Magnesium in PDB 1dxi: Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution
Enzymatic activity of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution
All present enzymatic activity of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution:
5.3.1.5;
Protein crystallography data
The structure of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution, PDB code: 1dxi
was solved by
H.Rasmussen,
T.La Cour,
J.Nyborg,
M.Schulein,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
6.00 /
2.60
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
137.650,
137.650,
132.200,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
n/a /
n/a
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution
(pdb code 1dxi). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution, PDB code: 1dxi:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1dxi
Go back to
Magnesium Binding Sites List in 1dxi
Magnesium binding site 1 out
of 4 in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg389
b:17.1
occ:1.00
|
OE2
|
A:GLU181
|
2.1
|
18.6
|
1.0
|
OE2
|
A:GLU217
|
2.1
|
17.2
|
1.0
|
OD2
|
A:ASP245
|
2.1
|
17.0
|
1.0
|
OD2
|
A:ASP287
|
2.3
|
16.4
|
1.0
|
OE1
|
A:GLU181
|
2.6
|
21.3
|
1.0
|
O
|
A:HOH391
|
2.6
|
36.0
|
1.0
|
CD
|
A:GLU181
|
2.7
|
18.8
|
1.0
|
CD
|
A:GLU217
|
3.2
|
17.9
|
1.0
|
CG
|
A:ASP245
|
3.3
|
18.8
|
1.0
|
CG
|
A:GLU217
|
3.4
|
20.2
|
1.0
|
CG
|
A:ASP287
|
3.5
|
19.9
|
1.0
|
CB
|
A:ASP245
|
3.9
|
16.3
|
1.0
|
CB
|
A:ASP287
|
4.1
|
17.5
|
1.0
|
CG
|
A:GLU181
|
4.2
|
20.5
|
1.0
|
CE1
|
A:HIS220
|
4.2
|
18.3
|
1.0
|
OD1
|
A:ASP245
|
4.2
|
21.1
|
1.0
|
OE1
|
A:GLU217
|
4.3
|
16.7
|
1.0
|
ND2
|
A:ASN215
|
4.6
|
16.6
|
1.0
|
OD1
|
A:ASP287
|
4.6
|
19.5
|
1.0
|
NE2
|
A:HIS220
|
4.6
|
16.6
|
1.0
|
O
|
A:HOH392
|
4.6
|
21.6
|
1.0
|
CB
|
A:GLU217
|
4.7
|
20.0
|
1.0
|
ND1
|
A:HIS220
|
4.9
|
18.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1dxi
Go back to
Magnesium Binding Sites List in 1dxi
Magnesium binding site 2 out
of 4 in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg390
b:12.0
occ:1.00
|
O
|
A:HOH392
|
1.8
|
21.6
|
1.0
|
OD1
|
A:ASP257
|
2.0
|
25.5
|
1.0
|
OE1
|
A:GLU217
|
2.1
|
16.7
|
1.0
|
OD2
|
A:ASP255
|
2.1
|
22.6
|
1.0
|
OD1
|
A:ASP255
|
2.6
|
21.9
|
1.0
|
CG
|
A:ASP255
|
2.7
|
21.9
|
1.0
|
NE2
|
A:HIS220
|
2.8
|
16.6
|
1.0
|
CG
|
A:ASP257
|
2.9
|
26.9
|
1.0
|
CD
|
A:GLU217
|
3.0
|
17.9
|
1.0
|
OD2
|
A:ASP257
|
3.0
|
28.7
|
1.0
|
CD2
|
A:HIS220
|
3.1
|
17.4
|
1.0
|
OE2
|
A:GLU217
|
3.3
|
17.2
|
1.0
|
ND2
|
A:ASN247
|
3.7
|
21.4
|
1.0
|
CE1
|
A:HIS220
|
4.0
|
18.3
|
1.0
|
CB
|
A:ASP255
|
4.2
|
19.0
|
1.0
|
CB
|
A:ASP257
|
4.3
|
24.7
|
1.0
|
CG
|
A:GLU217
|
4.3
|
20.2
|
1.0
|
CG
|
A:HIS220
|
4.4
|
18.2
|
1.0
|
O
|
A:HOH391
|
4.6
|
36.0
|
1.0
|
OD2
|
