Magnesium in PDB 8h47: Blasnase-T13A/P55F
Protein crystallography data
The structure of Blasnase-T13A/P55F, PDB code: 8h47
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)
|
19.98 /
1.90
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.513,
92.513,
230.783,
90,
90,
90
|
R / Rfree (%)
|
19.2 /
20.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Blasnase-T13A/P55F
(pdb code 8h47). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Blasnase-T13A/P55F, PDB code: 8h47:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8h47
Go back to
Magnesium Binding Sites List in 8h47
Magnesium binding site 1 out
of 4 in the Blasnase-T13A/P55F
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:37.0
occ:0.00
|
O1
|
A:FMT403
|
2.3
|
36.8
|
0.0
|
O
|
A:ASN246
|
2.5
|
33.7
|
1.0
|
O
|
A:HOH549
|
2.5
|
40.8
|
1.0
|
OD2
|
A:ASP250
|
2.7
|
42.6
|
1.0
|
C
|
A:FMT403
|
3.2
|
37.2
|
0.0
|
C
|
A:ASN246
|
3.6
|
39.5
|
1.0
|
CG
|
A:ASP250
|
3.6
|
38.2
|
1.0
|
NH1
|
A:ARG223
|
3.8
|
34.2
|
1.0
|
OD1
|
A:ASP250
|
3.9
|
38.2
|
1.0
|
O2
|
A:FMT403
|
4.2
|
37.8
|
0.0
|
O
|
A:HOH595
|
4.3
|
35.7
|
1.0
|
CA
|
A:ASN246
|
4.3
|
37.4
|
1.0
|
N
|
A:GLY219
|
4.3
|
30.9
|
1.0
|
CB
|
A:ASN246
|
4.5
|
32.5
|
1.0
|
CA
|
A:GLY219
|
4.5
|
32.1
|
1.0
|
N
|
A:MET247
|
4.6
|
32.4
|
1.0
|
CA
|
A:MET247
|
4.8
|
32.9
|
1.0
|
N
|
A:ASP250
|
4.9
|
33.3
|
1.0
|
CB
|
A:ASP250
|
4.9
|
33.7
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8h47
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Magnesium Binding Sites List in 8h47
Magnesium binding site 2 out
of 4 in the Blasnase-T13A/P55F
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:33.1
occ:0.00
|
O
|
A:ASP295
|
2.3
|
31.4
|
1.0
|
O
|
A:HOH664
|
2.5
|
36.2
|
1.0
|
O
|
A:HOH560
|
2.8
|
31.2
|
1.0
|
O
|
A:HOH647
|
3.0
|
36.4
|
1.0
|
O
|
A:GLU268
|
3.2
|
31.6
|
1.0
|
C
|
A:ASP295
|
3.5
|
31.1
|
1.0
|
O
|
A:HOH583
|
3.5
|
36.3
|
1.0
|
C
|
A:GLU268
|
4.1
|
29.3
|
1.0
|
CB
|
A:ASP295
|
4.1
|
30.4
|
1.0
|
N
|
A:ASP297
|
4.1
|
28.6
|
1.0
|
O
|
A:HOH550
|
4.1
|
36.6
|
1.0
|
CA
|
A:ASP295
|
4.2
|
31.8
|
1.0
|
C
|
A:TYR296
|
4.3
|
30.0
|
1.0
|
O
|
A:ALA267
|
4.5
|
31.2
|
1.0
|
CD1
|
A:TYR159
|
4.5
|
34.2
|
1.0
|
N
|
A:TYR296
|
4.5
|
30.9
|
1.0
|
CE1
|
A:TYR159
|
4.6
|
34.3
|
1.0
|
O
|
A:HOH612
|
4.6
|
42.6
|
1.0
|
CA
|
A:TYR296
|
4.7
|
29.5
|
1.0
|
CA
|
A:GLU269
|
4.8
|
31.8
|
1.0
|
CG
|
A:ASP295
|
4.8
