Iron in PDB 6po0: The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution
Enzymatic activity of The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution
All present enzymatic activity of The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution:
1.11.1.6;
Protein crystallography data
The structure of The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution, PDB code: 6po0
was solved by
A.Mcpherson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
119.57 /
1.75
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.984,
140.386,
228.177,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.3 /
20.7
|
Iron Binding Sites:
The binding sites of Iron atom in the The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution
(pdb code 6po0). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution, PDB code: 6po0:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6po0
Go back to
Iron Binding Sites List in 6po0
Iron binding site 1 out
of 4 in the The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:33.0
occ:1.00
|
FE
|
A:HEM601
|
0.0
|
33.0
|
1.0
|
|
ND
|
A:HEM601
|
1.9
|
32.3
|
1.0
|
|
OH
|
A:TYR357
|
1.9
|
29.3
|
1.0
|
|
NA
|
A:HEM601
|
2.0
|
29.7
|
1.0
|
|
NC
|
A:HEM601
|
2.1
|
40.5
|
1.0
|
|
NB
|
A:HEM601
|
2.1
|
34.5
|
1.0
|
|
C4D
|
A:HEM601
|
2.9
|
32.5
|
1.0
|
|
C1A
|
A:HEM601
|
3.0
|
32.4
|
1.0
|
|
C1D
|
A:HEM601
|
3.0
|
33.1
|
1.0
|
|
CZ
|
A:TYR357
|
3.0
|
27.8
|
1.0
|
|
C4B
|
A:HEM601
|
3.0
|
36.8
|
1.0
|
|
C4A
|
A:HEM601
|
3.0
|
32.3
|
1.0
|
|
C4C
|
A:HEM601
|
3.1
|
41.1
|
1.0
|
|
C1C
|
A:HEM601
|
3.1
|
43.4
|
1.0
|
|
C1B
|
A:HEM601
|
3.1
|
36.1
|
1.0
|
|
CHA
|
A:HEM601
|
3.3
|
31.0
|
1.0
|
|
CHC
|
A:HEM601
|
3.4
|
36.5
|
1.0
|
|
HE
|
A:ARG353
|
3.4
|
31.4
|
1.0
|
|
CHD
|
A:HEM601
|
3.5
|
33.6
|
1.0
|
|
CHB
|
A:HEM601
|
3.5
|
31.7
|
1.0
|
|
HH21
|
A:ARG353
|
3.6
|
36.0
|
1.0
|
|
HE2
|
A:TYR357
|
3.6
|
26.8
|
1.0
|
|
CE2
|
A:TYR357
|
3.7
|
26.8
|
1.0
|
|
O
|
A:HOH862
|
3.8
|
60.0
|
1.0
|
|
CE1
|
A:TYR357
|
3.9
|
26.7
|
1.0
|
|
HE1
|
A:TYR357
|
3.9
|
26.7
|
1.0
|
|
HZ
|
A:PHE160
|
3.9
|
33.2
|
1.0
|
|
