Iron in PDB 3gas: Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
Enzymatic activity of Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
All present enzymatic activity of Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme:
1.14.99.3;
Protein crystallography data
The structure of Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme, PDB code: 3gas
was solved by
F.Jiang,
Y.L.Hu,
Y.Guo,
G.Guo,
Q.M.Zou,
D.C.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.87 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.330,
139.340,
152.900,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.2 /
22.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
(pdb code 3gas). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme, PDB code: 3gas:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3gas
Go back to
Iron Binding Sites List in 3gas
Iron binding site 1 out
of 6 in the Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
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 Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1290
b:19.7
occ:1.00
|
FE
|
A:HEM1290
|
0.0
|
19.7
|
1.0
|
ND
|
A:HEM1290
|
2.0
|
16.8
|
1.0
|
NC
|
A:HEM1290
|
2.0
|
21.3
|
1.0
|
NA
|
A:HEM1290
|
2.0
|
15.1
|
1.0
|
NB
|
A:HEM1290
|
2.0
|
18.1
|
1.0
|
NE2
|
A:HIS245
|
2.2
|
22.5
|
1.0
|
N1
|
A:AZI1296
|
2.3
|
29.1
|
1.0
|
C1D
|
A:HEM1290
|
3.0
|
22.5
|
1.0
|
C4C
|
A:HEM1290
|
3.0
|
18.0
|
1.0
|
C4D
|
A:HEM1290
|
3.0
|
19.6
|
1.0
|
C1C
|
A:HEM1290
|
3.0
|
20.8
|
1.0
|
C1B
|
A:HEM1290
|
3.0
|
22.2
|
1.0
|
C4A
|
A:HEM1290
|
3.0
|
18.1
|
1.0
|
C1A
|
A:HEM1290
|
3.0
|
16.0
|
1.0
|
N2
|
A:AZI1296
|
3.1
|
26.7
|
1.0
|
C4B
|
A:HEM1290
|
3.1
|
19.6
|
1.0
|
CD2
|
A:HIS245
|
3.1
|
21.3
|
1.0
|
CE1
|
A:HIS245
|
3.2
|
21.2
|
1.0
|
CHD
|
A:HEM1290
|
3.3
|
19.6
|
1.0
|
CHB
|
A:HEM1290
|
3.4
|
16.9
|
1.0
|
CHA
|
A:HEM1290
|
3.4
|
15.4
|
1.0
|
CHC
|
A:HEM1290
|
3.4
|
20.6
|
1.0
|
N3
|
A:AZI1296
|
4.0
|
18.3
|
1.0
|
C3D
|
A:HEM1290
|
4.2
|
20.0
|
1.0
|
C3A
|
A:HEM1290
|
4.3
|
14.0
|
1.0
|
C2D
|
A:HEM1290
|
4.3
|
20.0
|
1.0
|
C2C
|
A:HEM1290
|
4.3
|
18.5
|
1.0
|
C2A
|
A:HEM1290
|
4.3
|
13.4
|
1.0
|
ND1
|
A:HIS245
|
4.3
|
23.4
|
1.0
|
C3C
|
A:HEM1290
|
4.3
|
18.2
|
1.0
|
CG
|
A:HIS245
|
4.3
|
24.1
|
1.0
|
C2B
|
A:HEM1290
|
4.3
|
19.5
|
1.0
|
C3B
|
A:HEM1290
|
4.3
|
21.2
|
1.0
|
N
|
A:GLY225
|
4.4
|
16.3
|
1.0
|
CA
|
A:PHE224
|
5.0
|
16.8
|
1.0
|
|
Iron binding site 2 out
of 6 in 3gas
Go back to
Iron Binding Sites List in 3gas
Iron binding site 2 out
of 6 in the Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
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 Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1293
