Magnesium in PDB 8h49: Blasnase-M57P
Protein crystallography data
The structure of Blasnase-M57P, PDB code: 8h49
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)
|
41.39 /
2.00
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.674,
91.674,
231.918,
90,
90,
90
|
R / Rfree (%)
|
19.1 /
21.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Blasnase-M57P
(pdb code 8h49). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Blasnase-M57P, PDB code: 8h49:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 8h49
Go back to
Magnesium Binding Sites List in 8h49
Magnesium binding site 1 out
of 7 in the Blasnase-M57P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Blasnase-M57P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:36.7
occ:0.00
|
O
|
A:ASP295
|
2.2
|
38.4
|
1.0
|
O
|
A:HOH559
|
2.4
|
35.5
|
1.0
|
O
|
A:HOH637
|
3.0
|
41.6
|
1.0
|
O
|
A:GLU268
|
3.1
|
38.1
|
1.0
|
C
|
A:ASP295
|
3.2
|
38.4
|
1.0
|
C
|
A:GLU268
|
3.9
|
37.5
|
1.0
|
CB
|
A:ASP295
|
3.9
|
35.1
|
1.0
|
CA
|
A:ASP295
|
4.0
|
34.6
|
1.0
|
O
|
A:HOH582
|
4.0
|
42.2
|
1.0
|
N
|
A:ASP297
|
4.0
|
31.5
|
1.0
|
C
|
A:TYR296
|
4.2
|
36.8
|
1.0
|
O
|
A:ALA267
|
4.2
|
34.7
|
1.0
|
N
|
A:TYR296
|
4.3
|
35.6
|
1.0
|
O
|
A:HOH542
|
4.4
|
42.6
|
1.0
|
CA
|
A:TYR296
|
4.5
|
33.5
|
1.0
|
O
|
A:HOH624
|
4.5
|
45.0
|
1.0
|
CA
|
A:GLU269
|
4.5
|
32.8
|
1.0
|
N
|
A:GLU269
|
4.5
|
33.9
|
1.0
|
O
|
A:GLY270
|
4.6
|
36.0
|
1.0
|
O
|
A:TYR296
|
4.7
|
38.1
|
1.0
|
CG
|
A:ASP295
|
4.7
|
40.4
|
1.0
|
CA
|
A:ASP297
|
4.8
|
30.8
|
1.0
|
CA
|
A:GLU268
|
4.8
|
35.5
|
1.0
|
CD1
|
A:TYR159
|
4.8
|
37.8
|
1.0
|
CE1
|
A:TYR159
|
4.9
|
36.1
|
1.0
|
C
|
A:GLU269
|
5.0
|
34.7
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 8h49
Go back to
Magnesium Binding Sites List in 8h49
Magnesium binding site 2 out
of 7 in the Blasnase-M57P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Blasnase-M57P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:45.9
occ:0.00
|
MG
|
B:MG403
|
2.3
|
46.0
|
0.0
|
O
|
B:HOH684
|
2.6
|
58.6
|
1.0
|
O
|
A:HOH636
|
3.5
|
44.4
|
1.0
|
O
|
A:HOH587
|
3.9
|
40.4
|
1.0
|
O
|
A:HOH564
|
4.0
|
38.8
|
1.0
|
O1
|
B:FMT406
|
4.2
|
41.0
|
0.0
|
O
|
A:HOH560
|
4.2
|
43.6
|
1.0
|
O
|
B:HOH602
|
4.7
|
43.0
|
1.0
|
O
|
A:HOH642
|
4.7
|
47.6
|
1.0
|
C
|
B:FMT406
|
4.8
|
40.7
|
0.0
|
CD
|
B:GLU207
|
4.8
|
49.2
|
1.0
|
OD2
|
A:ASP218
|
4.9
|
41.7
|
1.0
|
OE1
|
B:GLU207
|
4.9
|
54.8
|
1.0
|
OE2
|
B:GLU207
|
4.9
|
50.4
|
1.0
|
OD1
|
A:ASP216
|
5.0
|
37.0
|
1.0
|
OD2
|
A:ASP216
|
5.0
