Iron in PDB 5nhb: Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
All present enzymatic activity of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions:
5.3.1.5;
Protein crystallography data
The structure of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions, PDB code: 5nhb
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)
|
45.30 /
2.40
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.539,
79.510,
92.230,
115.57,
89.96,
116.69
|
R / Rfree (%)
|
24.5 /
28.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
(pdb code 5nhb). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions, PDB code: 5nhb:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 5nhb
Go back to
Iron Binding Sites List in 5nhb
Iron binding site 1 out
of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:27.9
occ:1.00
|
OD2
|
A:ASP297
|
2.0
|
24.3
|
1.0
|
OE2
|
A:GLU233
|
2.0
|
23.5
|
1.0
|
OE1
|
A:GLU269
|
2.2
|
23.1
|
1.0
|
OD2
|
A:ASP340
|
2.2
|
24.2
|
1.0
|
CD
|
A:GLU233
|
2.8
|
23.9
|
1.0
|
OE1
|
A:GLU233
|
2.9
|
24.5
|
1.0
|
CG
|
A:ASP297
|
3.1
|
24.1
|
1.0
|
CG
|
A:ASP340
|
3.2
|
24.4
|
1.0
|
CD
|
A:GLU269
|
3.5
|
22.5
|
1.0
|
CB
|
A:ASP340
|
3.7
|
24.3
|
1.0
|
CB
|
A:ASP297
|
3.7
|
23.4
|
1.0
|
FE
|
A:FE2502
|
4.1
|
21.9
|
1.0
|
OD1
|
A:ASP297
|
4.2
|
24.6
|
1.0
|
OD1
|
A:ASP340
|
4.3
|
24.9
|
1.0
|
CG
|
A:GLU233
|
4.3
|
23.5
|
1.0
|
OE2
|
A:GLU269
|
4.3
|
22.4
|
1.0
|
CG
|
A:GLU269
|
4.4
|
22.1
|
1.0
|
CB
|
A:GLU269
|
4.6
|
22.0
|
1.0
|
CE1
|
A:HIS272
|
4.6
|
22.4
|
1.0
|
O
|
A:HOH703
|
4.6
|
19.7
|
1.0
|
ND2
|
A:ASN267
|
4.8
|
24.6
|
1.0
|
NE2
|
A:HIS272
|
4.9
|
22.2
|
1.0
|
CZ2
|
A:TRP50
|
4.9
|
26.6
|
1.0
|
|
Iron binding site 2 out
of 8 in 5nhb
Go back to
Iron Binding Sites List in 5nhb
Iron binding site 2 out
of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:21.9
occ:1.00
|
OE2
|
A:GLU269
|
2.2
|
22.4
|
1.0
|
NE2
|
A:HIS272
|
2.4
|
22.2
|
1.0
|
OD2
|
A:ASP308
|
2.6
|
22.6
|
1.0
|
O
|
A:HOH647
|
2.7
|
5.1
|
1.0
|
CD
|
A:GLU269
|
2.9
|
22.5
|
1.0
|
OE1
|
A:GLU269
|
2.9
|
23.1
|
1.0
|
CE1
|
A:HIS272
|
3.3
|
22.4
|
1.0
|
CD2
|
A:HIS272
|
3.5
|
21.6
|
1.0
|
OD2
|
A:ASP340
|
3.5
|
24.2
|
1.0
|
CG
|
A:ASP308
|
3.7
|
22.2
|
1.0
|
OD1
|
A:ASP310
|
3.9
|
22.8
|
1.0
|
FE
|
A:FE2501
|
4.1
|
27.9
|
1.0
|
NZ
|
A:LYS235
|
4.1
|
22.8
|
1.0
|
OD1
|
A:ASP308
