Calcium in PDB 8ekg: Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
Enzymatic activity of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
All present enzymatic activity of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP:
3.1.1.102;
Protein crystallography data
The structure of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP, PDB code: 8ekg
was solved by
J.W.Saunders,
R.L.Frkic,
C.J.Jackson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
43.87 /
2.65
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.967,
120.514,
126.29,
90.44,
95.15,
90.2
|
|
R / Rfree (%)
|
18.4 /
24.1
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
(pdb code 8ekg). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP, PDB code: 8ekg:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 8ekg
Go back to
Calcium Binding Sites List in 8ekg
Calcium binding site 1 out
of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca701
b:55.5
occ:1.00
|
O
|
A:ILE313
|
2.3
|
55.6
|
1.0
|
|
OD1
|
A:ASP311
|
2.4
|
62.5
|
1.0
|
|
OD1
|
A:ASP304
|
2.6
|
47.3
|
1.0
|
|
OD1
|
A:ASP307
|
2.6
|
51.1
|
1.0
|
|
O
|
A:LEU309
|
2.7
|
50.4
|
1.0
|
|
O
|
A:ASP304
|
2.7
|
44.0
|
1.0
|
|
OD2
|
A:ASP307
|
2.8
|
61.1
|
1.0
|
|
CG
|
A:ASP307
|
2.9
|
56.0
|
1.0
|
|
CG
|
A:ASP311
|
3.3
|
61.6
|
1.0
|
|
OD2
|
A:ASP311
|
3.5
|
58.3
|
1.0
|
|
C
|
A:ILE313
|
3.5
|
45.4
|
1.0
|
|
C
|
A:ASP304
|
3.8
|
42.3
|
1.0
|
|
CG
|
A:ASP304
|
3.8
|
53.0
|
1.0
|
|
C
|
A:LEU309
|
3.9
|
44.4
|
1.0
|
|
O
|
A:HOH820
|
4.0
|
35.8
|
1.0
|
|
OD2
|
A:ASP315
|
4.2
|
65.3
|
1.0
|
|
CA
|
A:ASP304
|
4.3
|
47.3
|
1.0
|
|
CB
|
A:ASP307
|
4.3
|
41.8
|
1.0
|
|
N
|
A:ASP311
|
4.3
|
41.4
|
1.0
|
|
N
|
A:ILE313
|
4.3
|
50.0
|
1.0
|
|
N
|
A:ASP315
|
4.3
|
45.8
|
1.0
|
|
CA
|
A:ILE313
|
4.3
|
49.2
|
1.0
|
|
N
|
A:VAL314
|
4.5
|
39.2
|
1.0
|
|
CB
|
A:ILE313
|
4.5
|
42.4
|
1.0
|
|
CA
|
A:VAL314
|
4.6
|
44.3
|
1.0
|
|
OD2
|
A:ASP304
|
4.6
|
42.9
|
1.0
|
|
CB
|
A:ASP311
|
4.7
|
42.7
|
1.0
|
|
CB
|
A:ASP304
|
4.7
|
51.9
|
1.0
|
|
CA
|
A:LEU309
|
4.7
|
46.6
|
1.0
|
|
N
|
A:LEU309
|
4.7
|
51.4
|
1.0
|
|
CB
|
A:ASP315
|
4.8
|
48.1
|
1.0
|
|
CG2
|
A:ILE313
|
4.8
|
39.0
|
1.0
|
|
CB
|
A:LEU309
|
4.8
|
41.2
|
1.0
|
|
N
|
A:ALA310
|
4.8
|
47.5
|
1.0
|
|
CA
|
A:ALA310
|
4.9
|
43.0
|
1.0
|
|
CG
|
A:ASP315
|
4.9
|
64.1
|
1.0
|
|
N
|
A:ALA305
|
4.9
|
45.3
|
1.0
|
|
CA
|
A:ASP311
|
5.0
|
36.7
|
1.0
|
|
Calcium binding site 2 out
of 6 in 8ekg
Go back to
Calcium Binding Sites List in 8ekg
Calcium binding site 2 out
of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca701
b:53.9
occ:1.00
|
OD1
|
B:ASP311
|
2.3
|
51.8
|
1.0
|
|
O
|
B:ILE313
|
2.3
|
53.0
|
1.0
|
|
O
|
B:LEU309
|
2.4
|
49.5
|
1.0
|
|
OD2
|
B:ASP307
|
2.5
|
60.1
|
1.0
|
|
OD1
|
B:ASP304
|
2.5
|
48.4
|
1.0
|
|
O
|
B:ASP304
|
2.6
|
52.8
|
1.0
|
|
OD1
|
B:ASP307
|
2.9
|
73.8
|
1.0
|
|
CG
|
B:ASP307
|
3.0
|
64.6
|
1.0
|
|
CG
|
B:ASP311
|
3.4
|
55.5
|
1.0
|
|
C
|
B:ILE313
|
3.5
|
47.9
|
1.0
|
|
C
|
B:ASP304
|
3.6
|
50.6
|
1.0
|
|
C
|
B:LEU309
|
3.6
|
50.0
|
1.0
|
|
CG
|
B:ASP304
|
3.7
|
49.5
|
1.0
|
|
OD2
|
B:ASP315
|
3.7
|
73.5
|
1.0
|
|
OD2
|
B:ASP311
|
3.9
|
56.6
|
1.0
|
|
CA
|
B:ASP304
|
4.0
|
50.6
|
1.0
|
|
N
|
B:ASP311
|
4.0
|
40.1
|
1.0
|
|
N
|
B:ILE313
|
4.2
|
39.1
|
1.0
|
|
CA
|
B:ILE313
|
4.3
|
35.8
|
1.0
|
|
CB
|
B:ASP304
|
4.5
|
53.5
|
1.0
|
|
N
|
B:ALA310
|
4.5
|
45.1
|
1.0
|
|
CA
|
B:LEU309
|
4.5
|
50.3
|
1.0
|
|
N
|
B:VAL314
|
4.5
|
46.4
|
1.0
|
|
CB
|
B:ASP307
|
4.5
|
59.4
|
1.0
|
|
O
|
B:HOH810
|
4.5
|
50.5
|
1.0
|
|
CA
|
B:ALA310
|
4.5
|
44.4
|
1.0
|
|
N
|
B:ASP315
|
4.5
|
64.5
|
1.0
|
|
CB
|
B:ILE313
|
4.6
|
44.0
|
1.0
|
|
N
|
B:LEU309
|
4.6
|
51.9
|
1.0
|
|
OD2
|
B:ASP304
|
4.6
|
44.2
|
1.0
|
|
CB
|
B:ASP311
|
4.6
|
52.3
|
1.0
|
|
N
|
B:ALA305
|
4.6
|
50.3
|
1.0
|
|
CB
|
B:LEU309
|
4.7
|
42.7
|
1.0
|
|
CA
|
B:VAL314
|
4.7
|
51.3
|
1.0
|
|
O
|
B:HOH838
|
4.8
|
42.1
|
1.0
|
|
C
|
B:ALA310
|
4.8
|
47.1
|
1.0
|
|
CA
|
B:ASP311
|
4.8
|
41.7
|
1.0
|
|
CG
|
B:ASP315
|
4.8
|
75.3
|
1.0
|
|
N
|
B:GLY312
|
4.9
|
49.3
|
1.0
|
|
CA
|
B:ALA305
|
5.0
|
53.7
|
1.0
|
|
Calcium binding site 3 out
of 6 in 8ekg
Go back to
Calcium Binding Sites List in 8ekg
Calcium binding site 3 out
of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca701
b:58.0
occ:1.00
|
O
|
C:LEU309
|
2.2
|
63.3
|
1.0
|
|
OD1
|
C:ASP307
|
2.4
|
66.7
|
1.0
|
|
O
|
C:ASP304
|
2.5
|
51.1
|
1.0
|
|
OD1
|
C:ASP311
|
2.5
|
52.1
|
1.0
|
|
OD1
|
C:ASP304
|
2.6
|
68.1
|
1.0
|
|
O
|
C:ILE313
|
2.7
|
54.1
|
1.0
|
|
OD2
|
C:ASP307
|
3.0
|
68.5
|
1.0
|
|
CG
|
C:ASP307
|
3.1
|
71.9
|
1.0
|
|
C
|
C:LEU309
|
3.4
|
50.0
|
1.0
|
|
CG
|
C:ASP311
|
3.6
|
55.1
|
1.0
|
|
C
|
C:ASP304
|
3.6
|
58.3
|
1.0
|
|
CG
|
C:ASP304
|
3.7
|
68.2
|
1.0
|
|
OD1
|
C:ASP315
|
3.7
|
87.2
|
1.0
|
|
C
|
C:ILE313
|
3.9
|
50.5
|
1.0
|
|
N
|
C:ASP311
|
4.0
|
55.6
|
1.0
|
|
OD2
|
C:ASP311
|
4.0
|
54.6
|
1.0
|
|
CA
|
C:ASP304
|
4.2
|
56.4
|
1.0
|
|
CA
|
C:LEU309
|
4.3
|
49.3
|
1.0
|
|
N
|
C:LEU309
|
4.4
|
58.7
|
1.0
|
|
N
|
C:ALA310
|
4.4
|
56.5
|
1.0
|
|
OD2
|
C:ASP304
|
4.4
|
59.7
|
1.0
|
|
N
|
C:ILE313
|
4.4
|
54.9
|
1.0
|
|
CA
|
C:ALA310
|
4.5
|
58.1
|
1.0
|
|
CB
|
C:ASP304
|
4.5
|
58.4
|
1.0
|
|
CB
|
C:LEU309
|
4.5
|
46.2
|
1.0
|
|
CB
|
C:ASP307
|
4.5
|
66.5
|
1.0
|
|
N
|
C:ALA305
|
4.6
|
61.9
|
1.0
|
|
CA
|
C:ILE313
|
4.6
|
56.3
|
1.0
|
|
CB
|
C:ASP311
|
4.7
|
52.0
|
1.0
|
|
C
|
C:ALA310
|
4.7
|
55.7
|
1.0
|
|
CA
|
C:ASP311
|
4.8
|
50.6
|
1.0
|
|
N
|
C:VAL314
|
4.9
|
52.7
|
1.0
|
|
CG
|
C:ASP315
|
4.9
|
72.6
|
1.0
|
|
N
|
C:ASP315
|
4.9
|
47.7
|
1.0
|
|
CA
|
C:ALA305
|
4.9
|
59.5
|
1.0
|
|
CB
|
C:ILE313
|
4.9
|
52.3
|
1.0
|
|
Calcium binding site 4 out
of 6 in 8ekg
Go back to
Calcium Binding Sites List in 8ekg
Calcium binding site 4 out
of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca701
b:60.4
occ:1.00
|
OD1
|
D:ASP311
|
2.3
|
61.5
|
1.0
|
|
OD1
|
D:ASP307
|
2.3
|
60.3
|
1.0
|
|
O
|
D:ILE313
|
2.4
|
61.5
|
1.0
|
|
O
|
D:LEU309
|
2.4
|
69.5
|
1.0
|
|
OD2
|
D:ASP307
|
2.6
|
66.3
|
1.0
|
|
CG
|
D:ASP307
|
2.8
|
62.0
|
1.0
|
|
OD1
|
D:ASP304
|
2.8
|
58.0
|
1.0
|
|
O
|
D:ASP304
|
3.0
|
51.1
|
1.0
|
|
CG
|
D:ASP311
|
3.1
|
66.8
|
1.0
|
|
OD2
|
D:ASP311
|
3.4
|
62.3
|
1.0
|
|
C
|
D:LEU309
|
3.6
|
60.9
|
1.0
|
|
C
|
D:ILE313
|
3.6
|
51.1
|
1.0
|
|
OD2
|
D:ASP315
|
3.9
|
71.7
|
1.0
|
|
C
|
D:ASP304
|
4.0
|
52.2
|
1.0
|
|
CG
|
D:ASP304
|
4.0
|
61.3
|
1.0
|
|
N
|
D:ASP311
|
4.1
|
58.1
|
1.0
|
|
CB
|
D:ASP307
|
4.3
|
56.8
|
1.0
|
|
N
|
D:ILE313
|
4.3
|
54.6
|
1.0
|
|
CA
|
D:LEU309
|
4.4
|
63.9
|
1.0
|
|
CA
|
D:ILE313
|
4.4
|
52.5
|
1.0
|
|
N
|
D:LEU309
|
4.4
|
61.9
|
1.0
|
|
CA
|
D:ASP304
|
4.4
|
54.0
|
1.0
|
|
N
|
D:ASP315
|
4.5
|
60.4
|
1.0
|
|
CB
|
D:ASP311
|
4.5
|
65.8
|
1.0
|
|
CB
|
D:LEU309
|
4.5
|
56.6
|
1.0
|
|
N
|
D:ALA310
|
4.5
|
57.9
|
1.0
|
|
N
|
D:VAL314
|
4.6
|
59.7
|
1.0
|
|
CB
|
D:ILE313
|
4.6
|
53.9
|
1.0
|
|
CA
|
D:ALA310
|
4.7
|
57.3
|
1.0
|
|
CA
|
D:VAL314
|
4.7
|
61.4
|
1.0
|
|
CG
|
D:ASP315
|
4.7
|
74.1
|
1.0
|
|
CA
|
D:ASP311
|
4.8
|
62.7
|
1.0
|
|
C
|
D:ALA310
|
4.9
|
63.9
|
1.0
|
|
CB
|
D:ASP304
|
4.9
|
64.5
|
1.0
|
|
OD2
|
D:ASP304
|
4.9
|
54.8
|
1.0
|
|
CG2
|
D:ILE313
|
4.9
|
51.6
|
1.0
|
|
Calcium binding site 5 out
of 6 in 8ekg
Go back to
Calcium Binding Sites List in 8ekg
Calcium binding site 5 out
of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca701
b:64.1
occ:1.00
|
OD1
|
E:ASP311
|
2.3
|
77.9
|
1.0
|
|
O
|
E:LEU309
|
2.3
|
74.5
|
1.0
|
|
OD1
|
E:ASP307
|
2.4
|
63.9
|
1.0
|
|
OD1
|
E:ASP304
|
2.6
|
68.6
|
1.0
|
|
O
|
E:ILE313
|
2.6
|
66.6
|
1.0
|
|
OD2
|
E:ASP307
|
2.8
|
77.1
|
1.0
|
|
O
|
E:ASP304
|
2.8
|
81.9
|
1.0
|
|
CG
|
E:ASP307
|
2.9
|
72.2
|
1.0
|
|
CG
|
E:ASP311
|
3.2
|
71.0
|
1.0
|
|
OD2
|
E:ASP311
|
3.4
|
60.9
|
1.0
|
|
C
|
E:LEU309
|
3.5
|
73.9
|
1.0
|
|
OD2
|
E:ASP315
|
3.7
|
93.1
|
1.0
|
|
C
|
E:ASP304
|
3.8
|
84.7
|
1.0
|
|
CG
|
E:ASP304
|
3.8
|
72.6
|
1.0
|
|
C
|
E:ILE313
|
3.8
|
70.2
|
1.0
|
|
N
|
E:ASP311
|
4.0
|
68.3
|
1.0
|
|
CA
|
E:ASP304
|
4.2
|
80.8
|
1.0
|
|
CA
|
E:ALA310
|
4.4
|
71.6
|
1.0
|
|
N
|
E:ALA310
|
4.4
|
77.2
|
1.0
|
|
CB
|
E:ASP307
|
4.4
|
76.8
|
1.0
|
|
CA
|
E:LEU309
|
4.5
|
68.8
|
1.0
|
|
N
|
E:ILE313
|
4.5
|
57.1
|
1.0
|
|
CB
|
E:ASP311
|
4.5
|
64.3
|
1.0
|
|
N
|
E:LEU309
|
4.6
|
62.8
|
1.0
|
|
C
|
E:ALA310
|
4.6
|
69.8
|
1.0
|
|
CB
|
E:ASP304
|
4.6
|
75.2
|
1.0
|
|
CA
|
E:ILE313
|
4.6
|
69.5
|
1.0
|
|
N
|
E:ASP315
|
4.7
|
73.3
|
1.0
|
|
OD2
|
E:ASP304
|
4.7
|
75.1
|
1.0
|
|
CB
|
E:LEU309
|
4.8
|
72.9
|
1.0
|
|
N
|
E:VAL314
|
4.8
|
72.1
|
1.0
|
|
CG
|
E:ASP315
|
4.8
|
102.7
|
1.0
|
|
