Calcium in PDB 7dya: Crystal Structure of Tmftn with Calcium Ions
Enzymatic activity of Crystal Structure of Tmftn with Calcium Ions
All present enzymatic activity of Crystal Structure of Tmftn with Calcium Ions:
1.16.3.2;
Protein crystallography data
The structure of Crystal Structure of Tmftn with Calcium Ions, PDB code: 7dya
was solved by
X.Zhang,
G.Zhao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.58 /
2.20
|
Space group
|
H 3 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
175.434,
175.434,
357.421,
90,
90,
120
|
R / Rfree (%)
|
17.5 /
20
|
Other elements in 7dya:
The structure of Crystal Structure of Tmftn with Calcium Ions also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Tmftn with Calcium Ions
(pdb code 7dya). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the
Crystal Structure of Tmftn with Calcium Ions, PDB code: 7dya:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Calcium binding site 1 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 1 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca203
b:37.5
occ:1.00
|
OE2
|
H:GLU132
|
2.2
|
32.0
|
1.0
|
O
|
H:HOH409
|
2.3
|
31.7
|
1.0
|
OE2
|
H:GLU51
|
2.4
|
40.1
|
1.0
|
O
|
H:HOH331
|
2.5
|
34.1
|
1.0
|
O
|
H:HOH345
|
2.5
|
34.9
|
1.0
|
OE1
|
H:GLN135
|
2.5
|
38.0
|
1.0
|
OE1
|
H:GLU51
|
2.6
|
35.0
|
1.0
|
CD
|
H:GLU51
|
2.8
|
35.6
|
1.0
|
CD
|
H:GLU132
|
3.4
|
32.7
|
1.0
|
CD
|
H:GLN135
|
3.5
|
38.8
|
1.0
|
NE2
|
H:GLN135
|
3.9
|
38.3
|
1.0
|
CG
|
H:GLU132
|
4.1
|
32.9
|
1.0
|
O
|
H:HOH403
|
4.2
|
38.6
|
1.0
|
OE1
|
H:GLN48
|
4.2
|
32.7
|
1.0
|
NH2
|
H:ARG163
|
4.3
|
29.1
|
1.0
|
CG
|
H:GLU51
|
4.4
|
32.9
|
1.0
|
OE1
|
H:GLU132
|
4.4
|
32.8
|
1.0
|
NE2
|
H:GLN48
|
4.4
|
32.8
|
1.0
|
OE1
|
H:GLU131
|
4.6
|
43.2
|
1.0
|
CA
|
H:GLU132
|
4.7
|
33.7
|
1.0
|
CD
|
H:GLN48
|
4.8
|
34.6
|
1.0
|
O
|
H:HOH318
|
4.8
|
30.0
|
1.0
|
OE2
|
H:GLU128
|
4.8
|
40.5
|
1.0
|
CG
|
H:GLN135
|
4.9
|
37.5
|
1.0
|
CB
|
H:GLU132
|
4.9
|
31.4
|
1.0
|
|
Calcium binding site 2 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 2 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:36.5