|
4.2
|
21.7
|
1.0
|
OD2
|
A:ASP310
|
4.3
|
23.9
|
1.0
|
OE2
|
A:GLU233
|
4.3
|
23.5
|
1.0
|
CG
|
A:GLU269
|
4.4
|
22.1
|
1.0
|
ND1
|
A:HIS272
|
4.4
|
22.0
|
1.0
|
CG
|
A:ASP340
|
4.4
|
24.4
|
1.0
|
CG
|
A:ASP310
|
4.5
|
23.4
|
1.0
|
CG
|
A:HIS272
|
4.5
|
21.5
|
1.0
|
CE
|
A:LYS235
|
4.7
|
22.2
|
1.0
|
ND2
|
A:ASN299
|
4.9
|
22.3
|
1.0
|
OD1
|
A:ASP340
|
5.0
|
24.9
|
1.0
|
|
Iron binding site 3 out
of 8 in 5nhb
Go back to
Iron Binding Sites List in 5nhb
Iron binding site 3 out
of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:22.8
occ:1.00
|
OE2
|
B:GLU233
|
1.8
|
21.0
|
1.0
|
OD2
|
B:ASP297
|
2.0
|
21.6
|
1.0
|
OE1
|
B:GLU269
|
2.1
|
20.6
|
1.0
|
OD2
|
B:ASP340
|
2.3
|
21.2
|
1.0
|
O
|
B:HOH671
|
2.7
|
15.5
|
1.0
|
CD
|
B:GLU233
|
2.7
|
21.3
|
1.0
|
OE1
|
B:GLU233
|
2.9
|
21.7
|
1.0
|
CG
|
B:ASP297
|
3.1
|
21.6
|
1.0
|
CD
|
B:GLU269
|
3.3
|
20.2
|
1.0
|
CG
|
B:ASP340
|
3.4
|
21.3
|
1.0
|
CB
|
B:ASP297
|
3.6
|
21.2
|
1.0
|
FE
|
B:FE2502
|
3.7
|
17.3
|
1.0
|
CB
|
B:ASP340
|
3.8
|
21.4
|
1.0
|
CG
|
B:GLU233
|
4.1
|
21.2
|
1.0
|
OE2
|
B:GLU269
|
4.1
|
20.0
|
1.0
|
CG
|
B:GLU269
|
4.2
|
20.1
|
1.0
|
OD1
|
B:ASP297
|
4.2
|
22.0
|
1.0
|
CB
|
B:GLU269
|
4.3
|
20.2
|
1.0
|
CE1
|
B:HIS272
|
4.4
|
20.1
|
1.0
|
OD1
|
B:ASP340
|
4.4
|
21.6
|
1.0
|
O
|
B:HOH632
|
4.5
|
2.9
|
1.0
|
NE2
|
B:HIS272
|
4.7
|
19.9
|
1.0
|
ND2
|
B:ASN267
|
4.7
|
22.1
|
1.0
|
|
Iron binding site 4 out
of 8 in 5nhb
Go back to
Iron Binding Sites List in 5nhb
Iron binding site 4 out
of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:17.3
occ:1.00
|
O
|
B:HOH632
|
1.8
|
2.9
|
1.0
|
OE2
|
B:GLU269
|
2.3
|
20.0
|
1.0
|
NE2
|
B:HIS272
|
2.3
|
19.9
|
1.0
|
O
|
B:HOH623
|
2.4
|
13.6
|
1.0
|
OE1
|
B:GLU269
|
2.8
|
20.6
|
1.0
|
CD
|
B:GLU269
|
2.8
|
20.2
|
1.0
|
OD2
|
B:ASP308
|
2.9
|
19.9
|
1.0
|
CE1
|
B:HIS272
|
3.1
|
20.1
|
1.0
|
OD2
|
B:ASP340
|
3.4
|
21.2
|
1.0
|
CD2
|
B:HIS272
|
3.4
|
19.6
|
1.0
|
FE
|
B:FE2501
|
3.7
|
22.8
|
1.0
|
CG
|
B:ASP308
|
4.0
|
19.6
|
1.0
|
OE2
|
B:GLU233
|
4.0
|
21.0
|
1.0
|
OD1
|
B:ASP310
|
4.2
|
20.1
|
1.0
|
NZ
|
B:LYS235
|
4.2
|
19.9
|
1.0
|
ND1
|
B:HIS272
|
4.2
|
20.0
|
1.0
|
CG
|
B:GLU269
|
4.3
|
20.1
|
1.0
|
CG
|
B:ASP340
|
4.4
|
21.3
|
1.0
|
OD1
|
B:ASP308
|
4.4
|
19.4
|
1.0
|
CG
|
B:HIS272
|
4.4
|
19.6
|
1.0
|
OD2
|
B:ASP310
|
4.6
|
20.7
|
1.0
|
CE
|
