Iron in PDB 3nwl: The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy
Enzymatic activity of The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy
All present enzymatic activity of The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy:
1.11.1.6;
Protein crystallography data
The structure of The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy, PDB code: 3nwl
was solved by
L.M.Foroughi,
Y.N.Kang,
A.J.Matzger,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.98 /
2.69
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.652,
173.744,
186.325,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.3 /
24.1
|
Iron Binding Sites:
The binding sites of Iron atom in the The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy
(pdb code 3nwl). 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 Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy, PDB code: 3nwl:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3nwl
Go back to
Iron Binding Sites List in 3nwl
Iron binding site 1 out
of 4 in the The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe527
b:10.0
occ:1.00
|
FE
|
A:HEM527
|
0.0
|
10.0
|
1.0
|
ND
|
A:HEM527
|
2.0
|
8.1
|
1.0
|
NB
|
A:HEM527
|
2.0
|
8.2
|
1.0
|
OH
|
A:TYR357
|
2.0
|
16.2
|
1.0
|
NC
|
A:HEM527
|
2.0
|
15.6
|
1.0
|
NA
|
A:HEM527
|
2.1
|
7.1
|
1.0
|
C4D
|
A:HEM527
|
3.0
|
8.6
|
1.0
|
C4B
|
A:HEM527
|
3.0
|
10.7
|
1.0
|
C1D
|
A:HEM527
|
3.0
|
8.6
|
1.0
|
C1C
|
A:HEM527
|
3.0
|
16.7
|
1.0
|
C1A
|
A:HEM527
|
3.0
|
5.1
|
1.0
|
C1B
|
A:HEM527
|
3.1
|
8.3
|
1.0
|
C4C
|
A:HEM527
|
3.1
|
16.5
|
1.0
|
C4A
|
A:HEM527
|
3.1
|
5.3
|
1.0
|
CZ
|
A:TYR357
|
3.1
|
16.1
|
1.0
|
CHA
|
A:HEM527
|
3.3
|
5.1
|
1.0
|
CHC
|
A:HEM527
|
3.4
|
11.5
|
1.0
|
CHD
|
A:HEM527
|
3.4
|
12.1
|
1.0
|
CHB
|
A:HEM527
|
3.5
|
6.5
|
1.0
|
CE2
|
A:TYR357
|
3.9
|
16.3
|
1.0
|
CE1
|
A:TYR357
|
3.9
|
16.0
|
1.0
|
C3D
|
A:HEM527
|
4.2
|
9.5
|
1.0
|
C3B
|
A:HEM527
|
4.2
|
11.5
|
1.0
|
C2D
|
A:HEM527
|
4.2
|
8.5
|
1.0
|
C2B
|
A:HEM527
|
4.3
|
8.3
|
1.0
|
C2C
|
A:HEM527
|
4.3
|
19.4
|
1.0
|
C2A
|
A:HEM527
|
4.3
|
5.4
|
1.0
|
C3C
|
A:HEM527
|
4.3
|
20.2
|
1.0
|
C3A
|
A:HEM527
|
4.3
|
5.7
|
1.0
|
NH2
|
A:ARG353
|
4.4
|
16.1
|
1.0
|
CZ
|
A:PHE160
|
4.4
|
17.2
|
1.0
|
NE
|
A:ARG353
|
4.5
|
16.4
|
1.0
|
NE2
|
A:HIS74
|
4.5
|
16.6
|
1.0
|
CG2
|
A:VAL73
|
4.6
|
16.8
|
1.0
|
CD2
|
A:HIS74
|
4.6
|
16.6
|
1.0
|
CZ
|
A:ARG353
|
4.7
|
16.3
|
1.0
|
CE1
|
A:PHE160
|
5.0
|
17.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 3nwl
