Calcium in PDB 1nug: Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)
Enzymatic activity of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)
All present enzymatic activity of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form):
2.3.2.13;
Protein crystallography data
The structure of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form), PDB code: 1nug
was solved by
B.Ahvazi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.40
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.510,
66.810,
116.530,
97.24,
90.28,
98.36
|
R / Rfree (%)
|
19.4 /
24.8
|
Other elements in 1nug:
The structure of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)
(pdb code 1nug). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form), PDB code: 1nug:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1nug
Go back to
Calcium Binding Sites List in 1nug
Calcium binding site 1 out
of 4 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca703
b:20.0
occ:1.00
|
OD1
|
A:ASN224
|
2.3
|
18.9
|
1.0
|
O
|
A:ALA221
|
2.3
|
14.8
|
1.0
|
O
|
A:ASN226
|
2.4
|
21.0
|
1.0
|
O
|
A:ASN224
|
2.4
|
18.3
|
1.0
|
OD1
|
A:ASP228
|
2.5
|
23.4
|
1.0
|
O
|
A:HOH957
|
2.5
|
20.2
|
1.0
|
OD2
|
A:ASP228
|
2.8
|
23.8
|
1.0
|
CG
|
A:ASP228
|
2.9
|
23.6
|
1.0
|
CG
|
A:ASN224
|
3.3
|
18.9
|
1.0
|
C
|
A:ALA221
|
3.4
|
15.1
|
1.0
|
C
|
A:ASN224
|
3.4
|
18.6
|
1.0
|
C
|
A:ASN226
|
3.5
|
20.9
|
1.0
|
N
|
A:ASN226
|
3.6
|
20.4
|
1.0
|
CA
|
A:ASN226
|
4.0
|
20.6
|
1.0
|
ND2
|
A:ASN224
|
4.0
|
18.8
|
1.0
|
C
|
A:SER225
|
4.1
|
20.1
|
1.0
|
CA
|
A:ALA221
|
4.2
|
14.9
|
1.0
|
N
|
A:MET222
|
4.2
|
15.3
|
1.0
|
N
|
A:ASP228
|
4.2
|
23.2
|
1.0
|
CA
|
A:ASN224
|
4.3
|
18.3
|
1.0
|
N
|
A:SER225
|
4.3
|
19.1
|
1.0
|
CA
|
A:MET222
|
4.3
|
15.8
|
1.0
|
N
|
A:ASN224
|
4.3
|
17.5
|
1.0
|
CB
|
A:ASN226
|
4.3
|
20.3
|
1.0
|
CB
|
A:ASP228
|
4.3
|
23.6
|
1.0
|
CB
|
A:ASN224
|
4.3
|
18.4
|
1.0
|
CA
|
A:SER225
|
4.4
|
19.8
|
1.0
|
O
|
A:PHE364
|
4.5
|
22.6
|
1.0
|
CA
|
A:GLY230
|
4.5
|
22.7
|
1.0
|
N
|
A:GLY230
|
4.6
|
23.6
|
1.0
|
OD2
|
A:ASP227
|
4.6
|
22.7
|
1.0
|
CB
|
A:ALA221
|
4.6
|
14.6
|
1.0
|
N
|
A:ASP227
|
4.6
|
21.6
|
1.0
|
O
|
A:SER225
|
4.7
|
20.6
|
1.0
|
C
|
A:MET222
|
4.7
|
16.2
|
1.0
|
CA
|
A:ASP228
|
4.8
|
23.6
|
1.0
|
CB
|
A:ASP227
|
4.8
|
22.5
