Magnesium in PDB 5nh4: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol
Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol
All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol:
5.3.1.5;
Protein crystallography data
The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol, PDB code: 5nh4
was solved by
H.J.Rozeboom,
D.B.Janssen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.46 /
1.80
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.606,
79.365,
92.096,
115.50,
90.15,
116.92
|
R / Rfree (%)
|
19.4 /
22.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol
(pdb code 5nh4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol, PDB code: 5nh4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5nh4
Go back to
Magnesium Binding Sites List in 5nh4
Magnesium binding site 1 out
of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:20.9
occ:1.00
|
OD2
|
A:ASP340
|
2.0
|
13.3
|
1.0
|
OD2
|
A:ASP297
|
2.0
|
14.7
|
1.0
|
OE1
|
A:GLU269
|
2.1
|
17.9
|
1.0
|
OE2
|
A:GLU233
|
2.1
|
16.9
|
1.0
|
O3
|
A:GOL503
|
2.1
|
26.0
|
1.0
|
O2
|
A:GOL503
|
2.2
|
17.9
|
1.0
|
CD
|
A:GLU233
|
3.0
|
13.9
|
1.0
|
C2
|
A:GOL503
|
3.1
|
21.0
|
1.0
|
CG
|
A:ASP340
|
3.1
|
13.0
|
1.0
|
C3
|
A:GOL503
|
3.1
|
23.6
|
1.0
|
CG
|
A:ASP297
|
3.2
|
14.5
|
1.0
|
OE1
|
A:GLU233
|
3.2
|
15.3
|
1.0
|
CD
|
A:GLU269
|
3.3
|
15.7
|
1.0
|
CB
|
A:ASP340
|
3.7
|
12.7
|
1.0
|
CB
|
A:ASP297
|
3.8
|
13.6
|
1.0
|
O
|
A:HOH841
|
4.0
|
24.2
|
1.0
|
OD1
|
A:ASP340
|
4.1
|
13.8
|
1.0
|
OE2
|
A:GLU269
|
4.1
|
18.5
|
1.0
|
OD1
|
A:ASP297
|
4.2
|
14.7
|
1.0
|
NE2
|
A:HIS272
|
4.3
|
19.4
|
1.0
|
CG
|
A:GLU269
|
4.3
|
14.3
|
1.0
|
CB
|
A:GLU269
|
4.3
|
12.6
|
1.0
|
CG
|
A:GLU233
|
4.4
|
12.7
|
1.0
|
C1
|
A:GOL503
|
4.4
|
18.5
|
1.0
|
CE1
|
A:HIS272
|
4.7
|
18.1
|
1.0
|
ND2
|
A:ASN267
|
4.8
|
16.8
|
1.0
|
CZ2
|
A:TRP50
|
4.9
|
13.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5nh4
Go back to
Magnesium Binding Sites List in 5nh4
Magnesium binding site 2 out
of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:17.0
occ:1.00
|
OD2
|
B:ASP297
|
1.9
|
12.5
|
1.0
|
OD2
|
B:ASP340
|
2.0
|
16.6
|
1.0
|
OE1
|
B:GLU269
|
2.0
|
15.0
|
1.0
|
OE2
|
B:GLU233
|
2.1
|
14.9
|
1.0
|
O2
|
B:GOL503
|
2.2
|
17.8
|
1.0
|
O1
|
B:GOL503
|
2.3
|
20.2
|
1.0
|
CD
|
B:GLU233
|
3.0
|
14.4
|
1.0
|
C2
|
B:GOL503
|
3.0
|
21.0
|
1.0
|
CG
|
B:ASP297
|
3.1
|
11.9
|
1.0
|
C1
|
B:GOL503
|
3.1
|
21.5
|
1.0
|
CG
|
B:ASP340
|
3.1
|
15.1
|
1.0
|
OE1
|
B:GLU233
|
3.2
|
15.2
|
1.0
|
CD
|
B:GLU269
|
3.3
|
13.9
|
1.0
|
CB
|
B:ASP340
|
3.7
|
13.1
|
1.0
|
CB
|
B:ASP297
|
3.7
|
11.2
|
1.0
|
O
|
B:HOH644
|
4.0
|
28.5
|
1.0
|
OD1
|
B:ASP297
|
4.1
|
12.4
|
1.0
|
OE2
|
B:GLU269
|
4.1
|
15.1
|
1.0
|
OD1
|
B:ASP340
|
4.1
|
16.6
|
1.0
|
CB
|
B:GLU269
|
4.2
|
12.7
|
1.0
|
CG
|
B:GLU269
|
4.2
|
12.7
|
1.0
|
C3
|
B:GOL503
|
4.3
|
21.7
|
1.0
|
CE1
|
B:HIS272
|
4.3
|
13.1
|
1.0
|
CG
|
B:GLU233
|
4.3
|
13.4
|
1.0
|
O
|
B:HOH613
|
4.6
|
39.4
|
1.0
|
ND2
|
B:ASN267
|
4.7
|
15.4
|
1.0
|
NE2
|
