Magnesium in PDB 8xim: Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites
Enzymatic activity of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites
All present enzymatic activity of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites:
5.3.1.5;
Protein crystallography data
The structure of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites, PDB code: 8xim
was solved by
J.Janin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
2.40
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
143.450,
143.450,
231.500,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
n/a /
n/a
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites
(pdb code 8xim). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites, PDB code: 8xim:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8xim
Go back to
Magnesium Binding Sites List in 8xim
Magnesium binding site 1 out
of 4 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg395
b:14.2
occ:1.00
|
OD2
|
A:ASP245
|
1.9
|
14.3
|
1.0
|
OE2
|
A:GLU181
|
2.0
|
11.5
|
1.0
|
OE1
|
A:GLU217
|
2.1
|
11.4
|
1.0
|
OD2
|
A:ASP292
|
2.1
|
8.1
|
1.0
|
O4
|
A:XLS397
|
2.2
|
13.4
|
1.0
|
O2
|
A:XLS397
|
2.3
|
13.4
|
1.0
|
CD
|
A:GLU181
|
2.9
|
10.7
|
1.0
|
OE1
|
A:GLU181
|
3.1
|
10.5
|
1.0
|
CG
|
A:ASP245
|
3.1
|
14.4
|
1.0
|
CG
|
A:ASP292
|
3.2
|
8.6
|
1.0
|
CD
|
A:GLU217
|
3.3
|
11.0
|
1.0
|
C2
|
A:XLS397
|
3.3
|
13.8
|
1.0
|
C4
|
A:XLS397
|
3.4
|
14.5
|
1.0
|
C3
|
A:XLS397
|
3.6
|
14.1
|
1.0
|
O3
|
A:XLS397
|
3.6
|
15.0
|
1.0
|
CB
|
A:ASP245
|
3.7
|
11.0
|
1.0
|
CB
|
A:ASP292
|
3.8
|
8.3
|
1.0
|
OE2
|
A:GLU217
|
3.9
|
11.4
|
1.0
|
O
|
A:HOH455
|
3.9
|
14.9
|
1.0
|
OD1
|
A:ASP245
|
4.1
|
15.0
|
1.0
|
OD1
|
A:ASP292
|
4.2
|
9.0
|
1.0
|
CG
|
A:GLU181
|
4.2
|
9.1
|
1.0
|
CE1
|
A:HIS220
|
4.3
|
10.7
|
1.0
|
CG
|
A:GLU217
|
4.3
|
10.2
|
1.0
|
CB
|
A:GLU217
|
4.4
|
9.3
|
1.0
|
O
|
A:HOH530
|
4.4
|
23.1
|
1.0
|
ND2
|
A:ASN215
|
4.5
|
5.6
|
1.0
|
C5
|
A:XLS397
|
4.6
|
14.1
|
1.0
|
NE2
|
A:HIS220
|
4.6
|
11.3
|
1.0
|
C1
|
A:XLS397
|
4.6
|
12.8
|
1.0
|
O
|
A:HOH398
|
4.6
|
27.1
|
1.0
|
O1
|
A:XLS397
|
5.0
|
14.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8xim
Go back to
Magnesium Binding Sites List in 8xim
Magnesium binding site 2 out