HG21
|
A:VAL73
|
4.0
|
37.7
|
1.0
|
|
NE
|
A:ARG353
|
4.2
|
31.4
|
1.0
|
|
C2A
|
A:HEM601
|
4.2
|
30.7
|
1.0
|
|
C3A
|
A:HEM601
|
4.2
|
31.4
|
1.0
|
|
C3D
|
A:HEM601
|
4.2
|
31.4
|
1.0
|
|
C2D
|
A:HEM601
|
4.2
|
31.1
|
1.0
|
|
HE2
|
A:HIS74
|
4.2
|
35.4
|
1.0
|
|
HHA
|
A:HEM601
|
4.3
|
31.0
|
1.0
|
|
C3B
|
A:HEM601
|
4.3
|
37.5
|
1.0
|
|
C2C
|
A:HEM601
|
4.3
|
47.8
|
1.0
|
|
HG23
|
A:VAL73
|
4.3
|
37.7
|
1.0
|
|
C3C
|
A:HEM601
|
4.3
|
45.8
|
1.0
|
|
NH2
|
A:ARG353
|
4.3
|
36.0
|
1.0
|
|
C2B
|
A:HEM601
|
4.3
|
35.8
|
1.0
|
|
HHC
|
A:HEM601
|
4.3
|
36.5
|
1.0
|
|
HD2
|
A:HIS74
|
4.4
|
37.1
|
1.0
|
|
HHD
|
A:HEM601
|
4.4
|
33.6
|
1.0
|
|
CZ
|
A:PHE160
|
4.4
|
33.2
|
1.0
|
|
HHB
|
A:HEM601
|
4.4
|
31.7
|
1.0
|
|
CG2
|
A:VAL73
|
4.6
|
37.7
|
1.0
|
|
NE2
|
A:HIS74
|
4.6
|
35.4
|
1.0
|
|
CZ
|
A:ARG353
|
4.7
|
34.4
|
1.0
|
|
CD2
|
A:HIS74
|
4.7
|
37.1
|
1.0
|
|
HG2
|
A:ARG353
|
4.7
|
28.2
|
1.0
|
|
HE1
|
A:PHE160
|
4.8
|
34.7
|
1.0
|
|
CE1
|
A:PHE160
|
4.9
|
34.7
|
1.0
|
|
HG22
|
A:VAL73
|
4.9
|
37.7
|
1.0
|
|
HH22
|
A:ARG353
|
4.9
|
36.0
|
1.0
|
|
CD2
|
A:TYR357
|
5.0
|
27.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 6po0
Go back to
Iron Binding Sites List in 6po0
Iron binding site 2 out
of 4 in the The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe601
b:30.3
occ:1.00
|
FE
|
B:HEM601
|
0.0
|
30.3
|
1.0
|
|
OH
|
B:TYR357
|
1.9
|
29.8
|
1.0
|
|
ND
|
B:HEM601
|
1.9
|
28.2
|
1.0
|
|
NA
|
B:HEM601
|
2.0
|
29.2
|
1.0
|
|
NC
|
B:HEM601
|
2.1
|
37.5
|
1.0
|
|
NB
|
B:HEM601
|
2.1
|
30.8
|
1.0
|
|
C4D
|
B:HEM601
|
3.0
|
30.1
|
1.0
|
|
C1D
|
B:HEM601
|
3.0
|
31.1
|
1.0
|
|
C1A
|
B:HEM601
|
3.0
|
28.6
|
1.0
|
|
C4B
|
B:HEM601
|
3.0
|
31.6
|
1.0
|
|
CZ
|
B:TYR357
|
3.0
|
28.1
|
1.0
|
|
C4C
|
B:HEM601
|
3.0
|
35.9
|
1.0
|
|
C4A
|
B:HEM601
|
3.0
|
29.0
|
1.0
|
|
C1B
|
B:HEM601
|
3.1
|
27.3
|
1.0
|
|
C1C
|
B:HEM601
|
3.1
|
36.3
|
1.0
|
|
CHC
|
B:HEM601
|
3.4
|
33.5
|
1.0
|
|
CHA
|
B:HEM601
|
3.4
|
28.4
|
1.0
|
|
CHD
|
B:HEM601
|
3.4
|
30.5
|
1.0
|
|
HE
|
B:ARG353
|
3.4
|
31.1
|
1.0
|
|
CHB
|
B:HEM601
|
3.5
|
28.8
|
1.0
|
|
HH21
|
B:ARG353