A:ASP287
|
4.7
|
16.4
|
1.0
|
ND1
|
A:HIS220
|
4.8
|
18.2
|
1.0
|
CG
|
A:ASN247
|
4.8
|
20.8
|
1.0
|
CA
|
A:ASP257
|
4.8
|
21.7
|
1.0
|
O
|
A:ASP287
|
4.9
|
16.8
|
1.0
|
CB
|
A:GLU217
|
4.9
|
20.0
|
1.0
|
N
|
A:ASP257
|
5.0
|
20.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1dxi
Go back to
Magnesium Binding Sites List in 1dxi
Magnesium binding site 3 out
of 4 in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg389
b:14.8
occ:1.00
|
OE1
|
B:GLU217
|
2.1
|
19.2
|
1.0
|
O
|
B:HOH391
|
2.2
|
32.4
|
1.0
|
OE1
|
B:GLU181
|
2.3
|
28.4
|
1.0
|
OD2
|
B:ASP245
|
2.4
|
23.9
|
1.0
|
OD2
|
B:ASP287
|
2.4
|
20.1
|
1.0
|
OE2
|
B:GLU181
|
2.7
|
30.4
|
1.0
|
CD
|
B:GLU181
|
2.9
|
27.3
|
1.0
|
CD
|
B:GLU217
|
3.4
|
19.9
|
1.0
|
O
|
B:HOH392
|
3.4
|
30.4
|
1.0
|
CG
|
B:ASP245
|
3.6
|
21.9
|
1.0
|
CG
|
B:ASP287
|
3.6
|
19.0
|
1.0
|
CB
|
B:ASP287
|
4.0
|
16.8
|
1.0
|
CE1
|
B:HIS220
|
4.0
|
17.4
|
1.0
|
CB
|
B:ASP245
|
4.0
|
20.5
|
1.0
|
OE2
|
B:GLU217
|
4.2
|
20.0
|
1.0
|
CG
|
B:GLU217
|
4.2
|
16.5
|
1.0
|
CB
|
B:GLU217
|
4.3
|
16.0
|
1.0
|
CG
|
B:GLU181
|
4.3
|
22.1
|
1.0
|
NE2
|
B:HIS220
|
4.6
|
17.5
|
1.0
|
OD1
|
B:ASP245
|
4.6
|
18.4
|
1.0
|
OD1
|
B:ASP287
|
4.6
|
16.9
|
1.0
|
ND1
|
B:HIS220
|
4.7
|
15.4
|
1.0
|
ND2
|
B:ASN215
|
4.8
|
17.9
|
1.0
|
MG
|
B:MG390
|
5.0
|
4.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1dxi
Go back to
Magnesium Binding Sites List in 1dxi
Magnesium binding site 4 out
of 4 in the Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg390
b:4.7
occ:1.00
|
OE2
|
B:GLU217
|
1.8
|
20.0
|
1.0
|
OD1
|
B:ASP257
|
1.8
|
18.2
|
1.0
|
O
|
B:HOH392
|
1.8
|
30.4
|
1.0
|
OD2
|
B:ASP255
|
1.9
|
24.0
|
1.0
|
OD1
|
B:ASP255
|
2.6
|
24.6
|
1.0
|
CG
|
B:ASP255
|
2.6
|
23.4
|
1.0
|
CD
|
B:GLU217
|
2.9
|
19.9
|
1.0
|
CG
|
B:ASP257
|
2.9
|
17.7
|
1.0
|
NE2
|
B:HIS220
|
3.0
|
17.5
|
1.0
|
OD2
|
B:ASP257
|
3.3
|
19.3
|
1.0
|
CD2
|
B:HIS220
|
3.5
|
16.8
|
1.0
|
OE1
|
B:GLU217
|
3.5
|
19.2
|
1.0
|
ND2
|
B:ASN247
|
3.8
|
17.0
|
1.0
|
CE1
|
B:HIS220
|
4.0
|
17.4
|
1.0
|
CB
|
B:ASP255
|
4.1
|
20.8
|
1.0
|
CG
|
B:GLU217
|
4.1
|
16.5
|
1.0
|
CB
|
B:ASP257
|
4.2
|
14.1
|
1.0
|
O
|
B:ASP287
|
4.6
|
12.4
|
1.0
|
CA
|
B:ASP257
|
4.7
|
15.8
|
1.0
|
O
|
B:HOH391
|
4.7
|
32.4
|
1.0
|
CG
|
B:HIS220
|
4.7
|
17.1
|
1.0
|
OD2
|
B:ASP287
|
4.8
|
20.1
|
1.0
|
ND1
|
B:HIS220
|
4.9
|
15.4
|
1.0
|
N
|
B:ASP257
|
5.0
|
15.9
|
1.0
|
MG
|
B:MG389
|
5.0
|
14.8
|
1.0
|
CA
|
B:ASP255
|
5.0
|
17.4
|
1.0
|
|
Reference:
H.Rasmussen,
T.La Cour,
J.Nyborg,
M.Schulein.
Structure Determination of Glucose Isomerase From Streptomyces Murinus at 2.6 A Resolution. Acta Crystallogr.,Sect.D V. 50 124 1994.
ISSN: ISSN 0907-4449
PubMed: 15299450
DOI: 10.1107/S0907444993009540
Page generated: Tue Aug 13 02:46:44 2024
|