B:HIS272
|
4.8
|
14.1
|
1.0
|
CZ2
|
B:TRP50
|
4.9
|
12.1
|
1.0
|
ND1
|
B:HIS272
|
5.0
|
13.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5nh4
Go back to
Magnesium Binding Sites List in 5nh4
Magnesium binding site 3 out
of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg501
b:13.9
occ:1.00
|
OD2
|
C:ASP340
|
2.0
|
14.7
|
1.0
|
O3
|
C:GOL504
|
2.0
|
23.4
|
1.0
|
O2
|
C:GOL504
|
2.0
|
20.0
|
1.0
|
OE2
|
C:GLU233
|
2.1
|
16.5
|
1.0
|
OE1
|
C:GLU269
|
2.1
|
14.2
|
1.0
|
OD2
|
C:ASP297
|
2.2
|
14.4
|
1.0
|
C2
|
C:GOL504
|
2.8
|
21.7
|
1.0
|
C3
|
C:GOL504
|
2.8
|
22.4
|
1.0
|
CD
|
C:GLU233
|
3.0
|
15.2
|
1.0
|
CG
|
C:ASP340
|
3.1
|
14.7
|
1.0
|
OE1
|
C:GLU233
|
3.3
|
17.2
|
1.0
|
CD
|
C:GLU269
|
3.3
|
13.0
|
1.0
|
CG
|
C:ASP297
|
3.4
|
13.4
|
1.0
|
O
|
C:HOH755
|
3.6
|
38.6
|
1.0
|
CB
|
C:ASP340
|
3.9
|
13.1
|
1.0
|
O
|
C:HOH828
|
4.0
|
31.6
|
1.0
|
CB
|
C:ASP297
|
4.1
|
12.7
|
1.0
|
OE2
|
C:GLU269
|
4.1
|
13.9
|
1.0
|
OD1
|
C:ASP340
|
4.1
|
16.7
|
1.0
|
CE1
|
C:HIS272
|
4.1
|
14.1
|
1.0
|
C1
|
C:GOL504
|
4.2
|
22.0
|
1.0
|
CG
|
C:GLU233
|
4.4
|
13.4
|
1.0
|
CG
|
C:GLU269
|
4.4
|
12.5
|
1.0
|
OD1
|
C:ASP297
|
4.4
|
12.9
|
1.0
|
CB
|
C:GLU269
|
4.4
|
12.5
|
1.0
|
NE2
|
C:HIS272
|
4.6
|
15.2
|
1.0
|
O
|
C:HOH734
|
4.6
|
39.0
|
1.0
|
ND1
|
C:HIS272
|
4.9
|
13.7
|
1.0
|
ND2
|
C:ASN267
|
4.9
|
15.8
|
1.0
|
CZ2
|
C:TRP50
|
5.0
|
15.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5nh4
Go back to
Magnesium Binding Sites List in 5nh4
Magnesium binding site 4 out
of 4 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with One MG2+ Ions and Glycerol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg501
b:14.9
occ:1.00
|
O1
|
D:GOL502
|
2.0
|
21.3
|
1.0
|
OE1
|
D:GLU269
|
2.0
|
15.0
|
1.0
|
OD2
|
D:ASP340
|
2.0
|
14.6
|
1.0
|
OE2
|
D:GLU233
|
2.0
|
17.4
|
1.0
|
OD2
|
D:ASP297
|
2.1
|
14.1
|
1.0
|
O2
|
D:GOL502
|
2.2
|
17.1
|
1.0
|
CD
|
D:GLU233
|
2.9
|
13.9
|
1.0
|
C1
|
D:GOL502
|
2.9
|
20.6
|
1.0
|
C2
|
D:GOL502
|
3.0
|
19.8
|
1.0
|
CG
|
D:ASP340
|
3.2
|
13.2
|
1.0
|
CG
|
D:ASP297
|
3.2
|
14.8
|
1.0
|
OE1
|
D:GLU233
|
3.2
|
15.6
|
1.0
|
CD
|
D:GLU269
|
3.3
|
13.1
|
1.0
|
CB
|
D:ASP340
|
3.8
|
12.7
|
1.0
|
CB
|
D:ASP297
|
3.9
|
13.2
|
1.0
|
O
|
D:HOH823
|
3.9
|
17.3
|
1.0
|
OE2
|
D:GLU269
|
4.1
|
13.7
|
1.0
|
CE1
|
D:HIS272
|
4.1
|
11.1
|
1.0
|
OD1
|
D:ASP340
|
4.2
|
14.6
|
1.0
|
OD1
|
D:ASP297
|
4.2
|
16.1
|
1.0
|
CG
|
D:GLU269
|
4.2
|
12.6
|
1.0
|
CB
|
D:GLU269
|
4.2
|
11.5
|
1.0
|
CG
|
D:GLU233
|
4.3
|
12.1
|
1.0
|
C3
|
D:GOL502
|
4.4
|
19.1
|
1.0
|
NE2
|
D:HIS272
|
4.6
|
10.9
|
1.0
|
ND2
|
D:ASN267
|
4.8
|
13.4
|
1.0
|
ND1
|
D:HIS272
|
4.9
|
11.7
|
1.0
|
|
Reference:
M.Lee,
H.J.Rozeboom,
P.P.De Waal,
R.M.De Jong,
H.M.Dudek,
D.B.Janssen.
Metal Dependence of the Xylose Isomerase From Piromyces Sp. E2 Explored By Activity Profiling and Protein Crystallography. Biochemistry V. 56 5991 2017.
ISSN: ISSN 1520-4995
PubMed: 29045784
DOI: 10.1021/ACS.BIOCHEM.7B00777
Page generated: Sun Sep 29 23:16:40 2024
|