occ:1.00
|
OE2
|
A:GLU132
|
2.3
|
37.7
|
1.0
|
O
|
A:HOH315
|
2.3
|
35.2
|
1.0
|
OE2
|
A:GLU51
|
2.3
|
38.6
|
1.0
|
OE1
|
A:GLN135
|
2.5
|
35.5
|
1.0
|
O
|
A:HOH414
|
2.5
|
35.9
|
1.0
|
OE1
|
A:GLU51
|
2.6
|
36.2
|
1.0
|
O
|
A:HOH320
|
2.7
|
34.9
|
1.0
|
CD
|
A:GLU51
|
2.8
|
34.4
|
1.0
|
CD
|
A:GLU132
|
3.5
|
33.9
|
1.0
|
CD
|
A:GLN135
|
3.5
|
39.2
|
1.0
|
NE2
|
A:GLN135
|
4.0
|
37.5
|
1.0
|
O
|
A:HOH405
|
4.0
|
29.9
|
1.0
|
CG
|
A:GLU132
|
4.2
|
36.8
|
1.0
|
OE1
|
A:GLN48
|
4.2
|
30.8
|
1.0
|
O
|
A:HOH419
|
4.2
|
39.5
|
1.0
|
NH2
|
A:ARG163
|
4.3
|
28.8
|
1.0
|
CG
|
A:GLU51
|
4.3
|
29.0
|
1.0
|
NE2
|
A:GLN48
|
4.4
|
29.5
|
1.0
|
OE1
|
A:GLU132
|
4.4
|
35.9
|
1.0
|
OE2
|
A:GLU131
|
4.5
|
37.5
|
1.0
|
O
|
A:HOH412
|
4.7
|
43.6
|
1.0
|
CA
|
A:GLU132
|
4.7
|
36.6
|
1.0
|
CD
|
A:GLN48
|
4.8
|
33.5
|
1.0
|
O
|
A:HOH307
|
4.8
|
29.0
|
1.0
|
CG
|
A:GLN135
|
4.9
|
32.5
|
1.0
|
OE2
|
A:GLU128
|
4.9
|
40.3
|
1.0
|
CB
|
A:GLU132
|
5.0
|
33.1
|
1.0
|
|
Calcium binding site 3 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 3 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca203
b:41.7
occ:1.00
|
O
|
B:HOH389
|
2.0
|
35.8
|
1.0
|
OE2
|
B:GLU132
|
2.3
|
39.6
|
1.0
|
OE2
|
B:GLU51
|
2.4
|
37.5
|
1.0
|
O
|
B:HOH327
|
2.5
|
41.3
|
1.0
|
OE1
|
B:GLN135
|
2.5
|
45.1
|
1.0
|
OE1
|
B:GLU51
|
2.6
|
39.5
|
1.0
|
O
|
B:HOH328
|
2.6
|
40.5
|
1.0
|
CD
|
B:GLU51
|
2.8
|
40.9
|
1.0
|
CD
|
B:GLN135
|
3.5
|
40.8
|
1.0
|
CD
|
B:GLU132
|
3.6
|
38.8
|
1.0
|
NE2
|
B:GLN135
|
3.8
|
42.5
|
1.0
|
O
|
B:HOH400
|
4.0
|
39.8
|
1.0
|
NH2
|
B:ARG163
|
4.1
|
35.0
|
1.0
|
OE1
|
B:GLN48
|
4.2
|
33.9
|
1.0
|
O
|
B:HOH401
|
4.2
|
42.9
|
1.0
|
CG
|
B:GLU132
|
4.3
|
35.3
|
1.0
|
CG
|
B:GLU51
|
4.3
|
35.2
|
1.0
|
NE2
|
B:GLN48
|
4.4
|
32.5
|
1.0
|
OE1
|
B:GLU132
|
4.5
|
36.4
|
1.0
|
OE2
|
B:GLU131
|
4.7
|
48.8
|
1.0
|
OE2
|
B:GLU128
|
4.7
|
43.2
|
1.0
|
CD
|
B:GLN48
|
4.7
|
35.5
|
1.0
|
O
|
B:HOH320
|
4.8
|
41.1
|
1.0
|
CA
|
B:GLU132
|
4.8
|
38.5
|
1.0
|
O
|
B:HOH392
|
4.9
|
53.0
|
1.0
|
CG
|
B:GLN135
|
4.9
|
39.1
|
1.0
|
CZ
|
B:ARG163
|
5.0
|
36.1
|
1.0
|
|