|
3.6
|
36.9
|
1.0
|
|
HE2
|
B:TYR357
|
3.7
|
28.6
|
1.0
|
|
CE2
|
B:TYR357
|
3.8
|
28.6
|
1.0
|
|
O
|
B:HOH803
|
3.8
|
47.9
|
1.0
|
|
HZ
|
B:PHE160
|
3.9
|
25.5
|
1.0
|
|
HE1
|
B:TYR357
|
3.9
|
27.1
|
1.0
|
|
CE1
|
B:TYR357
|
3.9
|
27.1
|
1.0
|
|
HG21
|
B:VAL73
|
4.0
|
37.0
|
1.0
|
|
NE
|
B:ARG353
|
4.1
|
31.1
|
1.0
|
|
C2A
|
B:HEM601
|
4.2
|
28.1
|
1.0
|
|
C3A
|
B:HEM601
|
4.2
|
31.7
|
1.0
|
|
C2D
|
B:HEM601
|
4.3
|
31.0
|
1.0
|
|
NH2
|
B:ARG353
|
4.3
|
36.9
|
1.0
|
|
C3D
|
B:HEM601
|
4.3
|
30.0
|
1.0
|
|
C3C
|
B:HEM601
|
4.3
|
45.4
|
1.0
|
|
C2C
|
B:HEM601
|
4.3
|
41.9
|
1.0
|
|
C2B
|
B:HEM601
|
4.3
|
30.0
|
1.0
|
|
C3B
|
B:HEM601
|
4.3
|
29.2
|
1.0
|
|
HG23
|
B:VAL73
|
4.3
|
37.0
|
1.0
|
|
CZ
|
B:PHE160
|
4.3
|
25.5
|
1.0
|
|
HHC
|
B:HEM601
|
4.3
|
33.5
|
1.0
|
|
HE2
|
B:HIS74
|
4.3
|
29.1
|
1.0
|
|
HHA
|
B:HEM601
|
4.3
|
28.4
|
1.0
|
|
HHD
|
B:HEM601
|
4.4
|
30.5
|
1.0
|
|
HHB
|
B:HEM601
|
4.4
|
28.8
|
1.0
|
|
HD2
|
B:HIS74
|
4.4
|
31.6
|
1.0
|
|
CG2
|
B:VAL73
|
4.6
|
37.0
|
1.0
|
|
CZ
|
B:ARG353
|
4.6
|
35.2
|
1.0
|
|
HG2
|
B:ARG353
|
4.7
|
28.2
|
1.0
|
|
NE2
|
B:HIS74
|
4.7
|
29.1
|
1.0
|
|
HE1
|
B:PHE160
|
4.8
|
28.5
|
1.0
|
|
CD2
|
B:HIS74
|
4.8
|
31.6
|
1.0
|
|
CE1
|
B:PHE160
|
4.8
|
28.5
|
1.0
|
|
HG22
|
B:VAL73
|
4.9
|
37.0
|
1.0
|
|
HH22
|
B:ARG353
|
4.9
|
36.9
|
1.0
|
|
CE2
|
B:PHE160
|
5.0
|
25.7
|
1.0
|
|
HE2
|
B:PHE160
|
5.0
|
25.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 6po0
Go back to
Iron Binding Sites List in 6po0
Iron binding site 3 out
of 4 in the The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe601
b:33.8
occ:1.00
|
FE
|
C:HEM601
|
0.0
|
33.8
|
1.0
|
|
OH
|
C:TYR357
|
1.8
|
28.8
|
1.0
|
|
ND
|
C:HEM601
|
1.9
|
32.5
|
1.0
|
|
NA
|
C:HEM601
|
2.0
|
34.1
|
1.0
|
|
NC
|
C:HEM601
|
2.1
|
43.4
|
1.0
|
|
NB
|
C:HEM601
|
2.1
|
36.4
|
1.0
|
|
O
|
C:HOH721
|
2.3
|
49.7
|
1.0
|
|
C1D
|
C:HEM601
|
2.9
|
33.7
|
1.0
|
|
CZ
|
C:TYR357
|
3.0
|
29.9
|
1.0
|
|
C4D
|
C:HEM601
|
3.0
|
31.4
|
1.0
|
|
C1A
|
C:HEM601
|
3.0
|
33.4
|
1.0
|
|
C4C
|
C:HEM601
|
3.0
|
43.7
|
1.0
|
|
C4A
|
C:HEM601
|
3.0
|
31.8
|
1.0