b:22.6
occ:1.00
|
FE
|
B:HEM1293
|
0.0
|
22.6
|
1.0
|
ND
|
B:HEM1293
|
2.0
|
24.0
|
1.0
|
NB
|
B:HEM1293
|
2.0
|
23.9
|
1.0
|
NC
|
B:HEM1293
|
2.0
|
25.0
|
1.0
|
NA
|
B:HEM1293
|
2.0
|
18.5
|
1.0
|
NE2
|
B:HIS245
|
2.2
|
25.9
|
1.0
|
N1
|
B:AZI1299
|
2.3
|
30.5
|
1.0
|
C4D
|
B:HEM1293
|
3.0
|
25.2
|
1.0
|
C4C
|
B:HEM1293
|
3.0
|
24.9
|
1.0
|
C1D
|
B:HEM1293
|
3.0
|
27.1
|
1.0
|
C1C
|
B:HEM1293
|
3.0
|
28.2
|
1.0
|
C1A
|
B:HEM1293
|
3.0
|
21.2
|
1.0
|
C1B
|
B:HEM1293
|
3.0
|
21.3
|
1.0
|
C4A
|
B:HEM1293
|
3.1
|
20.1
|
1.0
|
N2
|
B:AZI1299
|
3.1
|
32.8
|
1.0
|
C4B
|
B:HEM1293
|
3.1
|
24.9
|
1.0
|
CD2
|
B:HIS245
|
3.1
|
30.4
|
1.0
|
CE1
|
B:HIS245
|
3.2
|
25.6
|
1.0
|
CHA
|
B:HEM1293
|
3.4
|
22.2
|
1.0
|
CHD
|
B:HEM1293
|
3.4
|
25.3
|
1.0
|
CHB
|
B:HEM1293
|
3.4
|
20.2
|
1.0
|
CHC
|
B:HEM1293
|
3.4
|
28.8
|
1.0
|
N3
|
B:AZI1299
|
4.0
|
23.7
|
1.0
|
C3D
|
B:HEM1293
|
4.3
|
22.5
|
1.0
|
C2A
|
B:HEM1293
|
4.3
|
16.3
|
1.0
|
C3A
|
B:HEM1293
|
4.3
|
16.3
|
1.0
|
C2C
|
B:HEM1293
|
4.3
|
29.8
|
1.0
|
C3B
|
B:HEM1293
|
4.3
|
27.3
|
1.0
|
C2B
|
B:HEM1293
|
4.3
|
25.2
|
1.0
|
C2D
|
B:HEM1293
|
4.3
|
26.6
|
1.0
|
N
|
B:GLY225
|
4.3
|
21.1
|
1.0
|
CG
|
B:HIS245
|
4.3
|
32.2
|
1.0
|
C3C
|
B:HEM1293
|
4.3
|
26.9
|
1.0
|
ND1
|
B:HIS245
|
4.3
|
26.7
|
1.0
|
CA
|
B:PHE224
|
5.0
|
18.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 3gas
Go back to
Iron Binding Sites List in 3gas
Iron binding site 3 out
of 6 in the Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
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 Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1295
b:23.5
occ:1.00
|
FE
|
C:HEM1295
|
0.0
|
23.5
|
1.0
|
ND
|
C:HEM1295
|
2.0
|
22.9
|
1.0
|
NB
|
C:HEM1295
|
2.0
|
22.9
|
1.0
|
NC
|
C:HEM1295
|
2.0
|
24.1
|
1.0
|
NA
|
C:HEM1295
|
2.0
|
19.4
|
1.0
|
NE2
|
C:HIS245
|
2.2
|
26.9
|
1.0
|
N1
|
C:AZI1301
|
2.3
|
33.2
|
1.0
|
C4C
|
C:HEM1295
|
3.0
|
24.1
|
1.0
|
C4D
|
C:HEM1295
|
3.0
|
24.4
|
1.0
|
C1C
|
C:HEM1295
|
3.0
|
25.2
|
1.0
|
C1D
|
C:HEM1295
|
3.0
|
24.1
|
1.0
|
C1B
|
C:HEM1295
|
3.0
|
22.9
|
1.0
|
C1A
|
C:HEM1295
|
3.0
|
21.2
|
1.0
|
C4A
|
C:HEM1295
|
3.1
|
22.0
|
1.0
|
C4B
|
C:HEM1295
|
3.1
|
23.2
|
1.0
|
N2
|
C:AZI1301
|
3.1
|
34.4
|
1.0
|
CD2
|
C:HIS245
|
3.1
|
31.3
|
1.0
|
CE1
|
C:HIS245
|
3.2
|
24.2
|
1.0
|
CHA
|
C:HEM1295
|
3.4
|
19.4
|
1.0
|
CHB
|
C:HEM1295
|
3.4
|
22.7
|
1.0
|
CHD
|
C:HEM1295
|
3.4
|
25.5
|
1.0
|
CHC
|
C:HEM1295
|
3.4
|
25.4
|
1.0
|
N3
|
C:AZI1301
|
4.0
|
26.6
|
1.0
|
C3A
|
C:HEM1295
|
4.3
|
16.9
|
1.0
|
C2A
|
C:HEM1295
|
4.3
|
18.8
|
1.0
|
CG
|
C:HIS245
|
4.3
|
31.8
|
1.0