Calcium binding site 4 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 4 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca204
b:73.1
occ:1.00
|
O
|
B:HOH398
|
2.3
|
68.1
|
1.0
|
OE2
|
B:GLU131
|
2.6
|
48.8
|
1.0
|
O
|
B:HOH434
|
2.7
|
59.2
|
1.0
|
O
|
B:HOH325
|
2.8
|
51.5
|
1.0
|
OE1
|
B:GLU131
|
3.0
|
56.5
|
1.0
|
CD
|
B:GLU131
|
3.2
|
43.9
|
1.0
|
OE2
|
B:GLU128
|
4.3
|
43.2
|
1.0
|
OE1
|
B:GLU128
|
4.5
|
43.1
|
1.0
|
CG
|
B:GLU131
|
4.6
|
42.7
|
1.0
|
O
|
B:HOH327
|
4.8
|
41.3
|
1.0
|
CD
|
B:GLU128
|
4.8
|
40.0
|
1.0
|
|
Calcium binding site 5 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 5 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca203
b:38.2
occ:1.00
|
O
|
C:HOH375
|
2.0
|
39.2
|
1.0
|
O
|
C:HOH346
|
2.2
|
32.4
|
1.0
|
OE2
|
C:GLU132
|
2.2
|
41.1
|
1.0
|
OE2
|
C:GLU51
|
2.4
|
41.4
|
1.0
|
OE1
|
C:GLU51
|
2.5
|
35.5
|
1.0
|
O
|
C:HOH317
|
2.5
|
32.5
|
1.0
|
OE1
|
C:GLN135
|
2.5
|
34.7
|
1.0
|
CD
|
C:GLU51
|
2.8
|
37.9
|
1.0
|
CD
|
C:GLU132
|
3.5
|
35.3
|
1.0
|
CD
|
C:GLN135
|
3.5
|
40.2
|
1.0
|
NE2
|
C:GLN135
|
3.9
|
37.7
|
1.0
|
O
|
C:HOH380
|
4.0
|
37.1
|
1.0
|
O
|
C:HOH406
|
4.1
|
41.0
|
1.0
|
OE1
|
C:GLN48
|
4.2
|
31.4
|
1.0
|
NH2
|
C:ARG163
|
4.2
|
32.9
|
1.0
|
CG
|
C:GLU132
|
4.3
|
33.4
|
1.0
|
CG
|
C:GLU51
|
4.3
|
34.0
|
1.0
|
OE1
|
C:GLU132
|
4.4
|
37.7
|
1.0
|
OE2
|
C:GLU131
|
4.4
|
43.0
|
1.0
|
NE2
|
C:GLN48
|
4.4
|
28.1
|
1.0
|
CA
|
C:GLU132
|
4.7
|
34.5
|
1.0
|
CD
|
C:GLN48
|
4.7
|
35.5
|
1.0
|
O
|
C:HOH308
|
4.8
|
39.8
|
1.0
|
OE2
|
C:GLU128
|
4.8
|
44.9
|
1.0
|
CG
|
C:GLN135
|
4.9
|
36.9
|
1.0
|
|
Calcium binding site 6 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 6 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca203
b:30.8
occ:0.72
|
O
|
D:HOH377
|
2.1
|
42.5
|
1.0
|
OE2
|
D:GLU132
|
2.3
|
38.3
|
1.0
|
NE2
|
D:GLN135
|
2.3
|
35.9
|
1.0
|
OE2
|
D:GLU51
|
2.4
|
38.4
|
1.0
|
O
|
D:HOH315
|
2.5
|
38.9
|
1.0
|
OE1
|
D:GLU51
|
2.6
|
40.8
|
1.0
|
O
|
D:HOH322
|
2.6
|
39.8
|
1.0
|
CD
|
D:GLU51
|
2.9
|
38.5
|
1.0
|
CD
|
D:GLN135
|
3.3
|
43.8
|
1.0
|
CD
|
D:GLU132
|
3.5
|
37.4
|
1.0