Go back to
Iron Binding Sites List in 3nwl
Iron binding site 2 out
of 4 in the The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe527
b:12.7
occ:1.00
|
FE
|
B:HEM527
|
0.0
|
12.7
|
1.0
|
NC
|
B:HEM527
|
2.0
|
18.3
|
1.0
|
OH
|
B:TYR357
|
2.0
|
18.5
|
1.0
|
NA
|
B:HEM527
|
2.0
|
9.3
|
1.0
|
NB
|
B:HEM527
|
2.0
|
13.5
|
1.0
|
ND
|
B:HEM527
|
2.1
|
12.8
|
1.0
|
C1C
|
B:HEM527
|
3.0
|
21.1
|
1.0
|
C4C
|
B:HEM527
|
3.0
|
21.0
|
1.0
|
C4B
|
B:HEM527
|
3.0
|
16.8
|
1.0
|
CZ
|
B:TYR357
|
3.0
|
18.4
|
1.0
|
C1A
|
B:HEM527
|
3.0
|
8.1
|
1.0
|
C4A
|
B:HEM527
|
3.0
|
10.2
|
1.0
|
C4D
|
B:HEM527
|
3.1
|
14.2
|
1.0
|
C1B
|
B:HEM527
|
3.1
|
13.3
|
1.0
|
C1D
|
B:HEM527
|
3.1
|
13.7
|
1.0
|
CHC
|
B:HEM527
|
3.4
|
18.9
|
1.0
|
CHA
|
B:HEM527
|
3.4
|
11.2
|
1.0
|
CHD
|
B:HEM527
|
3.4
|
15.3
|
1.0
|
CHB
|
B:HEM527
|
3.4
|
11.7
|
1.0
|
CE2
|
B:TYR357
|
3.7
|
18.4
|
1.0
|
CE1
|
B:TYR357
|
4.0
|
18.2
|
1.0
|
C2C
|
B:HEM527
|
4.2
|
22.4
|
1.0
|
C3C
|
B:HEM527
|
4.2
|
23.5
|
1.0
|
C2A
|
B:HEM527
|
4.3
|
6.6
|
1.0
|
C3A
|
B:HEM527
|
4.3
|
8.6
|
1.0
|
C3B
|
B:HEM527
|
4.3
|
17.9
|
1.0
|
C2B
|
B:HEM527
|
4.3
|
14.9
|
1.0
|
C3D
|
B:HEM527
|
4.3
|
15.0
|
1.0
|
C2D
|
B:HEM527
|
4.3
|
15.4
|
1.0
|
NE
|
B:ARG353
|
4.4
|
18.5
|
1.0
|
CZ
|
B:PHE160
|
4.4
|
18.4
|
1.0
|
NE2
|
B:HIS74
|
4.6
|
19.5
|
1.0
|
NH2
|
B:ARG353
|
4.6
|
18.9
|
1.0
|
CD2
|
B:HIS74
|
4.6
|
19.3
|
1.0
|
CG2
|
B:VAL73
|
4.7
|
18.6
|
1.0
|
CZ
|
B:ARG353
|
4.7
|
18.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 3nwl
Go back to
Iron Binding Sites List in 3nwl
Iron binding site 3 out
of 4 in the The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe527
b:14.8
occ:1.00
|
FE
|
C:HEM527
|
0.0
|
14.8
|
1.0
|
NB
|
C:HEM527
|
2.0
|
12.0
|
1.0
|
OH
|
C:TYR357
|
2.0
|
19.6
|
1.0
|
ND
|
C:HEM527
|
2.0
|
11.0
|
1.0
|
NA
|
C:HEM527
|
2.1
|
12.9
|
1.0
|
NC
|
C:HEM527
|
2.1
|
16.8
|
1.0
|
C4B
|
C:HEM527
|
2.9
|
14.3
|
1.0
|
C4D
|
C:HEM527
|
3.0
|
14.2
|
1.0
|
C1A
|
C:HEM527
|
3.0
|
15.0
|
1.0
|
C1B
|
C:HEM527
|
3.0
|
12.4
|
1.0
|
C1C
|
C:HEM527
|
3.1
|
17.6
|
1.0
|
C1D
|
C:HEM527
|
3.1
|
13.9
|
1.0
|
C4A
|
C:HEM527
|
3.1
|
12.1
|
1.0
|
CZ
|
C:TYR357
|
3.1
|
19.4
|
1.0
|
C4C
|
C:HEM527
|
3.2
|
17.4
|
1.0
|
CHC
|
C:HEM527
|
3.3
|
15.6
|
1.0
|
CHA
|
C:HEM527
|
3.3
|
15.5
|
1.0
|
CHB
|
C:HEM527
|
3.5
|
11.1
|
1.0
|
CHD
|
C:HEM527
|
3.5
|
15.6
|
1.0
|
CE1
|
C:TYR357
|
3.7
|
19.2
|
1.0
|
CE2
|
C:TYR357
|
4.1
|
19.4
|
1.0
|
C3B
|
C:HEM527
