Atomistry » Calcium » PDB 7pod-7qfy » 7q87
Atomistry »
  Calcium »
    PDB 7pod-7qfy »
      7q87 »

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

Go back to Calcium Binding Sites List in 7q87
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: Fri Jul 19 03:24:03 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy