Magnesium in PDB 8h48: Blasnase-T13A/P55F with L-Asn
Protein crystallography data
The structure of Blasnase-T13A/P55F with L-Asn, PDB code: 8h48
was solved by
F.Lu,
W.Wang,
H.Chi,
T.Ran,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.06 /
1.80
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.695,
92.695,
232.755,
90,
90,
90
|
R / Rfree (%)
|
18 /
20.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Blasnase-T13A/P55F with L-Asn
(pdb code 8h48). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Blasnase-T13A/P55F with L-Asn, PDB code: 8h48:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8h48
Go back to
Magnesium Binding Sites List in 8h48
Magnesium binding site 1 out
of 6 in the Blasnase-T13A/P55F with L-Asn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Blasnase-T13A/P55F with L-Asn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:24.1
occ:0.00
|
O
|
A:HOH515
|
2.4
|
23.1
|
1.0
|
O
|
A:ASP295
|
2.5
|
22.6
|
1.0
|
O
|
A:HOH682
|
2.6
|
29.9
|
1.0
|
O
|
A:HOH634
|
2.8
|
30.8
|
1.0
|
O
|
A:GLU268
|
2.9
|
21.8
|
1.0
|
C
|
A:ASP295
|
3.6
|
21.4
|
1.0
|
C
|
A:GLU268
|
3.7
|
25.1
|
1.0
|
O
|
A:HOH622
|
3.9
|
27.5
|
1.0
|
O
|
A:ALA267
|
4.1
|
19.0
|
1.0
|
CB
|
A:ASP295
|
4.1
|
23.1
|
1.0
|
CA
|
A:ASP295
|
4.2
|
21.4
|
1.0
|
O
|
A:HOH548
|
4.3
|
36.0
|
1.0
|
CA
|
A:GLU269
|
4.3
|
19.5
|
1.0
|
N
|
A:ASP297
|
4.4
|
18.3
|
1.0
|
O
|
A:HOH518
|
4.4
|
29.6
|
1.0
|
N
|
A:GLU269
|
4.4
|
21.1
|
1.0
|
C
|
A:TYR296
|
4.5
|
22.5
|
1.0
|
O
|
A:GLY270
|
4.6
|
24.2
|
1.0
|
N
|
A:TYR296
|
4.6
|
21.4
|
1.0
|
O
|
A:HOH656
|
4.6
|
30.1
|
1.0
|
CA
|
A:GLU268
|
4.7
|
23.3
|
1.0
|
CD1
|
A:TYR159
|
4.8
|
23.9
|
1.0
|
CE1
|
A:TYR159
|
4.8
|
24.2
|
1.0
|
C
|
A:GLU269
|
4.8
|
20.7
|
1.0
|
CG
|
A:ASP295
|
4.8
|
25.1
|
1.0
|
CA
|
A:TYR296
|
4.9
|
21.8
|
1.0
|
O
|
A:TYR296
|
4.9
|
22.5
|
1.0
|
N
|
A:GLY270
|
5.0
|
22.1
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8h48
Go back to
Magnesium Binding Sites List in 8h48
Magnesium binding site 2 out
of 6 in the Blasnase-T13A/P55F with L-Asn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Blasnase-T13A/P55F with L-Asn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:32.3
occ:0.00
|
O
|
A:HOH692
|
2.1
|
33.5
|
1.0
|
O
|
B:HOH507
|
2.3
|
36.6
|
1.0
|
O
|
B:HOH710
|
2.5
|
38.8
|
1.0
|
OD2
|
A:ASP218
|
2.5
|
31.5
|
1.0
|
CB
|
A:ASP218
|
3.3
|
24.5
|
1.0
|
CG
|
A:ASP218
|
3.4
|
29.5
|
1.0
|
O
|
A:HOH685
|
3.4
|
39.1
|
1.0
|
O1
|
A:FMT405
|
3.6
|
30.5
|
0.0
|
MG
|
A:MG403
|
3.7
|
33.3
|
0.0
|
O
|
A:HOH567
|
3.8
|
36.7
|
1.0
|
C
|
A:FMT405
|
3.8
|
29.5
|
0.0
|
O
|
A:HOH557
|
3.9
|
26.9
|
1.0
|
O
|
B:HOH635
|
4.0
|
41.0
|
1.0
|
O
|
A:HOH594
|
4.2
|
22.9
|
1.0
|
O
|
B:HOH734
|
4.3
|
30.0
|
1.0
|
OE2
|
B:GLU207
|
4.4
|
33.8
|
1.0
|
O
|
B:HOH518
|
4.5
|
30.0
|
1.0
|
OD1
|
A:ASP218
|
4.6
|
25.1
|
1.0
|
O2
|
A:FMT405
|
4.8
|
28.8
|
0.0
|
CA
|
A:ASP218
|
4.8
|
24.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8h48
Go back to
Magnesium Binding Sites List in 8h48
Magnesium binding site 3 out
of 6 in the Blasnase-T13A/P55F with L-Asn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Blasnase-T13A/P55F with L-Asn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:33.3
occ:0.00
|
O
|
A:HOH692
|
2.1
|
33.5
|
1.0
|
O
|
B:HOH635
|
2.5
|
41.0
|
1.0
|
O
|
A:HOH513
|
2.7
|
39.5
|
1.0
|
O
|
B:HOH734
|
3.1
|
30.0
|
1.0
|
O
|
B:HOH507
|
3.5
|
36.6
|
1.0
|
O
|
A:HOH536
|
3.6
|
28.9
|
1.0
|
MG
|
A:MG402
|
3.7
|
32.3
|
0.0
|
O
|
A:HOH594
|
3.9
|
22.9
|
1.0
|
O
|
B:HOH710
|
4.1
|
38.8
|
1.0
|
O
|
A:HOH557
|
4.4
|
26.9
|
1.0
|
O
|
B:HOH532
|
4.4
|
39.8
|
1.0
|
O1
|
B:FMT404
|
4.4
|
29.2
|
0.0
|
OD2
|
A:ASP216
|
4.7
|
24.2
|
1.0
|
OD1
|
A:ASP216
|
4.7
|
24.8
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8h48
Go back to
Magnesium Binding Sites List in 8h48
Magnesium binding site 4 out
of 6 in the Blasnase-T13A/P55F with L-Asn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Blasnase-T13A/P55F with L-Asn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:29.7
occ:0.00
|
O2
|
A:FMT405
|
2.1
|
28.8
|
0.0
|
O
|
A:HOH681
|
2.4
|
36.1
|
1.0
|
O
|
A:HOH543
|
2.4
|
32.5
|
1.0
|
OD2
|
A:ASP250
|
2.4
|
30.6
|
1.0
|
O
|
A:ASN246
|
2.5
|
24.3
|
1.0
|
O
|
A:HOH673
|
2.6
|
38.3
|
1.0
|
C
|
A:FMT405
|
2.9
|
29.5
|
0.0
|
CG
|
A:ASP250
|
3.4
|
29.6
|
1.0
|
NH1
|
A:ARG223
|
3.5
|
27.2
|
1.0
|
C
|
A:ASN246
|
3.7
|
25.7
|
1.0
|
OD1
|
A:ASP250
|
3.8
|
30.3
|
1.0
|
O1
|
A:FMT405
|
4.0
|
30.5
|
0.0
|
N
|
A:GLY219
|
4.0
|
22.0
|
1.0
|
CA
|
A:GLY219
|
4.2
|
24.9
|
1.0
|
O
|
A:HOH679
|
4.4
|
45.5
|
1.0
|
CA
|
A:ASN246
|
4.5
|
23.9
|
1.0
|
O
|
A:HOH637
|
4.6
|
42.4
|
1.0
|
CB
|
A:ASN246
|
4.6
|
24.5
|
1.0
|
N
|
A:MET247
|
4.7
|
22.6
|
1.0
|
O
|
A:HOH685
|
4.7
|
39.1
|
1.0
|
CB
|
A:ASP250
|
4.7
|
23.4
|
1.0
|
O
|
A:HOH605
|
4.7
|
26.4
|
1.0
|
CZ
|
A:ARG223
|
4.7
|
30.6
|
1.0
|
CA
|
A:MET247
|
4.8
|
23.8
|
1.0
|
N
|
A:ASP250
|
4.9
|
24.4
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8h48
Go back to