B:LYS235
|
4.7
|
19.6
|
1.0
|
CG
|
B:ASP310
|
4.8
|
20.4
|
1.0
|
OD1
|
B:ASP340
|
5.0
|
21.6
|
1.0
|
CB
|
B:GLU269
|
5.0
|
20.2
|
1.0
|
CD
|
B:LYS235
|
5.0
|
19.8
|
1.0
|
|
Iron binding site 5 out
of 8 in 5nhb
Go back to
Iron Binding Sites List in 5nhb
Iron binding site 5 out
of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:25.7
occ:1.00
|
OE1
|
C:GLU269
|
2.1
|
23.9
|
1.0
|
OD2
|
C:ASP297
|
2.1
|
25.3
|
1.0
|
OE2
|
C:GLU233
|
2.1
|
24.4
|
1.0
|
OD2
|
C:ASP340
|
2.1
|
25.1
|
1.0
|
CD
|
C:GLU233
|
2.9
|
24.7
|
1.0
|
O
|
C:HOH646
|
3.0
|
10.7
|
1.0
|
OE1
|
C:GLU233
|
3.1
|
25.4
|
1.0
|
CG
|
C:ASP340
|
3.1
|
25.4
|
1.0
|
CG
|
C:ASP297
|
3.2
|
25.2
|
1.0
|
CD
|
C:GLU269
|
3.3
|
23.3
|
1.0
|
CB
|
C:ASP340
|
3.6
|
25.2
|
1.0
|
CB
|
C:ASP297
|
3.7
|
24.4
|
1.0
|
FE
|
C:FE2502
|
3.9
|
24.0
|
1.0
|
OE2
|
C:GLU269
|
4.1
|
23.0
|
1.0
|
O
|
C:HOH632
|
4.2
|
10.7
|
1.0
|
OD1
|
C:ASP340
|
4.2
|
25.8
|
1.0
|
OD1
|
C:ASP297
|
4.2
|
25.7
|
1.0
|
CG
|
C:GLU269
|
4.3
|
22.8
|
1.0
|
CG
|
C:GLU233
|
4.4
|
24.3
|
1.0
|
CB
|
C:GLU269
|
4.5
|
22.8
|
1.0
|
CE1
|
C:HIS272
|
4.5
|
23.0
|
1.0
|
NE2
|
C:HIS272
|
4.8
|
22.8
|
1.0
|
ND2
|
C:ASN267
|
4.9
|
25.6
|
1.0
|
CZ2
|
C:TRP50
|
4.9
|
27.7
|
1.0
|
|
Iron binding site 6 out
of 8 in 5nhb
Go back to
Iron Binding Sites List in 5nhb
Iron binding site 6 out
of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe502
b:24.0
occ:1.00
|
O
|
C:HOH632
|
2.1
|
10.7
|
1.0
|
OE2
|
C:GLU269
|
2.3
|
23.0
|
1.0
|
NE2
|
C:HIS272
|
2.5
|
22.8
|
1.0
|
OD2
|
C:ASP308
|
2.6
|
23.0
|
1.0
|
OE1
|
C:GLU269
|
3.0
|
23.9
|
1.0
|
CD
|
C:GLU269
|
3.0
|
23.3
|
1.0
|
CE1
|
C:HIS272
|
3.3
|
23.0
|
1.0
|
OD2
|
C:ASP340
|
3.5
|
25.1
|
1.0
|
CD2
|
C:HIS272
|
3.5
|
22.2
|
1.0
|
CG
|
C:ASP308
|
3.7
|
22.5
|
1.0
|
FE
|
C:FE2501
|
3.9
|
25.7
|
1.0
|
OD1
|
C:ASP310
|
4.0
|
23.3
|
1.0
|
NZ
|
C:LYS235
|
4.1
|
23.1
|
1.0
|
OD1
|
C:ASP308
|
4.2
|
22.0
|
1.0
|
OD2
|
C:ASP310
|
4.3
|
24.5
|
1.0
|
OE2
|
C:GLU233
|
4.3
|
24.4
|
1.0
|
CG
|
C:ASP340
|
4.4
|
25.4
|
1.0
|
CG
|
C:GLU269
|
4.5
|
22.8
|
1.0
|
ND1
|
C:HIS272
|
4.5
|
22.6
|
1.0
|
CG
|
C:ASP310
|
4.6
|
23.9
|
1.0
|
CG
|
C:HIS272
|
4.6
|
22.0
|
1.0
|
CE
|
C:LYS235
|
4.7
|
22.5
|
1.0
|
OD1
|
C:ASP340
|
4.9
|
25.8
|
1.0
|
CZ
|
A:PHE61
|
5.0
|
28.1
|
1.0
|
ND2
|
C:ASN299
|
5.0
|
23.1
|
1.0
|
|
Iron binding site 7 out