|
OE1
|
D:GLN135
|
3.6
|
45.8
|
1.0
|
O
|
D:HOH360
|
4.0
|
37.3
|
1.0
|
O
|
D:HOH395
|
4.3
|
43.5
|
1.0
|
NH2
|
D:ARG163
|
4.3
|
33.0
|
1.0
|
OE1
|
D:GLN48
|
4.3
|
34.4
|
1.0
|
NE2
|
D:GLN48
|
4.3
|
31.8
|
1.0
|
CG
|
D:GLU132
|
4.4
|
37.7
|
1.0
|
CG
|
D:GLU51
|
4.4
|
33.9
|
1.0
|
OE1
|
D:GLU132
|
4.4
|
40.7
|
1.0
|
OE1
|
D:GLU131
|
4.5
|
46.1
|
1.0
|
CG
|
D:GLN135
|
4.7
|
39.0
|
1.0
|
CA
|
D:GLU132
|
4.7
|
34.5
|
1.0
|
O
|
D:HOH372
|
4.7
|
48.5
|
1.0
|
CD
|
D:GLN48
|
4.8
|
36.1
|
1.0
|
O
|
D:HOH320
|
4.8
|
37.2
|
1.0
|
|
Calcium binding site 7 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 7 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca203
b:43.8
occ:1.00
|
O
|
E:HOH316
|
2.2
|
36.6
|
1.0
|
OE2
|
E:GLU132
|
2.3
|
42.6
|
1.0
|
O
|
E:HOH333
|
2.4
|
39.1
|
1.0
|
OE2
|
E:GLU51
|
2.4
|
38.9
|
1.0
|
OE1
|
E:GLN135
|
2.4
|
42.1
|
1.0
|
O
|
E:HOH390
|
2.5
|
42.7
|
1.0
|
OE1
|
E:GLU51
|
2.5
|
41.1
|
1.0
|
CD
|
E:GLU51
|
2.8
|
42.2
|
1.0
|
CD
|
E:GLN135
|
3.5
|
44.2
|
1.0
|
CD
|
E:GLU132
|
3.5
|
40.5
|
1.0
|
NE2
|
E:GLN135
|
3.9
|
44.9
|
1.0
|
OE1
|
E:GLN48
|
4.2
|
38.7
|
1.0
|
O
|
E:HOH391
|
4.2
|
44.8
|
1.0
|
NH2
|
E:ARG163
|
4.3
|
35.1
|
1.0
|
CG
|
E:GLU132
|
4.3
|
36.0
|
1.0
|
O
|
E:HOH388
|
4.3
|
48.6
|
1.0
|
OE1
|
E:GLU132
|
4.3
|
44.0
|
1.0
|
O
|
E:HOH358
|
4.3
|
38.0
|
1.0
|
CG
|
E:GLU51
|
4.4
|
36.2
|
1.0
|
NE2
|
E:GLN48
|
4.4
|
38.9
|
1.0
|
OE2
|
E:GLU131
|
4.6
|
41.9
|
1.0
|
O
|
E:HOH308
|
4.7
|
38.2
|
1.0
|
CD
|
E:GLN48
|
4.7
|
39.2
|
1.0
|
CA
|
E:GLU132
|
4.7
|
37.9
|
1.0
|
OE2
|
E:GLU128
|
4.8
|
41.5
|
1.0
|
CG
|
E:GLN135
|
4.8
|
40.4
|
1.0
|
|
Calcium binding site 8 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 8 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca203
b:35.8
occ:1.00
|
O
|
F:HOH310
|
2.3
|
37.9
|
1.0
|
O
|
F:HOH322
|
2.4
|
35.4
|
1.0
|
OE2
|
F:GLU51
|
2.4
|
37.5
|
1.0
|
OE2
|
F:GLU132
|
2.4
|
36.0
|
1.0
|
O
|
F:HOH394
|
2.5
|
34.8
|
1.0
|
OE1
|
F:GLN135
|
2.5
|
36.2
|
1.0
|
OE1
|
F:GLU51
|
2.6
|
37.7
|
1.0
|
CD
|
F:GLU51
|
2.8
|
37.2
|
1.0
|
CD
|
F:GLN135
|
3.6
|
39.8
|
1.0
|
CD
|
F:GLU132