|
|
C4B
|
C:HEM601
|
3.0
|
38.2
|
1.0
|
|
C1B
|
C:HEM601
|
3.1
|
34.2
|
1.0
|
|
C1C
|
C:HEM601
|
3.1
|
46.7
|
1.0
|
|
CHD
|
C:HEM601
|
3.4
|
33.5
|
1.0
|
|
CHA
|
C:HEM601
|
3.4
|
32.9
|
1.0
|
|
CHB
|
C:HEM601
|
3.5
|
34.8
|
1.0
|
|
CHC
|
C:HEM601
|
3.5
|
40.1
|
1.0
|
|
HE
|
C:ARG353
|
3.5
|
36.3
|
1.0
|
|
HE2
|
C:TYR357
|
3.6
|
29.8
|
1.0
|
|
HH21
|
C:ARG353
|
3.6
|
34.2
|
1.0
|
|
CE2
|
C:TYR357
|
3.7
|
29.8
|
1.0
|
|
HZ
|
C:PHE160
|
3.9
|
37.3
|
1.0
|
|
CE1
|
C:TYR357
|
3.9
|
28.0
|
1.0
|
|
HG21
|
C:VAL73
|
3.9
|
41.4
|
1.0
|
|
HE1
|
C:TYR357
|
3.9
|
28.0
|
1.0
|
|
C2D
|
C:HEM601
|
4.2
|
31.5
|
1.0
|
|
C3A
|
C:HEM601
|
4.2
|
34.8
|
1.0
|
|
NE
|
C:ARG353
|
4.2
|
36.3
|
1.0
|
|
C2A
|
C:HEM601
|
4.2
|
30.8
|
1.0
|
|
C3D
|
C:HEM601
|
4.2
|
30.4
|
1.0
|
|
C3C
|
C:HEM601
|
4.3
|
50.4
|
1.0
|
|
HG23
|
C:VAL73
|
4.3
|
41.4
|
1.0
|
|
NH2
|
C:ARG353
|
4.3
|
34.2
|
1.0
|
|
C2C
|
C:HEM601
|
4.3
|
47.5
|
1.0
|
|
C3B
|
C:HEM601
|
4.3
|
39.1
|
1.0
|
|
C2B
|
C:HEM601
|
4.3
|
35.5
|
1.0
|
|
HHD
|
C:HEM601
|
4.3
|
33.5
|
1.0
|
|
HE2
|
C:HIS74
|
4.3
|
37.3
|
1.0
|
|
HHA
|
C:HEM601
|
4.4
|
32.9
|
1.0
|
|
O
|
C:HOH795
|
4.4
|
20.0
|
1.0
|
|
HD2
|
C:HIS74
|
4.4
|
38.4
|
1.0
|
|
HHB
|
C:HEM601
|
4.4
|
34.8
|
1.0
|
|
CZ
|
C:PHE160
|
4.4
|
37.3
|
1.0
|
|
HHC
|
C:HEM601
|
4.4
|
40.1
|
1.0
|
|
CG2
|
C:VAL73
|
4.5
|
41.4
|
1.0
|
|
CZ
|
C:ARG353
|
4.7
|
35.5
|
1.0
|
|
NE2
|
C:HIS74
|
4.7
|
37.3
|
1.0
|
|
CD2
|
C:HIS74
|
4.7
|
38.4
|
1.0
|
|
HG2
|
C:ARG353
|
4.8
|
37.2
|
1.0
|
|
HG22
|
C:VAL73
|
4.8
|
41.4
|
1.0
|
|
HE1
|
C:PHE160
|
4.8
|
39.0
|
1.0
|
|
HH22
|
C:ARG353
|
4.9
|
34.2
|
1.0
|
|
CE1
|
C:PHE160
|
4.9
|
39.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 6po0
Go back to
Iron Binding Sites List in 6po0
Iron binding site 4 out
of 4 in the The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Structure of the Orthorhombic (P212121) Crystal Form of Beef Liver Catalase at 1.85 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe601
b:44.3
occ:1.00
|
FE
|
D:HEM601
|
0.0
|
44.3
|
1.0
|
|
ND
|
D:HEM601
|
1.9
|
45.4
|
1.0
|
|
OH
|
D:TYR357
|
1.9
|