|
36.1
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 8h49
Go back to
Magnesium Binding Sites List in 8h49
Magnesium binding site 3 out
of 7 in the Blasnase-M57P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Blasnase-M57P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:41.6
occ:0.00
|
O1
|
A:FMT404
|
2.1
|
41.2
|
0.0
|
O
|
A:HOH594
|
2.2
|
43.6
|
1.0
|
OD2
|
A:ASP250
|
2.4
|
43.3
|
1.0
|
O
|
A:ASN246
|
2.8
|
41.4
|
1.0
|
C
|
A:FMT404
|
2.8
|
41.4
|
0.0
|
CG
|
A:ASP250
|
3.3
|
42.1
|
1.0
|
NH1
|
A:ARG223
|
3.5
|
40.3
|
1.0
|
OD1
|
A:ASP250
|
3.6
|
44.7
|
1.0
|
C
|
A:ASN246
|
3.9
|
45.0
|
1.0
|
O2
|
A:FMT404
|
4.0
|
41.5
|
0.0
|
N
|
A:GLY219
|
4.4
|
39.7
|
1.0
|
CA
|
A:GLY219
|
4.5
|
39.7
|
1.0
|
O
|
A:HOH552
|
4.5
|
42.2
|
1.0
|
CA
|
A:ASN246
|
4.6
|
43.5
|
1.0
|
CB
|
A:ASP250
|
4.6
|
38.8
|
1.0
|
CB
|
A:ASN246
|
4.6
|
34.0
|
1.0
|
N
|
A:ASP250
|
4.7
|
38.3
|
1.0
|
CZ
|
A:ARG223
|
4.8
|
46.4
|
1.0
|
N
|
A:MET247
|
5.0
|
37.9
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 8h49
Go back to
Magnesium Binding Sites List in 8h49
Magnesium binding site 4 out
of 7 in the Blasnase-M57P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Blasnase-M57P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:46.6
occ:0.00
|
O1
|
B:FMT405
|
2.1
|
45.6
|
0.0
|
O
|
B:HOH613
|
2.4
|
52.0
|
1.0
|
OD2
|
B:ASP250
|
2.7
|
48.5
|
1.0
|
O
|
B:ASN246
|
2.7
|
45.8
|
1.0
|
C
|
B:FMT405
|
2.9
|
45.7
|
0.0
|
CG
|
B:ASP250
|
3.7
|
48.2
|
1.0
|
C
|
B:ASN246
|
3.9
|
46.1
|
1.0
|
OD1
|
B:ASP250
|
3.9
|
51.8
|
1.0
|
O2
|
B:FMT405
|
4.0
|
45.4
|
0.0
|
NH1
|
B:ARG223
|
4.1
|
45.8
|
1.0
|
CA
|
B:ASN246
|
4.5
|
41.3
|
1.0
|
O
|
B:HOH548
|
4.5
|
48.5
|
1.0
|
CB
|
B:ASN246
|
4.6
|
47.7
|
1.0
|
N
|
B:GLY219
|
4.7
|
43.1
|
1.0
|
N
|
B:ASP250
|
4.8
|
43.5
|
1.0
|
CA
|
B:GLY219
|
4.9
|
39.3
|
1.0
|
O
|
B:HOH666
|
4.9
|
57.1
|
1.0
|
N
|
B:MET247
|
4.9
|
41.1
|
1.0
|
CB
|
B:ASP250
|
5.0
|
42.8
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 8h49
Go back to
Magnesium Binding Sites List in 8h49
Magnesium binding site 5 out
of 7 in the Blasnase-M57P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Blasnase-M57P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:39.1
occ:0.00
|
O
|
B:HOH654
|
2.4
|
45.5
|
1.0
|
O
|
B:HOH586
|
2.4
|
38.8
|
1.0
|
O
|
B:ASP295
|
2.5
|
37.6
|
1.0
|
O
|
B:GLU268
|
2.9
|
38.1
|
1.0
|
C
|
B:ASP295
|
3.6
|
42.1
|
1.0
|
O
|
B:HOH598
|
3.6
|
44.2
|
1.0
|
C
|
B:GLU268
|
3.7
|
38.8
|
1.0
|
O
|
B:HOH568
|
4.1
|
39.0
|
1.0
|
CB
|
B:ASP295