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1nug
Go back to
Calcium Binding Sites List in 1nug
Calcium binding site 2 out
of 4 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca704
b:29.5
occ:1.00
|
O
|
A:SER415
|
2.3
|
27.0
|
1.0
|
O
|
A:HOH1027
|
2.5
|
19.8
|
1.0
|
OD1
|
A:ASN393
|
2.6
|
23.9
|
1.0
|
O
|
A:HOH851
|
2.7
|
14.4
|
1.0
|
OE1
|
A:GLU443
|
2.7
|
34.1
|
1.0
|
OE2
|
A:GLU443
|
2.8
|
33.6
|
1.0
|
OE2
|
A:GLU448
|
2.8
|
36.1
|
1.0
|
CD
|
A:GLU443
|
3.1
|
33.8
|
1.0
|
CG
|
A:ASN393
|
3.4
|
23.6
|
1.0
|
C
|
A:SER415
|
3.5
|
27.1
|
1.0
|
CD
|
A:GLU448
|
3.6
|
36.4
|
1.0
|
NH1
|
A:ARG449
|
3.7
|
36.0
|
1.0
|
ND2
|
A:ASN393
|
3.8
|
23.9
|
1.0
|
CA
|
A:HIS416
|
4.1
|
27.1
|
1.0
|
OE1
|
A:GLU448
|
4.2
|
36.4
|
1.0
|
N
|
A:HIS416
|
4.3
|
27.0
|
1.0
|
CG
|
A:GLU448
|
4.4
|
36.5
|
1.0
|
O
|
A:HOH870
|
4.5
|
14.6
|
1.0
|
O
|
A:ASN393
|
4.5
|
22.4
|
1.0
|
NZ
|
A:LYS440
|
4.5
|
21.3
|
1.0
|
CA
|
A:SER415
|
4.5
|
27.2
|
1.0
|
CB
|
A:ASN393
|
4.6
|
22.8
|
1.0
|
CA
|
A:ASN393
|
4.7
|
22.1
|
1.0
|
CG
|
A:GLU443
|
4.7
|
33.6
|
1.0
|
OD1
|
A:ASP395
|
4.7
|
24.4
|
1.0
|
C
|
A:ASN393
|
4.7
|
22.2
|
1.0
|
CB
|
A:SER415
|
4.7
|
27.2
|
1.0
|
CG
|
A:HIS416
|
4.9
|
30.4
|
1.0
|
CD2
|
A:HIS416
|
4.9
|
31.1
|
1.0
|
CZ
|
A:ARG449
|
4.9
|
36.2
|
1.0
|
CB
|
A:HIS416
|
4.9
|
28.6
|
1.0
|
O
|
A:ILE418
|
5.0
|
20.4
|
1.0
|
C
|
A:HIS416
|
5.0
|
26.1
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1nug
Go back to
Calcium Binding Sites List in 1nug
Calcium binding site 3 out
of 4 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca703
b:21.1
occ:1.00
|
O
|
B:ASN226
|
2.3
|
17.8
|
1.0
|
O
|
B:ASN224
|
2.4
|
15.8
|
1.0
|
O
|
B:ALA221
|
2.5
|
14.6
|
1.0
|
OD1
|
B:ASP228
|
2.5
|
21.6
|
1.0
|
OD1
|
B:ASN224
|
2.5
|
14.3
|
1.0
|
O
|
B:HOH972
|
2.6
|
16.5
|
1.0
|
OD2
|
B:ASP228
|
2.8
|
21.5
|
1.0
|
CG
|
B:ASP228
|
2.9
|
21.8
|
1.0
|
C
|
B:ASN224
|
3.4
|
15.8
|
1.0
|
C
|
B:ASN226
|
3.4
|
18.1
|
1.0
|
C
|
B:ALA221
|
3.4
|
14.7
|
1.0
|
CG
|
B:ASN224
|
3.4
|
14.7
|
1.0
|
N
|
B:ASN226
|
3.6
|
17.7
|
1.0
|
C
|
B:SER225
|
3.8
|
17.3
|
1.0
|
CA
|
B:ASN226
|
4.0
|
17.9
|
1.0
|
N
|
B:SER225
|
4.2
|
16.2
|
1.0
|
ND2
|
B:ASN224
|
4.2
|
14.3
|
1.0
|
N
|
B:ASP228
|
4.2
|
21.3
|
1.0
|
CA
|
B:SER225
|
4.2
|
16.8
|
1.0
|
CA
|
B:MET222
|
4.2
|
14.5
|