CA
|
E:ASP311
|
4.8
|
68.4
|
1.0
|
|
N
|
E:ALA305
|
4.8
|
84.9
|
1.0
|
|
CA
|
E:VAL314
|
4.9
|
72.5
|
1.0
|
|
CB
|
E:ILE313
|
4.9
|
71.0
|
1.0
|
|
CD1
|
E:LEU309
|
5.0
|
71.5
|
1.0
|
|
Calcium binding site 6 out
of 6 in 8ekg
Go back to
Calcium Binding Sites List in 8ekg
Calcium binding site 6 out
of 6 in the Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Mhetase Variant THR159VAL, MET192TYR, TYR252PHE, TYR503TRP within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca701
b:60.6
occ:1.00
|
OD1
|
F:ASP311
|
2.3
|
66.7
|
1.0
|
|
O
|
F:LEU309
|
2.3
|
65.0
|
1.0
|
|
O
|
F:ILE313
|
2.5
|
61.8
|
1.0
|
|
OD2
|
F:ASP307
|
2.5
|
75.4
|
1.0
|
|
OD1
|
F:ASP307
|
2.5
|
69.5
|
1.0
|
|
O
|
F:ASP304
|
2.8
|
65.9
|
1.0
|
|
OD1
|
F:ASP304
|
2.8
|
60.1
|
1.0
|
|
CG
|
F:ASP307
|
2.9
|
72.7
|
1.0
|
|
CG
|
F:ASP311
|
3.4
|
66.3
|
1.0
|
|
C
|
F:LEU309
|
3.6
|
65.1
|
1.0
|
|
C
|
F:ILE313
|
3.7
|
63.8
|
1.0
|
|
C
|
F:ASP304
|
3.7
|
68.9
|
1.0
|
|
OD2
|
F:ASP311
|
3.8
|
68.7
|
1.0
|
|
N
|
F:ASP311
|
3.9
|
61.3
|
1.0
|
|
CG
|
F:ASP304
|
4.0
|
65.3
|
1.0
|
|
CA
|
F:ASP304
|
4.1
|
70.1
|
1.0
|
|
OD2
|
F:ASP315
|
4.2
|
88.5
|
1.0
|
|
N
|
F:ILE313
|
4.3
|
50.7
|
1.0
|
|
CA
|
F:ALA310
|
4.3
|
64.8
|
1.0
|
|
CB
|
F:ASP307
|
4.4
|
73.4
|
1.0
|
|
N
|
F:ALA310
|
4.4
|
63.8
|
1.0
|
|
CA
|
F:ILE313
|
4.4
|
61.3
|
1.0
|
|
N
|
F:ASP315
|
4.5
|
63.5
|
1.0
|
|
CA
|
F:LEU309
|
4.6
|
65.2
|
1.0
|
|
CB
|
F:ASP311
|
4.6
|
65.6
|
1.0
|
|
C
|
F:ALA310
|
4.6
|
63.2
|
1.0
|
|
N
|
F:LEU309
|
4.6
|
69.9
|
1.0
|
|
CB
|
F:ASP304
|
4.6
|
68.6
|
1.0
|
|
CB
|
F:ILE313
|
4.7
|
56.1
|
1.0
|
|
N
|
F:VAL314
|
4.7
|
68.0
|
1.0
|
|
CA
|
F:ASP311
|
4.7
|
65.1
|
1.0
|
|
N
|
F:ALA305
|
4.7
|
75.0
|
1.0
|
|
CA
|
F:VAL314
|
4.8
|
60.2
|
1.0
|
|
CG
|
F:ASP315
|
4.9
|
88.8
|
1.0
|
|
OD2
|
F:ASP304
|
4.9
|
74.3
|
1.0
|
|
CB
|
F:LEU309
|
4.9
|
58.6
|
1.0
|
|
CB
|
F:ASP315
|
5.0
|
72.9
|
1.0
|
|
Reference:
J.W.Saunders,
A.D.Damry,
V.Vongsouthi,
R.L.Frkic,
M.A.Spence,
P.M.Yates,
M.D.Mcleod,
N.Tokuriki,
C.J.Jackson.
Mhetase Protein Engineering Using A Novel Colorimetric Assay To Be Published.
Page generated: Thu Dec 28 01:38:18 2023
|
