Iron in PDB 1p80: Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli
Enzymatic activity of Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli
All present enzymatic activity of Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli:
1.11.1.6;
Protein crystallography data
The structure of Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli, PDB code: 1p80
was solved by
P.Chelikani,
X.Carpena,
I.Fita,
P.C.Loewen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.80 /
1.65
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.760,
133.130,
122.500,
90.00,
109.50,
90.00
|
R / Rfree (%)
|
16.8 /
20.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli
(pdb code 1p80). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli, PDB code: 1p80:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1p80
Go back to
Iron Binding Sites List in 1p80
Iron binding site 1 out
of 4 in the Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli
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 the D181Q Variant of Catalase Hpii From E. Coli within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe760
b:10.6
occ:1.00
|
FE
|
A:HEM760
|
0.0
|
10.6
|
1.0
|
OH
|
A:TYR415
|
2.0
|
12.2
|
1.0
|
NB
|
A:HEM760
|
2.0
|
10.3
|
1.0
|
NC
|
A:HEM760
|
2.0
|
10.3
|
1.0
|
ND
|
A:HEM760
|
2.0
|
10.8
|
1.0
|
NA
|
A:HEM760
|
2.0
|
10.5
|
1.0
|
CZ
|
A:TYR415
|
3.0
|
10.1
|
1.0
|
C1B
|
A:HEM760
|
3.0
|
10.0
|
1.0
|
C1D
|
A:HEM760
|
3.0
|
10.4
|
1.0
|
C4A
|
A:HEM760
|
3.0
|
10.4
|
1.0
|
C4C
|
A:HEM760
|
3.0
|
9.6
|
1.0
|
C4B
|
A:HEM760
|
3.0
|
11.4
|
1.0
|
C1C
|
A:HEM760
|
3.1
|
10.4
|
1.0
|
C1A
|
A:HEM760
|
3.1
|
10.7
|
1.0
|
C4D
|
A:HEM760
|
3.1
|
10.5
|
1.0
|
CHB
|
A:HEM760
|
3.4
|
9.6
|
1.0
|
CHD
|
A:HEM760
|
3.4
|
10.1
|
1.0
|
CHC
|
A:HEM760
|
3.4
|
12.0
|
1.0
|
CHA
|
A:HEM760
|
3.5
|
10.4
|
1.0
|
CE1
|
A:TYR415
|
3.7
|
10.0
|
1.0
|
CE2
|
A:TYR415
|
3.9
|
10.6
|
1.0
|
NE
|
A:ARG411
|
4.1
|
11.3
|
1.0
|
NH2
|
A:ARG411
|
4.1
|
11.2
|
1.0
|
C2B
|
A:HEM760
|
4.2
|
11.6
|
1.0
|
C3B
|
A:HEM760
|
4.3
|
11.7
|
1.0
|
C3C
|
A:HEM760
|
4.3
|
10.2
|
1.0
|
C2C
|
A:HEM760
|
4.3
|
10.3
|
1.0
|
C2D
|
A:HEM760
|
4.3
|
10.7
|
1.0
|
C3A
|
A:HEM760
|
4.3
|
9.7
|
1.0
|
C3D
|
A:HEM760
|
4.3
|
11.4
|
1.0
|
C2A
|
A:HEM760
|
4.3
|
10.2
|
1.0
|
CZ
|
A:ARG411
|
4.5
|
11.4
|
1.0
|
O
|
A:HOH4173
|
4.7
|
14.1
|
1.0
|
CG2
|
A:VAL127
|
4.7
|
10.9
|
1.0
|
CZ
|
A:PHE214
|
4.7
|
11.8
|
1.0
|
CD2
|
A:HIS128
|
4.9
|
11.2
|
1.0
|
CD1
|
A:TYR415
|
4.9
|
11.2
|
1.0
|
NE2
|
A:HIS128
|
5.0
|
11.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 1p80
Go back to
Iron Binding Sites List in 1p80
Iron binding site 2 out
of 4 in the Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli
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 the D181Q Variant of Catalase Hpii From E. Coli within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe760
b:12.1
occ:1.00
|
FE
|
B:HEM760
|
0.0
|
12.1
|
1.0
|
OH
|
B:TYR415
|
2.0
|
13.9
|
1.0
|
NB
|
B:HEM760
|
2.0
|
12.9
|
1.0
|
NC
|
B:HEM760
|
2.0
|
12.6
|
1.0
|
NA
|
B:HEM760
|
2.0
|
12.6
|
1.0
|
ND
|
B:HEM760
|
2.0
|
12.8
|
1.0
|
CZ
|
B:TYR415
|
3.0
|
12.1
|
1.0
|
C4C
|
B:HEM760
|
3.0
|
12.1
|
1.0
|
C1B
|
B:HEM760
|
3.0
|
12.9
|
1.0
|
C4B
|
B:HEM760
|
3.0
|
12.9
|
1.0
|
C1C
|
B:HEM760
|
3.0
|
12.5
|
1.0
|
C1D
|
B:HEM760
|
3.1
|
12.3
|
1.0
|
C4A
|
B:HEM760
|
3.1
|
12.4
|
1.0
|
C1A
|
B:HEM760
|
3.1
|
12.2
|
1.0
|
C4D
|
B:HEM760
|
3.1
|
12.5
|
1.0
|
CHD
|
B:HEM760
|
3.4
|
13.4
|
1.0
|
CHC
|
B:HEM760
|
3.4
|
12.4
|
1.0
|
CHB
|
B:HEM760
|
3.4
|
11.9
|
1.0
|
CHA
|
B:HEM760
|
3.5
|
12.6
|
1.0
|
CE1
|
B:TYR415
|
3.6
|
12.5
|
1.0
|
CE2
|
B:TYR415
|
3.8
|
13.4
|
1.0
|
NE
|
B:ARG411
|
4.1
|
12.7
|
1.0
|
NH2
|
B:ARG411
|
4.2
|
10.0
|
1.0
|
C3C
|
B:HEM760
|
4.2
|
13.0
|
1.0
|
C2C
|
B:HEM760
|
4.2
|
13.2
|
1.0
|
C2B
|
B:HEM760
|
4.2
|
12.8
|
1.0
|
C3B
|
B:HEM760
|
4.3
|
12.5
|
1.0
|
C2D
|
B:HEM760
|
4.3
|
13.1
|
1.0
|
C2A
|
B:HEM760
|
4.3
|
11.2
|
1.0
|
C3A
|
B:HEM760
|
4.3
|
11.6
|
1.0
|
C3D
|
B:HEM760
|
4.3
|
12.8
|
1.0
|
CZ
|
B:ARG411
|
4.5
|
12.9
|
1.0
|
O
|
B:HOH4174
|
4.7
|
17.9
|
1.0
|
CZ
|
B:PHE214
|
4.7
|
15.2
|
1.0
|
CG2
|
B:VAL127
|
4.7
|
11.5
|
1.0
|
CD2
|
B:HIS128
|
4.9
|
12.7
|
1.0
|
CD1
|
B:TYR415
|
4.9
|
11.7
|
1.0
|
NE2
|
B:HIS128
|
4.9
|
13.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 1p80
Go back to
Iron Binding Sites List in 1p80
Iron binding site 3 out
of 4 in the Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli
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 the D181Q Variant of Catalase Hpii From E. Coli within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe760
b:11.7
occ:1.00
|
FE
|
C:HEM760
|
0.0
|
11.7
|
1.0
|
OH
|
C:TYR415
|
2.0
|
12.0
|
1.0
|
NC
|
C:HEM760
|
2.0
|
11.9
|
1.0
|
ND
|
C:HEM760
|
2.0
|
11.6
|
1.0
|
NA
|
C:HEM760
|
2.0
|
11.4
|
1.0
|
NB
|
C:HEM760
|
2.0
|
12.7
|
1.0
|
CZ
|
C:TYR415
|
3.0
|
13.0
|
1.0
|
C1D
|
C:HEM760
|
3.0
|
11.6
|
1.0
|
C4C
|
C:HEM760
|
3.0
|
11.1
|
1.0
|
C4B
|
C:HEM760
|
3.0
|
13.4
|
1.0
|
C1B
|
C:HEM760
|
3.0
|
12.0
|
1.0
|
C1C
|
C:HEM760
|
3.0
|
12.8
|
1.0
|
C4A
|
C:HEM760
|
3.1
|
11.3
|
1.0
|
C1A
|
C:HEM760
|
3.1
|
11.0
|
1.0
|
C4D
|
C:HEM760
|
3.1
|
11.0
|
1.0
|
CHD
|
C:HEM760
|
3.4
|
10.8
|
1.0
|
CHB
|
C:HEM760
|
3.4
|
11.3
|
1.0
|
CHC
|
C:HEM760
|
3.4
|
12.7
|
1.0
|
CHA
|
C:HEM760
|
3.5
|
11.8
|
1.0
|
CE1
|
C:TYR415
|
3.6
|
12.7
|
1.0
|
CE2