|
3.6
|
38.3
|
1.0
|
NE2
|
F:GLN135
|
3.9
|
38.0
|
1.0
|
O
|
F:HOH368
|
4.1
|
30.8
|
1.0
|
CG
|
F:GLU132
|
4.2
|
37.5
|
1.0
|
OE1
|
F:GLN48
|
4.3
|
33.2
|
1.0
|
O
|
F:HOH396
|
4.3
|
43.7
|
1.0
|
CG
|
F:GLU51
|
4.4
|
35.0
|
1.0
|
OE1
|
F:GLU131
|
4.4
|
37.7
|
1.0
|
NH2
|
F:ARG163
|
4.4
|
30.3
|
1.0
|
NE2
|
F:GLN48
|
4.5
|
33.5
|
1.0
|
OE1
|
F:GLU132
|
4.5
|
32.4
|
1.0
|
CA
|
F:GLU132
|
4.7
|
30.3
|
1.0
|
O
|
F:HOH305
|
4.7
|
35.5
|
1.0
|
OE2
|
F:GLU128
|
4.7
|
43.7
|
1.0
|
CD
|
F:GLN48
|
4.9
|
32.3
|
1.0
|
CG
|
F:GLN135
|
4.9
|
34.8
|
1.0
|
CB
|
F:GLU132
|
5.0
|
31.9
|
1.0
|
|
Calcium binding site 9 out
of 9 in 7dya
Go back to
Calcium Binding Sites List in 7dya
Calcium binding site 9 out
of 9 in the Crystal Structure of Tmftn with Calcium Ions
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Tmftn with Calcium Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca203
b:48.7
occ:1.00
|
O
|
G:HOH306
|
2.2
|
52.6
|
1.0
|
OE2
|
G:GLU51
|
2.4
|
50.0
|
1.0
|
OE2
|
G:GLU132
|
2.4
|
51.5
|
1.0
|
O
|
G:HOH321
|
2.4
|
48.2
|
1.0
|
O
|
G:HOH366
|
2.4
|
51.0
|
1.0
|
OE1
|
G:GLU51
|
2.5
|
46.6
|
1.0
|
OE1
|
G:GLN135
|
2.6
|
46.9
|
1.0
|
CD
|
G:GLU51
|
2.8
|
47.3
|
1.0
|
CD
|
G:GLN135
|
3.5
|
49.0
|
1.0
|
CD
|
G:GLU132
|
3.6
|
46.9
|
1.0
|
NE2
|
G:GLN135
|
3.7
|
50.7
|
1.0
|
OE1
|
G:GLN48
|
4.1
|
43.4
|
1.0
|
NH2
|
G:ARG163
|
4.2
|
43.1
|
1.0
|
O
|
G:HOH362
|
4.2
|
48.7
|
1.0
|
CG
|
G:GLU132
|
4.3
|
45.1
|
1.0
|
OE2
|
G:GLU131
|
4.3
|
55.8
|
1.0
|
CG
|
G:GLU51
|
4.4
|
41.2
|
1.0
|
NE2
|
G:GLN48
|
4.5
|
39.8
|
1.0
|
O
|
G:HOH303
|
4.5
|
45.5
|
1.0
|
OE1
|
G:GLU132
|
4.6
|
46.9
|
1.0
|
OE2
|
G:GLU128
|
4.7
|
46.7
|
1.0
|
CD
|
G:GLN48
|
4.8
|
44.0
|
1.0
|
CA
|
G:GLU132
|
4.8
|
44.1
|
1.0
|
CG
|
G:GLN135
|
4.9
|
45.8
|
1.0
|
|
Reference:
X.Zhang,
Y.Liu,
B.Zheng,
J.Zang,
C.Lv,
T.Zhang,
H.Wang,
G.Zhao.
Protein Interface Redesign Facilitates the Transformation of Nanocage Building Blocks to 1D and 2D Nanomaterials. Nat Commun V. 12 4849 2021.
ISSN: ESSN 2041-1723
PubMed: 34381032
DOI: 10.1038/S41467-021-25199-X
Page generated: Fri Jul 19 00:14:51 2024
|