40.1
|
1.0
|
|
NA
|
D:HEM601
|
2.0
|
43.5
|
1.0
|
|
NC
|
D:HEM601
|
2.1
|
50.6
|
1.0
|
|
NB
|
D:HEM601
|
2.1
|
47.6
|
1.0
|
|
C1D
|
D:HEM601
|
2.9
|
47.0
|
1.0
|
|
C4D
|
D:HEM601
|
2.9
|
43.6
|
1.0
|
|
C1A
|
D:HEM601
|
3.0
|
42.3
|
1.0
|
|
C4C
|
D:HEM601
|
3.0
|
55.7
|
1.0
|
|
CZ
|
D:TYR357
|
3.1
|
44.3
|
1.0
|
|
C4B
|
D:HEM601
|
3.1
|
46.9
|
1.0
|
|
C4A
|
D:HEM601
|
3.1
|
42.1
|
1.0
|
|
C1B
|
D:HEM601
|
3.1
|
44.4
|
1.0
|
|
C1C
|
D:HEM601
|
3.1
|
54.3
|
1.0
|
|
CHD
|
D:HEM601
|
3.4
|
49.5
|
1.0
|
|
CHA
|
D:HEM601
|
3.4
|
41.3
|
1.0
|
|
HE
|
D:ARG353
|
3.4
|
44.0
|
1.0
|
|
CHC
|
D:HEM601
|
3.5
|
49.5
|
1.0
|
|
CHB
|
D:HEM601
|
3.5
|
41.5
|
1.0
|
|
HH21
|
D:ARG353
|
3.6
|
47.1
|
1.0
|
|
HE2
|
D:TYR357
|
3.7
|
40.9
|
1.0
|
|
O
|
D:HOH858
|
3.8
|
63.1
|
1.0
|
|
CE2
|
D:TYR357
|
3.8
|
40.9
|
1.0
|
|
HZ
|
D:PHE160
|
3.9
|
41.0
|
1.0
|
|
HG21
|
D:VAL73
|
3.9
|
42.0
|
1.0
|
|
CE1
|
D:TYR357
|
4.0
|
41.2
|
1.0
|
|
HE1
|
D:TYR357
|
4.0
|
41.2
|
1.0
|
|
C2D
|
D:HEM601
|
4.2
|
46.5
|
1.0
|
|
NE
|
D:ARG353
|
4.2
|
44.0
|
1.0
|
|
C3D
|
D:HEM601
|
4.2
|
44.4
|
1.0
|
|
HG23
|
D:VAL73
|
4.2
|
42.0
|
1.0
|
|
C2A
|
D:HEM601
|
4.2
|
39.6
|
1.0
|
|
HE2
|
D:HIS74
|
4.2
|
47.6
|
1.0
|
|
C3A
|
D:HEM601
|
4.3
|
43.6
|
1.0
|
|
NH2
|
D:ARG353
|
4.3
|
47.1
|
1.0
|
|
C3C
|
D:HEM601
|
4.3
|
57.4
|
1.0
|
|
HHD
|
D:HEM601
|
4.3
|
49.5
|
1.0
|
|
C2C
|
D:HEM601
|
4.3
|
54.2
|
1.0
|
|
HHA
|
D:HEM601
|
4.3
|
41.3
|
1.0
|
|
HD2
|
D:HIS74
|
4.3
|
44.3
|
1.0
|
|
C2B
|
D:HEM601
|
4.3
|
45.8
|
1.0
|
|
C3B
|
D:HEM601
|
4.3
|
46.6
|
1.0
|
|
CZ
|
D:PHE160
|
4.4
|
41.0
|
1.0
|
|
HHC
|
D:HEM601
|
4.4
|
49.5
|
1.0
|
|
HHB
|
D:HEM601
|
4.4
|
41.5
|
1.0
|
|
CG2
|
D:VAL73
|
4.5
|
42.0
|
1.0
|
|
NE2
|
D:HIS74
|
4.6
|
47.6
|
1.0
|
|
CZ
|
D:ARG353
|
4.6
|
45.3
|
1.0
|
|
CD2
|
D:HIS74
|
4.7
|
44.3
|
1.0
|
|
HG2
|
D:ARG353
|
4.7
|
40.1
|
1.0
|
|
HG22
|
D:VAL73
|
4.8
|
42.0
|
1.0
|
|
HE1
|
D:PHE160
|
4.8
|
44.9
|
1.0
|
|
HH22
|
D:ARG353
|
4.9
|
47.1
|
1.0
|
|
CE1
|
D:PHE160
|
4.9
|
44.9
|
1.0
|
|
Reference:
A.Mcpherson,
A.Mcpherson.
N/A N/A.
Page generated: Sun Dec 13 16:49:20 2020
|