of 8 in 5nhb
Go back to
Iron Binding Sites List in 5nhb
Iron binding site 7 out
of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:19.3
occ:1.00
|
O
|
D:HOH624
|
1.9
|
7.8
|
1.0
|
OE2
|
D:GLU233
|
2.0
|
19.3
|
1.0
|
OE1
|
D:GLU269
|
2.1
|
18.9
|
1.0
|
OD2
|
D:ASP297
|
2.1
|
19.8
|
1.0
|
OD2
|
D:ASP340
|
2.2
|
19.5
|
1.0
|
CD
|
D:GLU233
|
2.8
|
19.6
|
1.0
|
OE1
|
D:GLU233
|
3.0
|
20.0
|
1.0
|
CG
|
D:ASP297
|
3.2
|
19.9
|
1.0
|
CG
|
D:ASP340
|
3.3
|
19.6
|
1.0
|
CD
|
D:GLU269
|
3.3
|
18.6
|
1.0
|
CB
|
D:ASP297
|
3.7
|
19.4
|
1.0
|
CB
|
D:ASP340
|
3.8
|
19.6
|
1.0
|
OE2
|
D:GLU269
|
4.1
|
18.4
|
1.0
|
FE
|
D:FE2502
|
4.2
|
18.8
|
1.0
|
CG
|
D:GLU233
|
4.2
|
19.5
|
1.0
|
CG
|
D:GLU269
|
4.3
|
18.4
|
1.0
|
OD1
|
D:ASP297
|
4.3
|
20.3
|
1.0
|
OD1
|
D:ASP340
|
4.3
|
19.9
|
1.0
|
CB
|
D:GLU269
|
4.4
|
18.5
|
1.0
|
CE1
|
D:HIS272
|
4.5
|
18.5
|
1.0
|
O
|
D:HOH676
|
4.5
|
13.1
|
1.0
|
NE2
|
D:HIS272
|
4.7
|
18.4
|
1.0
|
ND2
|
D:ASN267
|
4.8
|
20.4
|
1.0
|
CZ2
|
D:TRP50
|
5.0
|
21.0
|
1.0
|
|
Iron binding site 8 out
of 8 in 5nhb
Go back to
Iron Binding Sites List in 5nhb
Iron binding site 8 out
of 8 in the Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Xylose Isomerase From Piromyces E2 in Complex with Two FE2+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe502
b:18.8
occ:1.00
|
OE2
|
D:GLU269
|
2.3
|
18.4
|
1.0
|
OD2
|
D:ASP308
|
2.4
|
18.4
|
1.0
|
NE2
|
D:HIS272
|
2.4
|
18.4
|
1.0
|
O
|
D:HOH676
|
2.5
|
13.1
|
1.0
|
CD
|
D:GLU269
|
3.1
|
18.6
|
1.0
|
OE1
|
D:GLU269
|
3.2
|
18.9
|
1.0
|
CE1
|
D:HIS272
|
3.3
|
18.5
|
1.0
|
CD2
|
D:HIS272
|
3.4
|
18.1
|
1.0
|
CG
|
D:ASP308
|
3.5
|
18.2
|
1.0
|
OD2
|
D:ASP340
|
3.7
|
19.5
|
1.0
|
OD1
|
D:ASP310
|
3.9
|
18.6
|
1.0
|
NZ
|
D:LYS235
|
3.9
|
18.6
|
1.0
|
OD1
|
D:ASP308
|
4.0
|
18.0
|
1.0
|
FE
|
D:FE2501
|
4.2
|
19.3
|
1.0
|
OD2
|
D:ASP310
|
4.3
|
19.2
|
1.0
|
ND1
|
D:HIS272
|
4.4
|
18.4
|
1.0
|
CE
|
D:LYS235
|
4.5
|
18.3
|
1.0
|
CG
|
D:GLU269
|
4.5
|
18.4
|
1.0
|
CG
|
D:ASP310
|
4.5
|
18.9
|
1.0
|
OE2
|
D:GLU233
|
4.5
|
19.3
|
1.0
|
CG
|
D:HIS272
|
4.5
|
18.1
|
1.0
|
CG
|
D:ASP340
|
4.7
|
19.6
|
1.0
|
CZ
|
B:PHE61
|
4.8
|
22.6
|
1.0
|
CD
|
D:LYS235
|
4.9
|
18.5
|
1.0
|
CB
|
D:ASP308
|
4.9
|
18.4
|
1.0
|
ND2
|
D:ASN299
|
5.0
|
18.4
|
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: Tue Aug 6 06:11:26 2024
|