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Calcium in PDB 4djl: Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine

Enzymatic activity of Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine

All present enzymatic activity of Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine:
3.4.17.18;

Protein crystallography data

The structure of Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine, PDB code: 4djl 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) 16.00 / 1.55
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 157.949, 157.949, 104.197, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 17.4

Other elements in 4djl:

The structure of Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine (pdb code 4djl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine, PDB code: 4djl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4djl

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Calcium binding site 1 out of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine


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 N-Sulfamoyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:21.5
occ:0.89
 OE1 A:GLU104 2.2 21.4 1.0
O A:HOH749 2.2 19.2 0.8
OE2 A:GLU61 2.3 18.0 1.0
OD1 A:ASP56 2.3 21.2 0.8
O A:HOH648 2.6 21.9 0.8
O A:GLU57 2.6 21.2 0.8
CD A:GLU104 3.3 18.4 0.6
CD A:GLU61 3.4 15.2 0.8
CG A:ASP56 3.5 22.1 0.4
OE2 A:GLU104 3.7 16.9 0.8
CG A:GLU61 3.8 14.9 1.0
NH2 A:ARG189 3.8 19.9 0.9
O A:HOH658 3.8 19.9 0.6
O A:GLU59 3.8 15.9 0.9
C A:GLU57 3.9 22.5 0.6
OD2 A:ASP56 4.0 19.2 0.5
N A:GLU57 4.1 22.2 0.9
N A:GLU59 4.4 22.7 1.0
OE1 A:GLU61 4.5 13.0 0.8
NE2 A:GLN196 4.5 18.0 1.0
C A:ASP56 4.5 23.3 0.9
CG A:GLU104 4.6 16.9 1.0
O A:HOH727 4.6 37.0 0.8
CA A:GLU57 4.6 23.7 1.0
CG A:GLN196 4.7 17.1 1.0
CB A:ASP56 4.7 24.1 1.0
CA A:ASP56 4.7 22.3 0.8
CB A:GLN196 4.7 15.0 1.0
CB A:GLU104 4.8 14.9 1.0
N A:ASN58 4.8 25.6 1.0
C A:GLU59 4.9 16.8 1.0
CA A:ASN58 4.9 26.3 0.9

Calcium binding site 2 out of 5 in 4djl

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Calcium binding site 2 out of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine


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 N-Sulfamoyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:18.4
occ:0.76
 OE1 A:GLU57 2.3 27.3 1.0
OG A:SER50 2.4 14.2 0.8
O A:ASP51 2.4 17.3 0.9
O A:HOH651 2.4 16.5 0.9
OD1 A:ASP51 2.4 23.0 0.9
OE1 A:GLU59 2.4 21.8 0.8
OE2 A:GLU59 3.1 29.6 0.8
CD A:GLU59 3.1 23.6 0.8
C A:ASP51 3.4 17.4 0.9
CB A:SER50 3.5 14.2 1.0
CD A:GLU57 3.5 25.2 0.7
CG A:ASP51 3.6 20.3 0.6
N A:ASP51 3.7 15.3 1.0
CA A:CA439 3.9 36.0 1.0
CA A:ASP51 4.1 17.3 1.0
CG A:GLU57 4.1 25.2 1.0
C A:SER50 4.2 15.0 0.8
CG A:GLU104 4.2 16.9 1.0
CB A:GLU57 4.3 23.5 1.0
CA A:SER50 4.3 14.3 1.0
O A:ASN52 4.4 20.7 1.0
CB A:ASP51 4.4 19.5 1.0
O A:ARG103 4.4 12.5 0.8
OD2 A:ASP51 4.4 20.3 0.6
OE2 A:GLU104 4.5 16.9 0.8
N A:ASN52 4.5 18.5 0.8
OE2 A:GLU57 4.5 24.9 0.3
CB A:ASN52 4.6 21.0 1.0
CG A:GLU59 4.6 24.2 1.0
C A:ASN52 4.6 18.5 0.9
O A:VAL100 4.6 15.0 0.9
O A:HOH769 4.7 25.0 0.3
CD A:GLU104 4.8 18.4 0.6
CA A:ASN52 4.8 19.7 0.9
OD1 A:ASN52 4.8 24.4 0.6
O A:SER50 4.9 14.7 0.9
O A:ASN101 4.9 14.5 0.8

Calcium binding site 3 out of 5 in 4djl

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Calcium binding site 3 out of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine


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 N-Sulfamoyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:17.1
occ:0.62
 O A:HOH762 2.3 21.6 1.0
O A:HOH767 2.4 30.8 1.0
O A:SER7 2.4 15.2 0.9
O A:TYR9 2.4 13.2 0.9
OE1 A:GLU14 2.5 13.6 0.8
O A:HOH646 2.6 22.7 0.8
OE2 A:GLU14 2.8 17.6 0.8
CD A:GLU14 3.0 14.6 0.8
C A:SER7 3.5 14.7 0.7
C A:TYR9 3.6 12.3 0.6
O A:HOH635 4.2 28.2 0.9
CA A:SER7 4.3 14.9 0.8
CA A:HIS10 4.3 12.3 1.0
N A:TYR9 4.4 12.3 1.0
C A:GLY8 4.4 13.8 0.9
N A:HIS10 4.4 11.9 1.0
CG A:GLU14 4.4 13.5 1.0
N A:GLY8 4.5 14.4 1.0
O A:HOH631 4.6 31.1 0.8
CA A:TYR9 4.6 11.6 1.0
O A:HOH603 4.6 20.6 0.7
N A:ASN11 4.6 12.0 1.0
O A:GLY8 4.6 14.9 1.0
CA A:GLY8 4.7 14.7 1.0
CB A:SER7 4.8 17.0 1.0
CB A:GLU14 4.9 13.4 1.0
C A:HIS10 5.0 12.6 1.0

Calcium binding site 4 out of 5 in 4djl

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Calcium binding site 4 out of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine


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 N-Sulfamoyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:24.0
occ:0.65
 O A:TYR5 2.4 19.8 0.9
O A:HOH765 2.4 33.4 1.0
OE2 A:GLU292 2.5 19.9 0.5
O A:HOH554 2.5 22.7 0.9
OD1 A:ASP291 2.5 13.8 0.9
O A:HOH766 2.6 41.5 1.0
OE1 A:GLU292 2.7 18.9 1.0
CD A:GLU292 2.9 19.0 0.4
O A:HOH678 3.2 33.3 0.9
CG A:ASP291 3.5 13.2 0.8
C A:TYR5 3.5 18.7 0.6
OD2 A:ASP291 3.9 14.7 0.9
CA A:TYR5 4.3 19.6 0.9
CG A:GLU292 4.4 17.8 0.7
OD1 A:ASP6 4.4 15.3 0.9
N A:ASP291 4.5 12.1 1.0
O A:HOH686 4.6 29.8 0.6
N A:ASP6 4.6 16.9 1.0
CB A:TYR5 4.6 21.8 1.0
N A:GLU292 4.6 12.8 1.0
CB A:ASP291 4.7 11.9 1.0
CA A:ASP6 4.8 15.2 1.0
O A:HOH778 4.9 32.0 1.0
O3 A:GOL422 4.9 32.9 0.3
CA A:ASP291 5.0 12.1 1.0

Calcium binding site 5 out of 5 in 4djl

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Calcium binding site 5 out of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine


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 N-Sulfamoyl-L-Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca439

b:36.0
occ:1.00
 OE2 A:GLU59 2.3 29.6 0.8
O A:HOH769 2.3 25.0 0.3
O A:ASN101 2.4 14.5 0.8
O A:HOH764 2.5 45.0 1.0
OD2 A:ASP51 2.7 20.3 0.6
OD1 A:ASP51 2.7 23.0 0.9
CG A:ASP51 3.1 20.3 0.6
OE1 A:GLU57 3.4 27.3 1.0
CD A:GLU59 3.5 23.6 0.8
C A:ASN101 3.5 14.9 0.8
CA A:CA403 3.9 18.4 0.8
CD A:GLU57 4.2 25.2 0.7
OE1 A:GLU59 4.2 21.8 0.8
OE2 A:GLU57 4.3 24.9 0.3
CA A:ASN101 4.4 16.3 1.0
O1 A:GOL433 4.4 40.7 0.7
CG A:GLU59 4.4 24.2 1.0
N A:ASN102 4.4 14.3 1.0
OD1 A:ASN52 4.5 24.4 0.6
CA A:ASN102 4.6 15.0 0.9
CB A:ASP51 4.6 19.5 1.0
OD1 A:ASN102 4.8 16.5 0.8
CB A:ASN101 4.9 17.4 1.0

Reference:

S.A.Kuznetsov, V.I.Timofeev, V.K.Akparov, I.P.Kuranova. Carboxypeptidase T with N-Sulfamoyl-L-Phenylalanine To Be Published.
Page generated: Sat Jul 13 23:28:08 2024

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