Magnesium Binding Sites List in 8h48
Magnesium binding site 5 out
of 6 in the Blasnase-T13A/P55F with L-Asn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Blasnase-T13A/P55F with L-Asn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:30.2
occ:0.00
|
O
|
B:ASN246
|
2.4
|
29.0
|
1.0
|
O1
|
B:FMT403
|
2.5
|
29.0
|
0.0
|
OD2
|
B:ASP250
|
2.6
|
33.6
|
1.0
|
O
|
B:HOH636
|
2.7
|
30.0
|
1.0
|
C
|
B:FMT403
|
3.0
|
29.7
|
0.0
|
C
|
B:ASN246
|
3.6
|
31.4
|
1.0
|
CG
|
B:ASP250
|
3.7
|
29.9
|
1.0
|
NH1
|
B:ARG223
|
3.8
|
28.0
|
1.0
|
OD1
|
B:ASP250
|
4.2
|
34.1
|
1.0
|
N
|
B:GLY219
|
4.2
|
23.9
|
1.0
|
O2
|
B:FMT403
|
4.2
|
30.7
|
0.0
|
CA
|
B:ASN246
|
4.3
|
26.4
|
1.0
|
CB
|
B:ASN246
|
4.4
|
27.2
|
1.0
|
CA
|
B:GLY219
|
4.4
|
25.5
|
1.0
|
O
|
B:HOH625
|
4.4
|
31.9
|
1.0
|
N
|
B:MET247
|
4.6
|
26.3
|
1.0
|
CA
|
B:MET247
|
4.7
|
26.5
|
1.0
|
CB
|
B:ASP250
|
4.9
|
26.3
|
1.0
|
N
|
B:ASP250
|
5.0
|
25.6
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8h48
Go back to
Magnesium Binding Sites List in 8h48
Magnesium binding site 6 out
of 6 in the Blasnase-T13A/P55F with L-Asn
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Blasnase-T13A/P55F with L-Asn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:26.5
occ:0.00
|
O
|
B:HOH709
|
2.2
|
30.0
|
1.0
|
O
|
B:HOH605
|
2.3
|
25.5
|
1.0
|
O
|
B:ASP295
|
2.5
|
24.0
|
1.0
|
O
|
B:HOH706
|
2.5
|
33.5
|
1.0
|
O
|
B:HOH623
|
2.5
|
36.0
|
1.0
|
O
|
B:GLU268
|
2.9
|
24.8
|
1.0
|
C
|
B:ASP295
|
3.5
|
26.4
|
1.0
|
C
|
B:GLU268
|
3.8
|
26.5
|
1.0
|
O
|
B:HOH599
|
3.8
|
29.6
|
1.0
|
CB
|
B:ASP295
|
4.0
|
26.4
|
1.0
|
O
|
B:ALA267
|
4.1
|
22.5
|
1.0
|
CA
|
B:ASP295
|
4.1
|
24.7
|
1.0
|
O
|
B:HOH659
|
4.2
|
30.0
|
1.0
|
O
|
B:HOH622
|
4.3
|
34.0
|
1.0
|
O
|
B:HOH519
|
4.3
|
32.5
|
1.0
|
CA
|
B:GLU269
|
4.3
|
20.9
|
1.0
|
N
|
B:ASP297
|
4.3
|
20.8
|
1.0
|
N
|
B:GLU269
|
4.4
|
22.2
|
1.0
|
C
|
B:TYR296
|
4.5
|
26.5
|
1.0
|
O
|
B:GLY270
|
4.6
|
25.2
|
1.0
|
N
|
B:TYR296
|
4.6
|
23.6
|
1.0
|
CA
|
B:GLU268
|
4.7
|
24.4
|
1.0
|
CG
|
B:ASP295
|
4.8
|
25.9
|
1.0
|
C
|
B:GLU269
|
4.8
|
25.1
|
1.0
|
CA
|
B:TYR296
|
4.9
|
24.1
|
1.0
|
CD1
|
B:TYR159
|
4.9
|
25.1
|
1.0
|
O
|
B:TYR296
|
4.9
|
25.9
|
1.0
|
CE1
|
B:TYR159
|
4.9
|
25.3
|
1.0
|
N
|
B:GLY270
|
5.0
|
24.2
|
1.0
|
|
Reference:
F.Lu,
W.Wang,
H.Chi,
T.Ran.
Structure-Based Rational Design of Bacillus Licheniformis L-Asparaginase with Low/No D-Asparaginase Activity For A Safer Enzyme To Be Published.
Page generated: Thu Dec 28 09:07:45 2023
|