|
32.6
|
1.0
|
N
|
A:GLU269
|
4.8
|
30.6
|
1.0
|
CA
|
A:ASP297
|
4.8
|
29.6
|
1.0
|
O
|
A:TYR296
|
4.8
|
31.3
|
1.0
|
CA
|
A:GLU268
|
4.9
|
31.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8h47
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Magnesium Binding Sites List in 8h47
Magnesium binding site 3 out
of 4 in the Blasnase-T13A/P55F
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:44.7
occ:0.00
|
O
|
A:HOH619
|
2.1
|
42.5
|
1.0
|
O
|
B:HOH505
|
2.5
|
51.4
|
1.0
|
OE1
|
B:GLU207
|
2.6
|
48.9
|
1.0
|
OE2
|
B:GLU207
|
2.7
|
43.3
|
1.0
|
O
|
B:GLU228
|
2.9
|
47.2
|
1.0
|
CD
|
B:GLU207
|
3.0
|
39.9
|
1.0
|
O2
|
B:FMT408
|
3.6
|
42.5
|
0.0
|
CB
|
B:GLU228
|
3.8
|
42.1
|
1.0
|
C
|
B:GLU228
|
3.9
|
41.6
|
1.0
|
OD2
|
A:ASP218
|
4.0
|
36.1
|
1.0
|
CE
|
A:LYS220
|
4.0
|
34.6
|
1.0
|
O
|
A:HOH640
|
4.1
|
49.5
|
1.0
|
NZ
|
A:LYS220
|
4.1
|
37.3
|
1.0
|
C
|
B:FMT408
|
4.3
|
42.7
|
0.0
|
CA
|
B:GLU228
|
4.5
|
41.9
|
1.0
|
CG
|
B:GLU207
|
4.5
|
42.5
|
1.0
|
OE1
|
B:GLU228
|
4.7
|
60.8
|
1.0
|
CG
|
B:GLU228
|
4.7
|
46.0
|
1.0
|
O1
|
B:FMT408
|
4.7
|
44.6
|
0.0
|
N
|
B:GLY229
|
4.9
|
36.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8h47
Go back to
Magnesium Binding Sites List in 8h47
Magnesium binding site 4 out
of 4 in the Blasnase-T13A/P55F
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 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:36.9
occ:0.00
|
O
|
B:HOH670
|
2.4
|
41.5
|
1.0
|
O
|
B:ASP295
|
2.6
|
32.8
|
1.0
|
O
|
B:HOH602
|
2.6
|
38.0
|
1.0
|
O
|
B:HOH652
|
2.9
|
44.2
|
1.0
|
O
|
B:GLU268
|
3.2
|
33.3
|
1.0
|
O
|
B:HOH611
|
3.5
|
35.6
|
1.0
|
O
|
B:HOH629
|
3.6
|
45.1
|
1.0
|
C
|
B:ASP295
|
3.7
|
36.7
|
1.0
|
C
|
B:GLU268
|
4.0
|
34.1
|
1.0
|
O
|
B:HOH547
|
4.1
|
42.1
|
1.0
|
N
|
B:ASP297
|
4.1
|
31.6
|
1.0
|
O
|
B:ALA267
|
4.2
|
33.0
|
1.0
|
O
|
B:HOH560
|
4.2
|
37.4
|
1.0
|
CB
|
B:ASP295
|
4.3
|
36.0
|
1.0
|
C
|
B:TYR296
|
4.3
|
33.5
|
1.0
|
CA
|
B:ASP295
|
4.4
|
35.9
|
1.0
|
N
|
B:TYR296
|
4.6
|
30.5
|
1.0
|
CA
|
B:ASP297
|
4.7
|
29.3
|
1.0
|
CD1
|
B:TYR159
|
4.7
|
35.3
|
1.0
|
CA
|
B:GLU268
|
4.7
|
35.5
|
1.0
|
N
|
B:GLU269
|
4.7
|
32.0
|
1.0
|
O
|
B:TYR296
|
4.7
|
32.9
|
1.0
|
CA
|
B:TYR296
|
4.8
|
32.9
|
1.0
|
CA
|
B:GLU269
|
4.8
|
35.2
|
1.0
|
CE1
|
B:TYR159
|
4.8
|
34.2
|
1.0
|
CB
|
B:ASP297
|
4.8
|
29.2
|
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 09:07:41 2023
|