|
4.1
|
38.4
|
1.0
|
O
|
B:ALA267
|
4.1
|
34.7
|
1.0
|
N
|
B:ASP297
|
4.2
|
36.1
|
1.0
|
CA
|
B:ASP295
|
4.2
|
42.7
|
1.0
|
N
|
B:GLU269
|
4.4
|
33.6
|
1.0
|
C
|
B:TYR296
|
4.5
|
40.7
|
1.0
|
CA
|
B:GLU269
|
4.5
|
39.1
|
1.0
|
CD1
|
B:TYR159
|
4.6
|
38.7
|
1.0
|
N
|
B:TYR296
|
4.6
|
37.6
|
1.0
|
CA
|
B:GLU268
|
4.6
|
35.9
|
1.0
|
CE1
|
B:TYR159
|
4.7
|
37.2
|
1.0
|
CA
|
B:TYR296
|
4.8
|
36.5
|
1.0
|
CG
|
B:ASP295
|
4.8
|
46.0
|
1.0
|
O
|
B:GLY270
|
4.9
|
39.8
|
1.0
|
O
|
B:HOH567
|
4.9
|
48.2
|
1.0
|
O
|
B:TYR296
|
4.9
|
38.1
|
1.0
|
CA
|
B:ASP297
|
4.9
|
37.3
|
1.0
|
C
|
B:GLU269
|
5.0
|
39.8
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 8h49
Go back to
Magnesium Binding Sites List in 8h49
Magnesium binding site 6 out
of 7 in the Blasnase-M57P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Blasnase-M57P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg403
b:46.0
occ:0.00
|
O
|
A:HOH636
|
2.2
|
44.4
|
1.0
|
MG
|
A:MG402
|
2.3
|
45.9
|
0.0
|
OE2
|
B:GLU207
|
2.7
|
50.4
|
1.0
|
O
|
A:HOH587
|
2.9
|
40.4
|
1.0
|
CD
|
B:GLU207
|
3.0
|
49.2
|
1.0
|
OD2
|
A:ASP218
|
3.1
|
41.7
|
1.0
|
OE1
|
B:GLU207
|
3.3
|
54.8
|
1.0
|
O
|
B:HOH684
|
3.4
|
58.6
|
1.0
|
MG
|
B:MG404
|
3.5
|
48.5
|
0.0
|
CG
|
B:GLU207
|
3.8
|
47.0
|
1.0
|
CG
|
A:ASP218
|
4.1
|
40.7
|
1.0
|
NZ
|
A:LYS220
|
4.5
|
42.4
|
1.0
|
O1
|
B:FMT406
|
4.5
|
41.0
|
0.0
|
CB
|
A:ASP218
|
4.7
|
41.0
|
1.0
|
CB
|
B:GLU207
|
4.7
|
46.0
|
1.0
|
C
|
B:FMT406
|
4.7
|
40.7
|
0.0
|
O
|
A:HOH564
|
4.7
|
38.8
|
1.0
|
O
|
B:HOH562
|
4.7
|
44.5
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 8h49
Go back to
Magnesium Binding Sites List in 8h49
Magnesium binding site 7 out
of 7 in the Blasnase-M57P
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Blasnase-M57P within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg404
b:48.5
occ:0.00
|
O
|
A:HOH636
|
2.3
|
44.4
|
1.0
|
OE2
|
B:GLU207
|
2.6
|
50.4
|
1.0
|
O
|
B:GLU228
|
2.7
|
54.0
|
1.0
|
OE1
|
B:GLU207
|
2.8
|
54.8
|
1.0
|
CD
|
B:GLU207
|
3.1
|
49.2
|
1.0
|
MG
|
B:MG403
|
3.5
|
46.0
|
0.0
|
C
|
B:GLU228
|
3.8
|
47.0
|
1.0
|
OD2
|
A:ASP218
|
3.8
|
41.7
|
1.0
|
CE
|
A:LYS220
|
3.9
|
41.0
|
1.0
|
CB
|
B:GLU228
|
3.9
|
44.5
|
1.0
|
NZ
|
A:LYS220
|
4.0
|
42.4
|
1.0
|
CA
|
B:GLU228
|
4.4
|
45.8
|
1.0
|
OE1
|
B:GLU228
|
4.4
|
65.1
|
1.0
|
CG
|
B:GLU207
|
4.6
|
47.0
|
1.0
|
N
|
B:GLY229
|
4.8
|
42.8
|
1.0
|
O
|
B:HOH684
|
4.9
|
58.6
|
1.0
|
CG
|
A:ASP218
|
4.9
|
40.7
|
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 09:07:34 2023
|