of 4 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg395
b:16.4
occ:1.00
|
OE1
|
B:GLU217
|
2.0
|
11.9
|
1.0
|
OD2
|
B:ASP292
|
2.0
|
11.7
|
1.0
|
OD2
|
B:ASP245
|
2.1
|
14.4
|
1.0
|
O4
|
B:XLS397
|
2.2
|
13.8
|
1.0
|
O2
|
B:XLS397
|
2.2
|
19.1
|
1.0
|
OE2
|
B:GLU181
|
2.2
|
13.1
|
1.0
|
CD
|
B:GLU181
|
3.1
|
13.7
|
1.0
|
CG
|
B:ASP292
|
3.1
|
12.7
|
1.0
|
CG
|
B:ASP245
|
3.2
|
13.7
|
1.0
|
CD
|
B:GLU217
|
3.2
|
11.2
|
1.0
|
C2
|
B:XLS397
|
3.2
|
17.1
|
1.0
|
C4
|
B:XLS397
|
3.2
|
15.7
|
1.0
|
OE1
|
B:GLU181
|
3.3
|
14.6
|
1.0
|
C3
|
B:XLS397
|
3.4
|
15.5
|
1.0
|
O3
|
B:XLS397
|
3.4
|
15.5
|
1.0
|
O
|
B:HOH458
|
3.7
|
14.3
|
1.0
|
CB
|
B:ASP292
|
3.7
|
11.6
|
1.0
|
OE2
|
B:GLU217
|
3.8
|
13.4
|
1.0
|
CB
|
B:ASP245
|
3.9
|
11.8
|
1.0
|
OD1
|
B:ASP245
|
4.1
|
13.9
|
1.0
|
O
|
B:HOH534
|
4.1
|
29.5
|
1.0
|
OD1
|
B:ASP292
|
4.1
|
13.8
|
1.0
|
CG
|
B:GLU217
|
4.3
|
10.4
|
1.0
|
CB
|
B:GLU217
|
4.3
|
10.3
|
1.0
|
CE1
|
B:HIS220
|
4.3
|
11.0
|
1.0
|
C5
|
B:XLS397
|
4.5
|
15.1
|
1.0
|
CG
|
B:GLU181
|
4.5
|
12.9
|
1.0
|
C1
|
B:XLS397
|
4.5
|
17.6
|
1.0
|
O
|
B:HOH404
|
4.5
|
27.2
|
1.0
|
NE2
|
B:HIS220
|
4.7
|
11.3
|
1.0
|
ND2
|
B:ASN215
|
4.8
|
11.8
|
1.0
|
O1
|
B:XLS397
|
4.8
|
17.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8xim
Go back to
Magnesium Binding Sites List in 8xim
Magnesium binding site 3 out
of 4 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg395
b:11.0
occ:1.00
|
OD2
|
C:ASP245
|
2.0
|
13.9
|
1.0
|
OD2
|
C:ASP292
|
2.0
|
9.9
|
1.0
|
OE1
|
C:GLU217
|
2.0
|
14.1
|
1.0
|
O2
|
C:XLS397
|
2.2
|
16.6
|
1.0
|
OE2
|
C:GLU181
|
2.2
|
10.6
|
1.0
|
O4
|
C:XLS397
|
2.2
|
12.9
|
1.0
|
CD
|
C:GLU181
|
3.0
|
10.1
|
1.0
|
CG
|
C:ASP292
|
3.1
|
11.2
|
1.0
|
CG
|
C:ASP245
|
3.2
|
11.4
|
1.0
|
CD
|
C:GLU217
|
3.2
|
11.7
|
1.0
|
OE1
|
C:GLU181
|
3.2
|
10.7
|
1.0
|
C2
|
C:XLS397
|
3.3
|
14.5
|
1.0
|
C4
|
C:XLS397
|
3.4
|
12.3
|
1.0
|
C3
|
C:XLS397
|
3.6
|
13.4
|
1.0
|
O3
|
C:XLS397
|
3.7
|
15.0
|
1.0
|
OE2
|
C:GLU217
|
3.7
|
14.8
|
1.0
|
CB
|
C:ASP292
|
3.8
|
9.3
|
1.0
|
CB
|
C:ASP245
|
3.8
|
9.3
|
1.0
|
O
|
C:HOH470
|
4.0
|
17.2
|
1.0
|
OD1
|
C:ASP245
|
4.1
|
11.9
|
1.0
|
OD1
|
C:ASP292
|
4.2
|
11.5
|
1.0
|
CG
|
C:GLU217
|
4.2
|
8.5
|
1.0
|
CE1
|
C:HIS220
|
4.2
|
8.7
