Iron in PDB 1th4: Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole
Enzymatic activity of Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole
All present enzymatic activity of Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole:
1.11.1.6;
Protein crystallography data
The structure of Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole, PDB code: 1th4
was solved by
R.Sugadev,
M.N.Ponnuswamy,
D.Kumaran,
S.Swaminathan,
K.Sekar,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.90 /
2.98
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.030,
141.090,
231.000,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.5 /
29.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole
(pdb code 1th4). 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 Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole, PDB code: 1th4:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1th4
Go back to
Iron Binding Sites List in 1th4
Iron binding site 1 out
of 4 in the Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole
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 Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe2000
b:83.9
occ:1.00
|
FE
|
A:HEM2000
|
0.0
|
83.9
|
1.0
|
NC
|
A:HEM2000
|
2.0
|
98.1
|
1.0
|
ND
|
A:HEM2000
|
2.0
|
89.1
|
1.0
|
NA
|
A:HEM2000
|
2.2
|
83.4
|
1.0
|
NB
|
A:HEM2000
|
2.3
|
91.4
|
1.0
|
OH
|
A:TYR357
|
2.3
|
50.1
|
1.0
|
C4D
|
A:HEM2000
|
3.0
|
84.7
|
1.0
|
C1C
|
A:HEM2000
|
3.0
|
98.8
|
1.0
|
C4C
|
A:HEM2000
|
3.1
|
0.5
|
1.0
|
C1D
|
A:HEM2000
|
3.1
|
92.8
|
1.0
|
C1A
|
A:HEM2000
|
3.1
|
82.9
|
1.0
|
C4B
|
A:HEM2000
|
3.2
|
94.5
|
1.0
|
C4A
|
A:HEM2000
|
3.3
|
82.7
|
1.0
|
C1B
|
A:HEM2000
|
3.3
|
93.6
|
1.0
|
CHA
|
A:HEM2000
|
3.4
|
81.5
|
1.0
|
CHC
|
A:HEM2000
|
3.5
|
96.0
|
1.0
|
CHD
|
A:HEM2000
|
3.5
|
98.7
|
1.0
|
CZ
|
A:TYR357
|
3.7
|
52.0
|
1.0
|
CHB
|
A:HEM2000
|
3.7
|
89.1
|
1.0
|
O
|
A:HOH2154
|
4.1
|
33.6
|
1.0
|
C3D
|
A:HEM2000
|
4.3
|
82.9
|
1.0
|
C2C
|
A:HEM2000
|
4.3
|
0.8
|
1.0
|
C2D
|
A:HEM2000
|
4.3
|
88.1
|
1.0
|
C3C
|
A:HEM2000
|
4.3
|
0.8
|
1.0
|
C2A
|
A:HEM2000
|
4.4
|
86.5
|
1.0
|
CE2
|
A:TYR357
|
4.4
|
51.3
|
1.0
|
C3A
|
A:HEM2000
|
4.4
|
82.6
|
1.0
|
C3B
|
A:HEM2000
|
4.5
|
98.3
|
1.0
|
CD
|
A:ARG353
|
4.5
|
80.5
|
1.0
|
NE
|
A:ARG353
|
4.5
|
95.0
|
1.0
|
C2B
|
A:HEM2000
|
4.5
|
99.7
|
1.0
|
CE1
|
A:TYR357
|
4.6
|
49.9
|
1.0
|
CG
|
A:ARG353
|
4.9
|
66.4
|
1.0
|
|
Iron binding site 2 out
of 4 in 1th4
Go back to
Iron Binding Sites List in 1th4
Iron binding site 2 out
of 4 in the Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole
