Calcium in PDB 6tnk: Carboxypeptidase T with N-Sulfamoyl-L-Valine
Enzymatic activity of Carboxypeptidase T with N-Sulfamoyl-L-Valine
All present enzymatic activity of Carboxypeptidase T with N-Sulfamoyl-L-Valine:
3.4.17.18;
Protein crystallography data
The structure of Carboxypeptidase T with N-Sulfamoyl-L-Valine, PDB code: 6tnk
was solved by
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)
|
19.99 /
1.90
|
Space group
|
P 63 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
157.531,
157.531,
104.523,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
14.2 /
15.6
|
Other elements in 6tnk:
The structure of Carboxypeptidase T with N-Sulfamoyl-L-Valine also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Carboxypeptidase T with N-Sulfamoyl-L-Valine
(pdb code 6tnk). 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-Valine, PDB code: 6tnk:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 6tnk
Go back to
Calcium Binding Sites List in 6tnk
Calcium binding site 1 out
of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Valine
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-Valine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:18.9
occ:1.00
|
OE1
|
A:GLU104
|
2.2
|
18.9
|
1.0
|
OD1
|
A:ASP56
|
2.3
|
18.8
|
1.0
|
O
|
A:HOH520
|
2.3
|
18.1
|
1.0
|
OE2
|
A:GLU61
|
2.4
|
16.4
|
1.0
|
O
|
A:GLU57
|
2.4
|
19.0
|
1.0
|
O
|
A:HOH625
|
2.4
|
17.0
|
1.0
|
CD
|
A:GLU104
|
3.4
|
18.3
|
1.0
|
CG
|
A:ASP56
|
3.4
|
21.0
|
1.0
|
CD
|
A:GLU61
|
3.5
|
17.2
|
1.0
|
C
|
A:GLU57
|
3.6
|
22.9
|
1.0
|
NH2
|
A:ARG189
|
3.8
|
20.7
|
1.0
|
OD2
|
A:ASP56
|
3.8
|
19.3
|
1.0
|
O
|
A:GLU59
|
3.9
|
15.8
|
1.0
|
OE2
|
A:GLU104
|
3.9
|
18.2
|
1.0
|
CG
|
A:GLU61
|
3.9
|
16.0
|
1.0
|
N
|
A:GLU57
|
4.0
|
18.1
|
1.0
|
O
|
A:HOH509
|
4.0
|
27.8
|
1.0
|
N
|
A:GLU59
|
4.3
|
20.2
|
1.0
|
C
|
A:ASP56
|
4.4
|
22.4
|
1.0
|
CA
|
A:GLU57
|
4.5
|
19.4
|
1.0
|
OE1
|
A:GLN196
|
4.5
|
15.7
|
1.0
|
OE1
|
A:GLU61
|
4.6
|
14.9
|
1.0
|
N
|
A:ASN58
|
4.6
|
23.3
|
1.0
|
CA
|
A:ASP56
|
4.6
|
19.8
|
1.0
|
CG
|
A:GLU104
|
4.6
|
16.8
|
1.0
|
CB
|
A:ASP56
|
4.6
|
21.2
|
1.0
|
CA
|
A:ASN58
|
4.7
|
27.5
|
1.0
|
CG
|
A:GLN196
|
4.7
|
14.5
|
1.0
|
CB
|
A:GLN196
|
4.7
|
13.2
|
1.0
|
C
|
A:GLU59
|
4.9
|
16.2
|
1.0
|
CB
|
A:GLU104
|
4.9
|
14.8
|
1.0
|
C
|
A:ASN58
|
5.0
|
25.6
|
1.0
|
|
Calcium binding site 2 out
of 5 in 6tnk
Go back to
Calcium Binding Sites List in 6tnk
Calcium binding site 2 out
of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Valine
