A:ASN101 4.8 16.5 1.0

Calcium binding site 6 out of 6 in 7q87

Go back to Calcium Binding Sites List in 7q87
Calcium binding site 6 out of 6 in the Carboxypeptidase T with (S)-3-Phenyllactic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Carboxypeptidase T with (S)-3-Phenyllactic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:32.4
occ:1.00
 OE1 A:GLN250 2.2 28.8 1.0
OD1 A:ASP220 2.3 17.9 1.0
O A:HOH591 2.4 33.5 1.0
O A:HOH506 2.4 23.6 1.0
O A:HOH746 2.6 27.1 1.0
O A:TYR218 2.6 13.9 1.0
CD A:GLN250 3.4 32.1 1.0
CG A:ASP220 3.6 25.1 1.0
OD1 A:ASP253 3.7 33.8 1.0
C A:TYR218 3.8 12.6 1.0
NE2 A:GLN250 3.8 32.4 1.0
O A:HOH615 4.1 29.5 1.0
O A:HOH701 4.2 20.3 1.0
N A:ASP220 4.2 14.3 1.0
O A:HOH507 4.3 20.1 1.0
CA A:ASP220 4.3 14.1 1.0
O A:HOH744 4.3 44.6 1.0
OG A:SER252 4.3 15.5 1.0
CA A:TYR218 4.3 15.6 1.0
OD2 A:ASP220 4.4 25.4 1.0
CB A:GLN250 4.4 13.7 1.0
C A:THR219 4.5 16.7 1.0
CG A:GLN250 4.5 17.3 1.0
CB A:ASP220 4.5 17.1 1.0
CG A:ASP253 4.6 28.2 1.0
OD2 A:ASP253 4.7 40.6 1.0
N A:THR219 4.8 15.3 1.0
O A:THR219 4.8 14.5 1.0
CB A:TYR218 4.9 17.5 1.0

Reference:

V.I.Timofeev, V.K.Akparov, M.B.Shevtsov, I.P.Kuranova. Carboxypeptidase T with (S)-3-Phenyllactic Acid To Be Published.
Page generated: Thu Jul 10 00:31:18 2025

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