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 Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe2001
b:64.2
occ:1.00
|
FE
|
B:HEM2001
|
0.0
|
64.2
|
1.0
|
ND
|
B:HEM2001
|
2.0
|
61.7
|
1.0
|
NB
|
B:HEM2001
|
2.0
|
33.4
|
1.0
|
NA
|
B:HEM2001
|
2.0
|
54.7
|
1.0
|
NC
|
B:HEM2001
|
2.3
|
56.0
|
1.0
|
OH
|
B:TYR357
|
2.8
|
6.4
|
1.0
|
C4D
|
B:HEM2001
|
3.0
|
62.9
|
1.0
|
C4B
|
B:HEM2001
|
3.0
|
23.6
|
1.0
|
C1A
|
B:HEM2001
|
3.0
|
57.4
|
1.0
|
C1D
|
B:HEM2001
|
3.0
|
59.5
|
1.0
|
C4A
|
B:HEM2001
|
3.1
|
50.1
|
1.0
|
C1B
|
B:HEM2001
|
3.1
|
34.6
|
1.0
|
C1C
|
B:HEM2001
|
3.2
|
56.4
|
1.0
|
CHC
|
B:HEM2001
|
3.3
|
36.7
|
1.0
|
CHA
|
B:HEM2001
|
3.4
|
63.5
|
1.0
|
C4C
|
B:HEM2001
|
3.4
|
66.2
|
1.0
|
CHB
|
B:HEM2001
|
3.5
|
36.2
|
1.0
|
CZ
|
B:TYR357
|
3.8
|
23.4
|
1.0
|
CHD
|
B:HEM2001
|
3.8
|
63.4
|
1.0
|
CD2
|
B:HIS74
|
3.9
|
38.3
|
1.0
|
NE2
|
B:HIS74
|
4.2
|
43.0
|
1.0
|
C3B
|
B:HEM2001
|
4.2
|
28.4
|
1.0
|
C2D
|
B:HEM2001
|
4.2
|
57.8
|
1.0
|
C3D
|
B:HEM2001
|
4.2
|
59.0
|
1.0
|
C2A
|
B:HEM2001
|
4.2
|
49.5
|
1.0
|
C3A
|
B:HEM2001
|
4.3
|
45.9
|
1.0
|
C2B
|
B:HEM2001
|
4.3
|
30.3
|
1.0
|
CE2
|
B:TYR357
|
4.3
|
28.0
|
1.0
|
C2C
|
B:HEM2001
|
4.5
|
65.5
|
1.0
|
NH2
|
B:ARG353
|
4.6
|
38.5
|
1.0
|
C3C
|
B:HEM2001
|
4.6
|
70.3
|
1.0
|
CE1
|
B:TYR357
|
4.6
|
29.1
|
1.0
|
CG
|
B:HIS74
|
4.6
|
39.3
|
1.0
|
CB
|
B:VAL73
|
4.6
|
24.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 1th4
Go back to
Iron Binding Sites List in 1th4
Iron binding site 3 out
of 4 in the Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole
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 Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe2002
b:68.1
occ:1.00
|
FE
|
C:HEM2002
|
0.0
|
68.1
|
1.0
|
ND
|
C:HEM2002
|
1.9
|
68.9
|
1.0
|
NC
|
C:HEM2002
|
2.0
|
66.5
|
1.0
|
NA
|
C:HEM2002
|
2.0
|
67.2
|
1.0
|
NB
|
C:HEM2002
|
2.0
|
55.9
|
1.0
|
OH
|
C:TYR357
|
2.8
|
36.0
|
1.0
|
C4D
|
C:HEM2002
|
3.0
|
67.9
|
1.0
|
C1A
|
C:HEM2002
|
3.0
|
70.6
|
1.0
|
C1D
|
C:HEM2002
|
3.0
|
63.7
|
1.0
|
C4C
|
C:HEM2002
|
3.0
|
71.4
|
1.0
|
C1C
|
C:HEM2002
|
3.0
|
66.3
|
1.0
|
C4A
|
C:HEM2002
|
3.1
|
58.1
|
1.0
|
C4B
|
C:HEM2002
|
3.1
|
51.8
|
1.0
|
C1B
|
C:HEM2002
|
3.1
|
57.8
|
1.0
|
CHA
|
C:HEM2002
|
3.4
|
72.5
|
1.0
|
CHD
|
C:HEM2002
|
3.4
|
67.2
|
1.0
|
CHC
|
C:HEM2002
|
3.4
|
55.7
|
1.0
|
CHB
|
C:HEM2002
|
3.5
|
53.5
|
1.0
|
CG2
|
C:VAL73
|
3.7
|
4.2
|
1.0
|
CZ
|
C:TYR357
|
3.8
|
52.7
|
1.0
|
CD2
|
C:HIS74
|
4.1
|
30.2
|
1.0
|
CE2
|
C:TYR357
|
4.2
|
49.7
|
1.0
|
NE2
|
C:HIS74
|
4.2
|
23.3
|
1.0
|
C2D
|
C:HEM2002
|
4.2
|
62.2
|
1.0
|
C3D
|
C:HEM2002
|