|
4.1
|
14.6
|
1.0
|
C2B
|
C:HEM527
|
4.2
|
11.5
|
1.0
|
NE
|
C:ARG353
|
4.2
|
19.9
|
1.0
|
NH2
|
C:ARG353
|
4.2
|
19.9
|
1.0
|
C3D
|
C:HEM527
|
4.2
|
12.8
|
1.0
|
C2A
|
C:HEM527
|
4.3
|
15.0
|
1.0
|
C2D
|
C:HEM527
|
4.3
|
14.4
|
1.0
|
C3A
|
C:HEM527
|
4.3
|
14.2
|
1.0
|
C2C
|
C:HEM527
|
4.3
|
17.5
|
1.0
|
C3C
|
C:HEM527
|
4.4
|
17.7
|
1.0
|
CZ
|
C:PHE160
|
4.4
|
18.6
|
1.0
|
CZ
|
C:ARG353
|
4.6
|
20.0
|
1.0
|
NE2
|
C:HIS74
|
4.6
|
20.7
|
1.0
|
CD2
|
C:HIS74
|
4.7
|
20.5
|
1.0
|
CE1
|
C:PHE160
|
4.9
|
18.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 3nwl
Go back to
Iron Binding Sites List in 3nwl
Iron binding site 4 out
of 4 in the The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Crystal Structure of the P212121 Form of Bovine Liver Catalase Previously Characterized By Electron Microscopy within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe527
b:11.9
occ:1.00
|
FE
|
D:HEM527
|
0.0
|
11.9
|
1.0
|
ND
|
D:HEM527
|
2.0
|
5.6
|
1.0
|
OH
|
D:TYR357
|
2.0
|
20.9
|
1.0
|
NC
|
D:HEM527
|
2.0
|
11.5
|
1.0
|
NA
|
D:HEM527
|
2.1
|
7.6
|
1.0
|
NB
|
D:HEM527
|
2.1
|
10.1
|
1.0
|
C4D
|
D:HEM527
|
2.9
|
2.9
|
1.0
|
C1A
|
D:HEM527
|
3.0
|
8.3
|
1.0
|
C1C
|
D:HEM527
|
3.0
|
14.7
|
1.0
|
C1D
|
D:HEM527
|
3.0
|
7.8
|
1.0
|
C4B
|
D:HEM527
|
3.0
|
11.4
|
1.0
|
C4C
|
D:HEM527
|
3.1
|
12.7
|
1.0
|
CZ
|
D:TYR357
|
3.1
|
20.6
|
1.0
|
C1B
|
D:HEM527
|
3.1
|
9.6
|
1.0
|
C4A
|
D:HEM527
|
3.1
|
9.1
|
1.0
|
CHA
|
D:HEM527
|
3.3
|
4.8
|
1.0
|
CHC
|
D:HEM527
|
3.4
|
12.0
|
1.0
|
CHD
|
D:HEM527
|
3.5
|
10.1
|
1.0
|
CHB
|
D:HEM527
|
3.5
|
9.1
|
1.0
|
CE2
|
D:TYR357
|
3.7
|
20.3
|
1.0
|
CE1
|
D:TYR357
|
4.0
|
20.6
|
1.0
|
C3D
|
D:HEM527
|
4.2
|
3.1
|
1.0
|
NH2
|
D:ARG353
|
4.2
|
21.8
|
1.0
|
C2D
|
D:HEM527
|
4.2
|
5.9
|
1.0
|
C2C
|
D:HEM527
|
4.2
|
15.5
|
1.0
|
C3C
|
D:HEM527
|
4.3
|
14.5
|
1.0
|
C3B
|
D:HEM527
|
4.3
|
11.5
|
1.0
|
NE
|
D:ARG353
|
4.3
|
21.7
|
1.0
|
C2A
|
D:HEM527
|
4.3
|
8.8
|
1.0
|
C2B
|
D:HEM527
|
4.3
|
10.1
|
1.0
|
C3A
|
D:HEM527
|
4.3
|
8.5
|
1.0
|
CZ
|
D:PHE160
|
4.4
|
18.1
|
1.0
|
NE2
|
D:HIS74
|
4.5
|
18.4
|
1.0
|
CG2
|
D:VAL73
|
4.5
|
17.8
|
1.0
|
CD2
|
D:HIS74
|
4.5
|
18.2
|
1.0
|
CZ
|
D:ARG353
|
4.6
|
22.0
|
1.0
|
|
Reference:
L.M.Foroughi,
Y.N.Kang,
A.J.Matzger.
Polymer-Induced Heteronucleation For Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms Cryst.Growth Des. V. 11 1294 2011.
ISSN: ISSN 1528-7483
DOI: 10.1021/CG101518F
Page generated: Sun Aug 4 16:47:57 2024
|