|
1.0
|
O
|
C:HOH540
|
4.2
|
20.5
|
1.0
|
CB
|
C:GLU217
|
4.3
|
7.3
|
1.0
|
CG
|
C:GLU181
|
4.4
|
8.8
|
1.0
|
C1
|
C:XLS397
|
4.5
|
14.9
|
1.0
|
NE2
|
C:HIS220
|
4.5
|
8.2
|
1.0
|
ND2
|
C:ASN215
|
4.5
|
5.5
|
1.0
|
C5
|
C:XLS397
|
4.6
|
9.3
|
1.0
|
O
|
C:HOH416
|
4.8
|
35.0
|
1.0
|
O1
|
C:XLS397
|
4.9
|
14.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8xim
Go back to
Magnesium Binding Sites List in 8xim
Magnesium binding site 4 out
of 4 in the Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site- Directed Mutagenesis of Metal Binding Sites within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg395
b:11.6
occ:1.00
|
OD2
|
D:ASP292
|
1.9
|
8.9
|
1.0
|
OE1
|
D:GLU217
|
2.0
|
9.7
|
1.0
|
OD2
|
D:ASP245
|
2.1
|
13.2
|
1.0
|
OE2
|
D:GLU181
|
2.2
|
11.6
|
1.0
|
O4
|
D:XLS397
|
2.2
|
13.8
|
1.0
|
O2
|
D:XLS397
|
2.4
|
13.6
|
1.0
|
CG
|
D:ASP292
|
3.0
|
9.4
|
1.0
|
CD
|
D:GLU181
|
3.1
|
10.7
|
1.0
|
CG
|
D:ASP245
|
3.2
|
12.5
|
1.0
|
CD
|
D:GLU217
|
3.2
|
9.9
|
1.0
|
C4
|
D:XLS397
|
3.3
|
13.8
|
1.0
|
O3
|
D:XLS397
|
3.4
|
14.6
|
1.0
|
C2
|
D:XLS397
|
3.4
|
13.1
|
1.0
|
OE1
|
D:GLU181
|
3.5
|
10.9
|
1.0
|
C3
|
D:XLS397
|
3.5
|
13.7
|
1.0
|
CB
|
D:ASP292
|
3.6
|
9.0
|
1.0
|
CB
|
D:ASP245
|
3.7
|
10.2
|
1.0
|
O
|
D:HOH483
|
3.9
|
11.6
|
1.0
|
OE2
|
D:GLU217
|
3.9
|
11.4
|
1.0
|
OD1
|
D:ASP292
|
4.0
|
8.7
|
1.0
|
O
|
D:HOH553
|
4.1
|
20.5
|
1.0
|
OD1
|
D:ASP245
|
4.2
|
13.1
|
1.0
|
CG
|
D:GLU217
|
4.2
|
7.5
|
1.0
|
CB
|
D:GLU217
|
4.3
|
7.5
|
1.0
|
CE1
|
D:HIS220
|
4.3
|
4.8
|
1.0
|
O
|
D:HOH429
|
4.3
|
16.9
|
1.0
|
CG
|
D:GLU181
|
4.5
|
8.9
|
1.0
|
C5
|
D:XLS397
|
4.6
|
13.5
|
1.0
|
C1
|
D:XLS397
|
4.6
|
11.7
|
1.0
|
NE2
|
D:HIS220
|
4.6
|
4.1
|
1.0
|
ND2
|
D:ASN215
|
4.7
|
8.2
|
1.0
|
O1
|
D:XLS397
|
4.9
|
9.5
|
1.0
|
|
Reference:
J.Jenkins,
J.Janin,
F.Rey,
M.Chiadmi,
H.Van Tilbeurgh,
I.Lasters,
M.De Maeyer,
D.Van Belle,
S.J.Wodak,
M.Lauwereys,
P.Stanssens,
G.Matthyssens,
A.M.Lambeir.
Protein Engineering of Xylose (Glucose) Isomerase From Actinoplanes Missouriensis. 1. Crystallography and Site-Directed Mutagenesis of Metal Binding Sites. Biochemistry V. 31 5449 1992.
ISSN: ISSN 0006-2960
PubMed: 1610791
DOI: 10.1021/BI00139A005
Page generated: Sat Oct 5 07:47:45 2024
|