|
C3D
|
C:HEM1295
|
4.3
|
22.6
|
1.0
|
C2C
|
C:HEM1295
|
4.3
|
24.8
|
1.0
|
C3B
|
C:HEM1295
|
4.3
|
25.3
|
1.0
|
C2B
|
C:HEM1295
|
4.3
|
22.7
|
1.0
|
ND1
|
C:HIS245
|
4.3
|
27.1
|
1.0
|
C2D
|
C:HEM1295
|
4.3
|
24.3
|
1.0
|
C3C
|
C:HEM1295
|
4.3
|
26.3
|
1.0
|
N
|
C:GLY225
|
4.4
|
19.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 3gas
Go back to
Iron Binding Sites List in 3gas
Iron binding site 4 out
of 6 in the Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
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 Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1294
b:22.6
occ:1.00
|
FE
|
D:HEM1294
|
0.0
|
22.6
|
1.0
|
ND
|
D:HEM1294
|
2.0
|
22.9
|
1.0
|
NC
|
D:HEM1294
|
2.0
|
24.6
|
1.0
|
NB
|
D:HEM1294
|
2.0
|
22.1
|
1.0
|
NA
|
D:HEM1294
|
2.0
|
19.7
|
1.0
|
NE2
|
D:HIS245
|
2.2
|
28.2
|
1.0
|
N1
|
D:AZI1300
|
2.2
|
24.9
|
1.0
|
N2
|
D:AZI1300
|
2.9
|
31.4
|
1.0
|
C1D
|
D:HEM1294
|
3.0
|
26.1
|
1.0
|
C4D
|
D:HEM1294
|
3.0
|
23.8
|
1.0
|
C4C
|
D:HEM1294
|
3.0
|
23.0
|
1.0
|
C1C
|
D:HEM1294
|
3.0
|
24.5
|
1.0
|
C1B
|
D:HEM1294
|
3.0
|
22.2
|
1.0
|
C1A
|
D:HEM1294
|
3.0
|
19.5
|
1.0
|
C4B
|
D:HEM1294
|
3.1
|
24.1
|
1.0
|
C4A
|
D:HEM1294
|
3.1
|
20.2
|
1.0
|
CD2
|
D:HIS245
|
3.1
|
27.8
|
1.0
|
CE1
|
D:HIS245
|
3.2
|
28.3
|
1.0
|
CHA
|
D:HEM1294
|
3.4
|
20.9
|
1.0
|
CHD
|
D:HEM1294
|
3.4
|
24.6
|
1.0
|
CHB
|
D:HEM1294
|
3.4
|
20.5
|
1.0
|
CHC
|
D:HEM1294
|
3.4
|
24.7
|
1.0
|
N3
|
D:AZI1300
|
3.9
|
19.6
|
1.0
|
C3D
|
D:HEM1294
|
4.2
|
24.2
|
1.0
|
C2C
|
D:HEM1294
|
4.3
|
25.2
|
1.0
|
C3B
|
D:HEM1294
|
4.3
|
25.1
|
1.0
|
C2A
|
D:HEM1294
|
4.3
|
16.8
|
1.0
|
C2D
|
D:HEM1294
|
4.3
|
24.7
|
1.0
|
CG
|
D:HIS245
|
4.3
|
28.3
|
1.0
|
C3A
|
D:HEM1294
|
4.3
|
18.7
|
1.0
|
ND1
|
D:HIS245
|
4.3
|
24.2
|
1.0
|
C2B
|
D:HEM1294
|
4.3
|
22.5
|
1.0
|
C3C
|
D:HEM1294
|
4.3
|
24.8
|
1.0
|
N
|
D:GLY225
|
4.4
|
19.1
|
1.0
|
CA
|
D:PHE224
|
5.0
|
16.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 3gas
Go back to
Iron Binding Sites List in 3gas
Iron binding site 5 out
of 6 in the Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
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 Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe1291
b:18.5
occ:1.00
|
FE
|
E:HEM1291
|
0.0
|
18.5
|
1.0
|
ND
|
E:HEM1291
|
2.0
|
15.7
|
1.0
|
NC
|
E:HEM1291
|
2.0
|
17.3
|
1.0
|
NB
|
E:HEM1291
|
2.0
|
19.7
|
1.0
|
NA
|
E:HEM1291
|
2.0
|
15.2
|
1.0
|
NE2
|
E:HIS245
|
2.2
|
20.2
|
1.0
|
N1
|
E:AZI1297
|
2.3
|
25.4
|
1.0
|
N2
|
E:AZI1297
|
3.0
|
28.9
|
1.0
|
C4C
|
E:HEM1291
|
3.0
|
18.7
|
1.0
|
C1D
|
E:HEM1291
|
3.0
|
19.3
|
1.0
|
C1C
|
E:HEM1291
|
3.0
|
18.1
|
1.0
|
C4D
