Magnesium in PDB 5nh5: Crystal Structure of Native Xylose Isomerase From Piromyces E2
Enzymatic activity of Crystal Structure of Native Xylose Isomerase From Piromyces E2
All present enzymatic activity of Crystal Structure of Native Xylose Isomerase From Piromyces E2:
5.3.1.5;
Protein crystallography data
The structure of Crystal Structure of Native Xylose Isomerase From Piromyces E2, PDB code: 5nh5
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)
|
41.20 /
1.80
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.720,
79.360,
92.210,
115.33,
90.31,
117.00
|
R / Rfree (%)
|
12.3 /
14.8
|
Other elements in 5nh5:
The structure of Crystal Structure of Native Xylose Isomerase From Piromyces E2 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Native Xylose Isomerase From Piromyces E2
(pdb code 5nh5). 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 Native Xylose Isomerase From Piromyces E2, PDB code: 5nh5:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5nh5
Go back to
Magnesium Binding Sites List in 5nh5
Magnesium binding site 1 out
of 4 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2
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 Native Xylose Isomerase From Piromyces E2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg503
b:8.0
occ:0.36
|
FE
|
A:FE2502
|
0.4
|
12.2
|
0.3
|
CA
|
A:CA501
|
0.5
|
21.0
|
0.4
|
OD2
|
A:ASP340
|
2.0
|
15.3
|
1.0
|
OD2
|
A:ASP297
|
2.1
|
14.1
|
1.0
|
OE1
|
A:GLU269
|
2.1
|
14.7
|
1.0
|
OE2
|
A:GLU233
|
2.3
|
15.3
|
1.0
|
O2
|
A:GOL507
|
2.4
|
15.9
|
1.0
|
O3
|
A:GOL507
|
2.4
|
22.6
|
1.0
|
CG
|
A:ASP340
|
3.1
|
12.7
|
1.0
|
C2
|
A:GOL507
|
3.2
|
19.1
|
1.0
|
C3
|
A:GOL507
|
3.2
|
22.6
|
1.0
|
CD
|
A:GLU233
|
3.2
|
13.4
|
1.0
|
CG
|
A:ASP297
|
3.2
|
13.0
|
1.0
|
CD
|
A:GLU269
|
3.3
|
13.6
|
1.0
|
OE1
|
A:GLU233
|
3.5
|
13.0
|
1.0
|
CB
|
A:ASP340
|
3.7
|
11.4
|
1.0
|
CB
|
A:ASP297
|
3.8
|
11.5
|
1.0
|
O
|
A:HOH673
|
4.0
|
32.6
|
1.0
|
OD1
|
A:ASP340
|
4.1
|
12.8
|
1.0
|
OE2
|
A:GLU269
|
4.2
|
15.0
|
1.0
|
OD1
|
A:ASP297
|
4.3
|
11.7
|
1.0
|
CE1
|
A:HIS272
|
4.3
|
12.7
|
1.0
|
CG
|
A:GLU269
|
4.3
|
11.8
|
1.0
|
CB
|
A:GLU269
|
4.3
|
10.7
|
1.0
|
CG
|
A:GLU233
|
4.5
|
12.4
|
1.0
|
C1
|
A:GOL507
|
4.6
|
17.6
|
1.0
|
NE2
|
A:HIS272
|
4.7
|
12.3
|
1.0
|
ND2
|
A:ASN267
|
4.9
|
11.8
|
1.0
|
CZ2
|
A:TRP50
|
4.9
|
12.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5nh5
Go back to
Magnesium Binding Sites List in 5nh5
Magnesium binding site 2 out
of 4 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2
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 Native Xylose Isomerase From Piromyces E2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg503
b:6.9
occ:0.38
|
FE
|
B:FE2502
|
0.2
|
13.5
|
0.3
|
CA
|
B:CA501
|
0.7
|
18.5
|
0.5
|
OD2
|
B:ASP297
|
2.0
|
14.0
|
1.0
|
OE1
|
B:GLU269
|
2.0
|
14.7
|
1.0
|
OE2
|
B:GLU233
|
2.2
|
13.7
|
1.0
|
OD2
|
B:ASP340
|
2.2
|
13.8
|
1.0
|
O2
|
B:GOL506
|
2.4
|
15.8
|
1.0
|
O3
|
B:GOL506
|
2.6
|
23.7
|
1.0
|
CD
|
B:GLU233
|
3.0
|
13.1
|
1.0
|
CG
|
B:ASP297
|
3.1
|
11.7
|
1.0
|
CD
|
B:GLU269
|
3.3
|
13.5
|
1.0
|
CG
|
B:ASP340
|
3.3
|
11.2
|
1.0
|
C2
|
B:GOL506
|
3.3
|
18.9
|
1.0
|
OE1
|
B:GLU233
|
3.3
|
13.7
|
1.0
|
C3
|
B:GOL506
|
3.4
|
23.4
|
1.0
|
CB
|
B:ASP297
|
3.7
|
10.3
|
1.0
|
CB
|
B:ASP340