4.2
|
63.4
|
1.0
|
C2A
|
C:HEM2002
|
4.2
|
62.0
|
1.0
|
C3C
|
C:HEM2002
|
4.3
|
75.6
|
1.0
|
C2C
|
C:HEM2002
|
4.3
|
72.1
|
1.0
|
C3A
|
C:HEM2002
|
4.3
|
56.2
|
1.0
|
C3B
|
C:HEM2002
|
4.3
|
52.0
|
1.0
|
C2B
|
C:HEM2002
|
4.3
|
55.1
|
1.0
|
NH1
|
C:ARG353
|
4.6
|
52.4
|
1.0
|
CZ
|
C:PHE160
|
4.6
|
46.8
|
1.0
|
CE1
|
C:TYR357
|
4.9
|
55.3
|
1.0
|
CG
|
C:HIS74
|
4.9
|
30.8
|
1.0
|
CB
|
C:VAL73
|
5.0
|
14.5
|
1.0
|
CE1
|
C:HIS74
|
5.0
|
33.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 1th4
Go back to
Iron Binding Sites List in 1th4
Iron binding site 4 out
of 4 in the Crystal Structure of Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole
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 Nadph Depleted Bovine Liver Catalase Complexed with 3-Amino-1,2,4-Triazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe2003
b:51.4
occ:1.00
|
FE
|
D:HEM2003
|
0.0
|
51.4
|
1.0
|
NC
|
D:HEM2003
|
1.8
|
51.6
|
1.0
|
NA
|
D:HEM2003
|
1.9
|
36.8
|
1.0
|
ND
|
D:HEM2003
|
2.0
|
41.8
|
1.0
|
NB
|
D:HEM2003
|
2.0
|
38.6
|
1.0
|
OH
|
D:TYR357
|
2.2
|
4.2
|
1.0
|
N3A
|
D:3TR3074
|
2.5
|
0.8
|
1.0
|
C3
|
D:3TR3074
|
2.8
|
99.3
|
1.0
|
C1C
|
D:HEM2003
|
2.8
|
55.1
|
1.0
|
C4C
|
D:HEM2003
|
2.8
|
56.0
|
1.0
|
C1A
|
D:HEM2003
|
2.9
|
35.4
|
1.0
|
C4A
|
D:HEM2003
|
3.0
|
34.4
|
1.0
|
C1D
|
D:HEM2003
|
3.0
|
43.8
|
1.0
|
C4D
|
D:HEM2003
|
3.0
|
36.0
|
1.0
|
C1B
|
D:HEM2003
|
3.0
|
38.8
|
1.0
|
C4B
|
D:HEM2003
|
3.1
|
46.4
|
1.0
|
N4
|
D:3TR3074
|
3.1
|
96.9
|
1.0
|
CHC
|
D:HEM2003
|
3.2
|
50.7
|
1.0
|
CHD
|
D:HEM2003
|
3.3
|
48.7
|
1.0
|
CZ
|
D:TYR357
|
3.3
|
18.0
|
1.0
|
CHB
|
D:HEM2003
|
3.4
|
30.1
|
1.0
|
N2
|
D:3TR3074
|
3.4
|
99.8
|
1.0
|
CHA
|
D:HEM2003
|
3.4
|
42.8
|
1.0
|
NH2
|
D:ARG353
|
3.6
|
52.8
|
1.0
|
CE2
|
D:TYR357
|
3.8
|
21.1
|
1.0
|
C5
|
D:3TR3074
|
3.9
|
90.0
|
1.0
|
C2C
|
D:HEM2003
|
4.0
|
55.1
|
1.0
|
C3C
|
D:HEM2003
|
4.1
|
59.2
|
1.0
|
N1
|
D:3TR3074
|
4.1
|
94.6
|
1.0
|
C2A
|
D:HEM2003
|
4.2
|
34.1
|
1.0
|
C3A
|
D:HEM2003
|
4.2
|
33.3
|
1.0
|
C2D
|
D:HEM2003
|
4.3
|
40.4
|
1.0
|
C3D
|
D:HEM2003
|
4.3
|
34.9
|
1.0
|
C2B
|
D:HEM2003
|
4.3
|
47.1
|
1.0
|
C3B
|
D:HEM2003
|
4.3
|
46.9
|
1.0
|
NE
|
D:ARG353
|
4.4
|
45.4
|
1.0
|
CE1
|
D:TYR357
|
4.4
|
18.5
|
1.0
|
CD2
|
D:HIS74
|
4.4
|
69.0
|
1.0
|
CZ
|
D:ARG353
|
4.4
|
51.3
|
1.0
|
CG2
|
D:VAL73
|
4.4
|
57.8
|
1.0
|
NE2
|
D:HIS74
|
4.5
|
77.3
|
1.0
|
CZ
|
D:PHE160
|
4.9
|
28.6
|
1.0
|
|
Reference:
R.Sugadev,
M.N.Ponnuswamy,
D.Kumaran,
S.Swaminathan,
K.Sekar.
Crystal Structure of Bovine Liver Catalase To Be Published.
Page generated: Sat Aug 3 15:16:16 2024
|