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-Valine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca404
b:17.3
occ:1.00
|
OD1
|
A:ASP51
|
2.2
|
20.2
|
1.0
|
O
|
A:HOH601
|
2.3
|
16.1
|
1.0
|
OE1
|
A:GLU57
|
2.3
|
22.7
|
1.0
|
OE1
|
A:GLU59
|
2.3
|
20.4
|
1.0
|
O
|
A:ASP51
|
2.4
|
15.9
|
1.0
|
OG
|
A:SER50
|
2.4
|
13.8
|
1.0
|
OE2
|
A:GLU59
|
2.9
|
32.3
|
1.0
|
CD
|
A:GLU59
|
3.0
|
23.1
|
1.0
|
C
|
A:ASP51
|
3.4
|
17.1
|
1.0
|
CB
|
A:SER50
|
3.4
|
13.8
|
1.0
|
CG
|
A:ASP51
|
3.4
|
20.3
|
1.0
|
CD
|
A:GLU57
|
3.5
|
27.3
|
1.0
|
N
|
A:ASP51
|
3.7
|
15.1
|
1.0
|
CA
|
A:CA405
|
3.9
|
29.3
|
1.0
|
CA
|
A:ASP51
|
3.9
|
16.4
|
1.0
|
CG
|
A:GLU57
|
4.1
|
21.9
|
1.0
|
C
|
A:SER50
|
4.2
|
14.6
|
1.0
|
CB
|
A:ASP51
|
4.3
|
18.4
|
1.0
|
CB
|
A:GLU57
|
4.3
|
19.4
|
1.0
|
CG
|
A:GLU104
|
4.3
|
16.8
|
1.0
|
CA
|
A:SER50
|
4.3
|
13.1
|
1.0
|
OD2
|
A:ASP51
|
4.3
|
22.9
|
1.0
|
OE2
|
A:GLU104
|
4.4
|
18.2
|
1.0
|
N
|
A:ASN52
|
4.4
|
18.0
|
1.0
|
CG
|
A:GLU59
|
4.5
|
23.1
|
1.0
|
O
|
A:ASN52
|
4.5
|
18.6
|
1.0
|
OE2
|
A:GLU57
|
4.5
|
32.1
|
1.0
|
O
|
A:ARG103
|
4.5
|
12.3
|
1.0
|
CB
|
A:ASN52
|
4.5
|
21.2
|
1.0
|
C
|
A:ASN52
|
4.6
|
18.8
|
1.0
|
O
|
A:VAL100
|
4.6
|
13.7
|
1.0
|
O
|
A:HOH512
|
4.6
|
39.5
|
1.0
|
OD1
|
A:ASN52
|
4.7
|
34.2
|
1.0
|
CA
|
A:ASN52
|
4.8
|
18.3
|
1.0
|
CD
|
A:GLU104
|
4.8
|
18.3
|
1.0
|
O
|
A:ASN101
|
4.8
|
16.7
|
1.0
|
O
|
A:SER50
|
4.9
|
15.5
|
1.0
|
|
Calcium binding site 3 out
of 5 in 6tnk
Go back to
Calcium Binding Sites List in 6tnk
Calcium binding site 3 out
of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Valine
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-Valine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca405
b:29.3
occ:1.00
|
O
|
A:ASN101
|
2.3
|
16.7
|
1.0
|
OE2
|
A:GLU59
|
2.3
|
32.3
|
1.0
|
OD2
|
A:ASP51
|
2.4
|
22.9
|
1.0
|
O
|
A:HOH692
|
2.4
|
33.4
|
1.0
|
O
|
A:HOH512
|
2.5
|
39.5
|
1.0
|
OD1
|
A:ASP51
|
2.7
|
20.2
|
1.0
|
CG
|
A:ASP51
|
2.9
|
20.3
|
1.0
|
C
|
A:ASN101
|
3.5
|
17.9
|
1.0
|
CD
|
A:GLU59
|
3.5
|
23.1
|
1.0
|
OE1
|
A:GLU57
|
3.6
|
22.7
|
1.0
|
CA
|
A:CA404
|
3.9
|
17.3
|
1.0
|
CA
|
A:ASN101
|
4.3
|
16.0
|
1.0
|
OE1
|
A:GLU59
|
4.3
|
20.4
|
1.0
|
CD
|
A:GLU57
|
4.3
|
27.3
|
1.0
|
N
|
A:ASN102
|
4.4
|
15.7
|
1.0
|
CB
|
A:ASP51
|
4.4
|
18.4
|
1.0
|
OE2
|
A:GLU57
|
4.4
|
32.1
|
1.0
|
CG
|
A:GLU59
|
4.4
|
23.1
|
1.0
|
OD1
|
A:ASN52
|
4.5
|
34.2
|
1.0
|
CA
|
A:ASN102
|
4.5
|
16.6
|
1.0
|
OD1
|
A:ASN102
|
4.7
|
18.1
|
1.0
|
CB
|
A:ASN101
|
4.8
|
17.8
|
1.0
|
|
Calcium binding site 4 out