|
C:TYR415
|
3.8
|
13.1
|
1.0
|
NE
|
C:ARG411
|
4.0
|
12.1
|
1.0
|
NH2
|
C:ARG411
|
4.1
|
10.4
|
1.0
|
C3B
|
C:HEM760
|
4.2
|
12.6
|
1.0
|
C3C
|
C:HEM760
|
4.2
|
12.4
|
1.0
|
C2C
|
C:HEM760
|
4.3
|
12.4
|
1.0
|
C2B
|
C:HEM760
|
4.3
|
13.4
|
1.0
|
C2D
|
C:HEM760
|
4.3
|
11.2
|
1.0
|
C2A
|
C:HEM760
|
4.3
|
11.3
|
1.0
|
C3D
|
C:HEM760
|
4.3
|
11.1
|
1.0
|
C3A
|
C:HEM760
|
4.3
|
11.0
|
1.0
|
CZ
|
C:ARG411
|
4.5
|
11.6
|
1.0
|
O
|
C:HOH4172
|
4.7
|
18.1
|
1.0
|
CG2
|
C:VAL127
|
4.7
|
11.8
|
1.0
|
CZ
|
C:PHE214
|
4.8
|
13.8
|
1.0
|
CD1
|
C:TYR415
|
4.9
|
13.3
|
1.0
|
CD2
|
C:HIS128
|
4.9
|
12.2
|
1.0
|
NE2
|
C:HIS128
|
4.9
|
11.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 1p80
Go back to
Iron Binding Sites List in 1p80
Iron binding site 4 out
of 4 in the Crystal Structure of the D181Q Variant of Catalase Hpii From E. Coli
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 the D181Q Variant of Catalase Hpii From E. Coli within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe760
b:10.6
occ:1.00
|
FE
|
D:HEM760
|
0.0
|
10.6
|
1.0
|
NC
|
D:HEM760
|
2.0
|
10.7
|
1.0
|
NB
|
D:HEM760
|
2.0
|
11.5
|
1.0
|
OH
|
D:TYR415
|
2.0
|
12.4
|
1.0
|
ND
|
D:HEM760
|
2.0
|
10.9
|
1.0
|
NA
|
D:HEM760
|
2.0
|
10.7
|
1.0
|
CZ
|
D:TYR415
|
3.0
|
11.8
|
1.0
|
C4B
|
D:HEM760
|
3.0
|
11.9
|
1.0
|
C4C
|
D:HEM760
|
3.0
|
10.7
|
1.0
|
C1C
|
D:HEM760
|
3.0
|
10.2
|
1.0
|
C1B
|
D:HEM760
|
3.0
|
11.8
|
1.0
|
C1D
|
D:HEM760
|
3.0
|
11.2
|
1.0
|
C4A
|
D:HEM760
|
3.1
|
10.2
|
1.0
|
C1A
|
D:HEM760
|
3.1
|
9.9
|
1.0
|
C4D
|
D:HEM760
|
3.1
|
10.8
|
1.0
|
CHC
|
D:HEM760
|
3.4
|
12.2
|
1.0
|
CHD
|
D:HEM760
|
3.4
|
10.6
|
1.0
|
CHB
|
D:HEM760
|
3.4
|
10.4
|
1.0
|
CHA
|
D:HEM760
|
3.5
|
10.1
|
1.0
|
CE1
|
D:TYR415
|
3.7
|
11.7
|
1.0
|
CE2
|
D:TYR415
|
3.8
|
11.6
|
1.0
|
NE
|
D:ARG411
|
4.0
|
10.0
|
1.0
|
NH2
|
D:ARG411
|
4.1
|
10.7
|
1.0
|
C2C
|
D:HEM760
|
4.2
|
11.0
|
1.0
|
C3B
|
D:HEM760
|
4.2
|
12.2
|
1.0
|
C3C
|
D:HEM760
|
4.2
|
11.1
|
1.0
|
C2B
|
D:HEM760
|
4.3
|
12.0
|
1.0
|
C2D
|
D:HEM760
|
4.3
|
11.9
|
1.0
|
C2A
|
D:HEM760
|
4.3
|
9.8
|
1.0
|
C3A
|
D:HEM760
|
4.3
|
9.1
|
1.0
|
C3D
|
D:HEM760
|
4.3
|
12.1
|
1.0
|
CZ
|
D:ARG411
|
4.4
|
9.6
|
1.0
|
O
|
D:HOH4171
|
4.7
|
14.6
|
1.0
|
CG2
|
D:VAL127
|
4.7
|
10.4
|
1.0
|
CZ
|
D:PHE214
|
4.8
|
12.3
|
1.0
|
CD2
|
D:HIS128
|
4.9
|
11.2
|
1.0
|
CD1
|
D:TYR415
|
4.9
|
11.5
|
1.0
|
NE2
|
D:HIS128
|
4.9
|
11.4
|
1.0
|
|
Reference:
P.Chelikani,
X.Carpena,
I.Fita,
P.C.Loewen.
An Electrical Potential in the Access Channel of Catalases Enhances Catalysis J.Biol.Chem. V. 278 31290 2003.
ISSN: ISSN 0021-9258
PubMed: 12777389
DOI: 10.1074/JBC.M304076200
Page generated: Sat Aug 3 13:00:24 2024
|