|
E:HEM1291
|
3.0
|
17.9
|
1.0
|
C1B
|
E:HEM1291
|
3.0
|
18.6
|
1.0
|
C4A
|
E:HEM1291
|
3.0
|
17.0
|
1.0
|
C1A
|
E:HEM1291
|
3.1
|
17.4
|
1.0
|
C4B
|
E:HEM1291
|
3.1
|
20.1
|
1.0
|
CD2
|
E:HIS245
|
3.2
|
25.7
|
1.0
|
CE1
|
E:HIS245
|
3.2
|
22.8
|
1.0
|
CHD
|
E:HEM1291
|
3.4
|
18.3
|
1.0
|
CHB
|
E:HEM1291
|
3.4
|
17.1
|
1.0
|
CHA
|
E:HEM1291
|
3.4
|
16.7
|
1.0
|
CHC
|
E:HEM1291
|
3.4
|
20.0
|
1.0
|
N3
|
E:AZI1297
|
3.9
|
18.7
|
1.0
|
C2C
|
E:HEM1291
|
4.3
|
20.6
|
1.0
|
C3A
|
E:HEM1291
|
4.3
|
15.8
|
1.0
|
C3D
|
E:HEM1291
|
4.3
|
17.4
|
1.0
|
C2A
|
E:HEM1291
|
4.3
|
12.5
|
1.0
|
C2D
|
E:HEM1291
|
4.3
|
19.7
|
1.0
|
C3C
|
E:HEM1291
|
4.3
|
18.2
|
1.0
|
C3B
|
E:HEM1291
|
4.3
|
22.2
|
1.0
|
C2B
|
E:HEM1291
|
4.3
|
20.6
|
1.0
|
ND1
|
E:HIS245
|
4.3
|
21.7
|
1.0
|
CG
|
E:HIS245
|
4.3
|
23.8
|
1.0
|
N
|
E:GLY225
|
4.4
|
15.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 3gas
Go back to
Iron Binding Sites List in 3gas
Iron binding site 6 out
of 6 in the Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme
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 Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1292
b:20.4
occ:1.00
|
FE
|
F:HEM1292
|
0.0
|
20.4
|
1.0
|
ND
|
F:HEM1292
|
2.0
|
20.1
|
1.0
|
NC
|
F:HEM1292
|
2.0
|
21.1
|
1.0
|
NB
|
F:HEM1292
|
2.0
|
20.5
|
1.0
|
NA
|
F:HEM1292
|
2.0
|
16.8
|
1.0
|
NE2
|
F:HIS245
|
2.2
|
22.7
|
1.0
|
N1
|
F:AZI1298
|
2.3
|
28.5
|
1.0
|
C1D
|
F:HEM1292
|
3.0
|
22.2
|
1.0
|
C4C
|
F:HEM1292
|
3.0
|
20.3
|
1.0
|
C4D
|
F:HEM1292
|
3.0
|
21.1
|
1.0
|
C1C
|
F:HEM1292
|
3.0
|
20.8
|
1.0
|
N2
|
F:AZI1298
|
3.0
|
31.6
|
1.0
|
C1B
|
F:HEM1292
|
3.1
|
21.4
|
1.0
|
C1A
|
F:HEM1292
|
3.1
|
18.3
|
1.0
|
C4A
|
F:HEM1292
|
3.1
|
17.2
|
1.0
|
C4B
|
F:HEM1292
|
3.1
|
21.7
|
1.0
|
CD2
|
F:HIS245
|
3.1
|
27.8
|
1.0
|
CE1
|
F:HIS245
|
3.2
|
22.3
|
1.0
|
CHD
|
F:HEM1292
|
3.4
|
21.4
|
1.0
|
CHA
|
F:HEM1292
|
3.4
|
19.4
|
1.0
|
CHB
|
F:HEM1292
|
3.4
|
18.6
|
1.0
|
CHC
|
F:HEM1292
|
3.4
|
22.1
|
1.0
|
N3
|
F:AZI1298
|
4.0
|
24.0
|
1.0
|
C3D
|
F:HEM1292
|
4.3
|
21.2
|
1.0
|
C2C
|
F:HEM1292
|
4.3
|
24.2
|
1.0
|
C3A
|
F:HEM1292
|
4.3
|
15.3
|
1.0
|
C2D
|
F:HEM1292
|
4.3
|
22.2
|
1.0
|
C2A
|
F:HEM1292
|
4.3
|
15.8
|
1.0
|
CG
|
F:HIS245
|
4.3
|
25.1
|
1.0
|
C3B
|
F:HEM1292
|
4.3
|
24.8
|
1.0
|
C3C
|
F:HEM1292
|
4.3
|
22.7
|
1.0
|
C2B
|
F:HEM1292
|
4.3
|
20.8
|
1.0
|
ND1
|
F:HIS245
|
4.3
|
23.0
|
1.0
|
N
|
F:GLY225
|
4.4
|
19.4
|
1.0
|
|
Reference:
F.Jiang,
Y.L.Hu,
Y.Guo,
G.Guo,
Q.M.Zou,
D.C.Wang.
Crystal Structure of Helicobacter Pylori Heme Oxygenase Hugz in Complex with Heme To Be Published.
Page generated: Sun Aug 4 10:26:34 2024
|