|
3.7
|
10.3
|
1.0
|
CG
|
B:GLU269
|
4.1
|
11.4
|
1.0
|
OD1
|
B:ASP297
|
4.1
|
11.5
|
1.0
|
OE2
|
B:GLU269
|
4.1
|
14.8
|
1.0
|
CB
|
B:GLU269
|
4.1
|
10.0
|
1.0
|
CE1
|
B:HIS272
|
4.2
|
9.0
|
1.0
|
OD1
|
B:ASP340
|
4.4
|
11.3
|
1.0
|
CG
|
B:GLU233
|
4.4
|
11.7
|
1.0
|
NE2
|
B:HIS272
|
4.7
|
9.5
|
1.0
|
ND2
|
B:ASN267
|
4.7
|
11.7
|
1.0
|
C1
|
B:GOL506
|
4.7
|
17.1
|
1.0
|
ND1
|
B:HIS272
|
5.0
|
9.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5nh5
Go back to
Magnesium Binding Sites List in 5nh5
Magnesium binding site 3 out
of 4 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2
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 Native Xylose Isomerase From Piromyces E2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg503
b:5.9
occ:0.37
|
CA
|
C:CA501
|
0.3
|
23.1
|
0.4
|
FE
|
C:FE2502
|
0.5
|
11.7
|
0.3
|
OE1
|
C:GLU269
|
1.9
|
15.0
|
1.0
|
OD2
|
C:ASP340
|
2.1
|
13.2
|
1.0
|
OD2
|
C:ASP297
|
2.1
|
12.7
|
1.0
|
OE2
|
C:GLU233
|
2.2
|
14.4
|
1.0
|
O2
|
C:GOL505
|
2.5
|
18.0
|
1.0
|
O1
|
C:GOL505
|
2.5
|
26.2
|
1.0
|
CD
|
C:GLU269
|
3.2
|
13.7
|
1.0
|
CD
|
C:GLU233
|
3.2
|
12.6
|
1.0
|
CG
|
C:ASP340
|
3.2
|
12.1
|
1.0
|
CG
|
C:ASP297
|
3.3
|
11.6
|
1.0
|
C1
|
C:GOL505
|
3.3
|
23.0
|
1.0
|
C2
|
C:GOL505
|
3.3
|
20.9
|
1.0
|
OE1
|
C:GLU233
|
3.5
|
13.2
|
1.0
|
CB
|
C:ASP340
|
3.7
|
11.1
|
1.0
|
CB
|
C:ASP297
|
3.8
|
10.6
|
1.0
|
OE2
|
C:GLU269
|
4.0
|
14.2
|
1.0
|
CG
|
C:GLU269
|
4.1
|
11.8
|
1.0
|
CE1
|
C:HIS272
|
4.1
|
11.0
|
1.0
|
CB
|
C:GLU269
|
4.1
|
10.7
|
1.0
|
OD1
|
C:ASP340
|
4.2
|
13.0
|
1.0
|
OD1
|
C:ASP297
|
4.3
|
10.9
|
1.0
|
CG
|
C:GLU233
|
4.5
|
11.7
|
1.0
|
NE2
|
C:HIS272
|
4.5
|
11.0
|
1.0
|
C3
|
C:GOL505
|
4.7
|
18.7
|
1.0
|
ND2
|
C:ASN267
|
4.9
|
11.6
|
1.0
|
O
|
C:HOH642
|
4.9
|
34.1
|
1.0
|
ND1
|
C:HIS272
|
4.9
|
10.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5nh5
Go back to
Magnesium Binding Sites List in 5nh5
Magnesium binding site 4 out
of 4 in the Crystal Structure of Native Xylose Isomerase From Piromyces E2
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 Native Xylose Isomerase From Piromyces E2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg503
b:14.5
occ:0.35
|
CA
|
D:CA501
|
0.1
|
13.4
|
0.4
|
FE
|
D:FE2502
|
0.7
|
10.4
|
0.3
|
OD2
|
D:ASP297
|
1.9
|
12.8
|
1.0
|
OD2
|
D:ASP340
|
2.1
|
14.6
|
1.0
|
O2
|
D:GOL505
|
2.1
|
17.9
|
1.0
|
OE1
|
D:GLU269
|
2.2
|
12.3
|
1.0
|
OE2
|
D:GLU233
|
2.2
|
14.8
|
1.0
|
O3
|
D:GOL505
|
2.4
|
22.9
|
1.0
|
CD
|
D:GLU233
|
3.0
|
11.7
|
1.0
|
CG
|
D:ASP297
|
3.1
|
11.1
|
1.0
|
C2
|
D:GOL505
|
3.2
|
20.2
|
1.0
|
OE1
|
D:GLU233
|
3.2
|
12.6
|
1.0
|
CG
|
D:ASP340
|
3.3
|
10.9
|
1.0
|
C3
|
D:GOL505
|
3.3
|
23.1
|
1.0
|
CD
|
D:GLU269
|
3.4
|
11.0
|
1.0
|
CB
|
D:ASP297
|
3.7
|
9.8
|
1.0
|
CB
|
D:ASP340
|
3.7
|
10.2
|
1.0
|
OD1
|
D:ASP297
|
4.0
|
11.2
|
1.0
|
CG
|
D:GLU269
|
4.3
|
10.0
|
1.0
|
OD1
|
D:ASP340
|
4.3
|
11.3
|
1.0
|
OE2
|
D:GLU269
|
4.3
|
11.7
|
1.0
|
CB
|
D:GLU269
|
4.3
|
9.0
|
1.0
|
CG
|
D:GLU233
|
4.4
|
10.9
|
1.0
|
CE1
|
D:HIS272
|
4.4
|
9.4
|
1.0
|
C1
|
D:GOL505
|
4.5
|
18.3
|
1.0
|
O
|
D:HOH604
|
4.6
|
34.4
|
1.0
|
ND2
|
D:ASN267
|
4.6
|
10.5
|
1.0
|
NE2
|
D:HIS272
|
4.9
|
10.3
|
1.0
|
CZ2
|
D:TRP50
|
4.9
|
9.1
|
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 23:16:49 2024
|