1.0
|
N
|
B:MET222
|
4.2
|
14.5
|
1.0
|
CA
|
B:ASN224
|
4.3
|
15.4
|
1.0
|
CB
|
B:ASP228
|
4.3
|
21.9
|
1.0
|
N
|
B:ASN224
|
4.3
|
15.3
|
1.0
|
O
|
B:SER225
|
4.3
|
17.5
|
1.0
|
CA
|
B:GLY230
|
4.3
|
21.9
|
1.0
|
CA
|
B:ALA221
|
4.4
|
14.9
|
1.0
|
CB
|
B:ASN224
|
4.4
|
15.0
|
1.0
|
N
|
B:GLY230
|
4.5
|
23.2
|
1.0
|
CB
|
B:ASN226
|
4.5
|
17.6
|
1.0
|
N
|
B:ASP227
|
4.6
|
18.9
|
1.0
|
C
|
B:MET222
|
4.6
|
15.0
|
1.0
|
O
|
B:PHE364
|
4.7
|
19.6
|
1.0
|
CB
|
B:ASP227
|
4.7
|
19.4
|
1.0
|
CA
|
B:ASP228
|
4.8
|
21.9
|
1.0
|
CB
|
B:ALA221
|
4.8
|
14.6
|
1.0
|
OD1
|
B:ASP227
|
4.8
|
19.2
|
1.0
|
O
|
B:MET222
|
4.9
|
15.2
|
1.0
|
C
|
B:ASP227
|
4.9
|
20.5
|
1.0
|
CA
|
B:ASP227
|
5.0
|
19.6
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1nug
Go back to
Calcium Binding Sites List in 1nug
Calcium binding site 4 out
of 4 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca704
b:36.4
occ:1.00
|
O
|
B:HOH978
|
2.2
|
34.9
|
1.0
|
OE2
|
B:GLU443
|
2.4
|
32.8
|
1.0
|
O
|
B:SER415
|
2.4
|
28.6
|
1.0
|
OD1
|
B:ASN393
|
2.4
|
24.2
|
1.0
|
OE1
|
B:GLU443
|
2.7
|
33.0
|
1.0
|
O
|
B:HOH805
|
2.8
|
29.2
|
1.0
|
OE2
|
B:GLU448
|
2.9
|
42.0
|
1.0
|
CD
|
B:GLU443
|
2.9
|
32.8
|
1.0
|
CG
|
B:ASN393
|
3.4
|
24.1
|
1.0
|
C
|
B:SER415
|
3.6
|
28.4
|
1.0
|
CD
|
B:GLU448
|
3.6
|
41.7
|
1.0
|
ND2
|
B:ASN393
|
4.0
|
24.0
|
1.0
|
CA
|
B:HIS416
|
4.1
|
28.1
|
1.0
|
OE1
|
B:GLU448
|
4.1
|
42.1
|
1.0
|
NH1
|
B:ARG449
|
4.2
|
40.9
|
1.0
|
N
|
B:HIS416
|
4.3
|
28.3
|
1.0
|
CG
|
B:GLU443
|
4.4
|
32.9
|
1.0
|
NZ
|
B:LYS440
|
4.4
|
22.5
|
1.0
|
ND1
|
B:HIS416
|
4.5
|
31.0
|
1.0
|
CG
|
B:GLU448
|
4.5
|
41.0
|
1.0
|
CE
|
B:LYS440
|
4.5
|
23.4
|
1.0
|
O
|
B:HOH927
|
4.6
|
7.0
|
1.0
|
O
|
B:ASN393
|
4.6
|
23.8
|
1.0
|
CB
|
B:ASN393
|
4.6
|
23.6
|
1.0
|
CA
|
B:ASN393
|
4.6
|
23.3
|
1.0
|
CA
|
B:SER415
|
4.6
|
28.4
|
1.0
|
C
|
B:ASN393
|
4.7
|
23.4
|
1.0
|
O
|
B:ILE418
|
4.8
|
23.1
|
1.0
|
OD1
|
B:ASP395
|
4.8
|
25.2
|
1.0
|
C
|
B:HIS416
|
4.9
|
27.2
|
1.0
|
CB
|
B:SER415
|
5.0
|
28.6
|
1.0
|
|
Reference:
B.Ahvazi,
K.M.Boeshans,
W.Idler,
U.Baxa,
P.M.Steinert.
Roles of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme J.Biol.Chem. V. 278 23834 2003.
ISSN: ISSN 0021-9258
PubMed: 12679341
DOI: 10.1074/JBC.M301162200
Page generated: Thu Jul 11 13:02:38 2024
|