of 5 in 6tnk
Go back to
Calcium Binding Sites List in 6tnk
Calcium binding site 4 out
of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Valine
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-Valine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca406
b:17.8
occ:1.00
|
O
|
A:HOH691
|
2.3
|
18.4
|
1.0
|
O
|
A:SER7
|
2.3
|
14.0
|
1.0
|
O
|
A:TYR9
|
2.4
|
11.9
|
1.0
|
O
|
A:HOH660
|
2.4
|
23.9
|
1.0
|
O
|
A:HOH725
|
2.5
|
21.0
|
1.0
|
OE1
|
A:GLU14
|
2.5
|
14.3
|
1.0
|
OE2
|
A:GLU14
|
2.6
|
16.4
|
1.0
|
CD
|
A:GLU14
|
2.9
|
17.1
|
1.0
|
C
|
A:SER7
|
3.5
|
14.6
|
1.0
|
C
|
A:TYR9
|
3.6
|
13.5
|
1.0
|
CA
|
A:SER7
|
4.1
|
15.5
|
1.0
|
O
|
A:HOH506
|
4.3
|
23.9
|
1.0
|
N
|
A:TYR9
|
4.3
|
11.0
|
1.0
|
C
|
A:GLY8
|
4.3
|
12.8
|
1.0
|
CA
|
A:HIS10
|
4.3
|
11.9
|
1.0
|
N
|
A:HIS10
|
4.4
|
11.8
|
1.0
|
CG
|
A:GLU14
|
4.4
|
15.5
|
1.0
|
N
|
A:GLY8
|
4.5
|
12.9
|
1.0
|
CA
|
A:TYR9
|
4.6
|
11.1
|
1.0
|
O
|
A:GLY8
|
4.6
|
11.6
|
1.0
|
N
|
A:ASN11
|
4.7
|
12.3
|
1.0
|
CB
|
A:SER7
|
4.7
|
16.9
|
1.0
|
O
|
A:HOH603
|
4.7
|
19.7
|
1.0
|
CA
|
A:GLY8
|
4.7
|
14.2
|
1.0
|
O
|
A:HOH534
|
4.8
|
42.6
|
1.0
|
CB
|
A:GLU14
|
5.0
|
13.8
|
1.0
|
OD1
|
A:ASP1
|
5.0
|
18.2
|
1.0
|
C
|
A:HIS10
|
5.0
|
12.9
|
1.0
|
CD2
|
A:PHE2
|
5.0
|
13.4
|
1.0
|
|
Calcium binding site 5 out
of 5 in 6tnk
Go back to
Calcium Binding Sites List in 6tnk
Calcium binding site 5 out
of 5 in the Carboxypeptidase T with N-Sulfamoyl-L-Valine
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-Valine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca407
b:27.3
occ:1.00
|
O
|
A:TYR5
|
2.3
|
16.3
|
1.0
|
OE2
|
A:GLU292
|
2.4
|
27.6
|
1.0
|
OD1
|
A:ASP291
|
2.4
|
14.1
|
1.0
|
O
|
A:HOH737
|
2.4
|
26.0
|
1.0
|
O
|
A:HOH724
|
2.5
|
35.4
|
1.0
|
O
|
A:HOH630
|
2.5
|
19.3
|
1.0
|
OE1
|
A:GLU292
|
2.6
|
17.3
|
1.0
|
CD
|
A:GLU292
|
2.8
|
21.7
|
1.0
|
O
|
A:HOH606
|
3.3
|
38.1
|
1.0
|
CG
|
A:ASP291
|
3.4
|
15.8
|
1.0
|
C
|
A:TYR5
|
3.5
|
17.3
|
1.0
|
OD2
|
A:ASP291
|
3.8
|
15.2
|
1.0
|
CA
|
A:TYR5
|
4.3
|
18.1
|
1.0
|
CG
|
A:GLU292
|
4.3
|
21.0
|
1.0
|
OD1
|
A:ASP6
|
4.4
|
12.5
|
1.0
|
N
|
A:ASP291
|
4.4
|
12.1
|
1.0
|
N
|
A:ASP6
|
4.5
|
13.9
|
1.0
|
N
|
A:GLU292
|
4.5
|
12.2
|
1.0
|
CB
|
A:ASP291
|
4.6
|
13.2
|
1.0
|
CB
|
A:TYR5
|
4.6
|
19.4
|
1.0
|
CA
|
A:ASP6
|
4.8
|
14.2
|
1.0
|
CA
|
A:ASP291
|
4.9
|
12.0
|
1.0
|
|
Reference:
V.I.Timofeev,
V.K.Akparov,
I.P.Kuranova.
Carboxypeptidase T with N-Sulfamoyl-L-Valine To Be Published.
Page generated: Tue Jul 16 15:23:02 2024
|