Iron in PDB 8dwr: Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis
Enzymatic activity of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis
All present enzymatic activity of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis:
1.11.1.21;
Protein crystallography data
The structure of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis, PDB code: 8dwr
was solved by
A.Diaz-Vilchis,
B.Uribe-Vazquez,
A.Avila-Linares,
E.Rudino-Pinera,
X.Soberon,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.99 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.671,
150.817,
127.037,
90,
90.45,
90
|
R / Rfree (%)
|
18.1 /
22.7
|
Other elements in 8dwr:
The structure of Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis
(pdb code 8dwr). 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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis, PDB code: 8dwr:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8dwr
Go back to
Iron Binding Sites List in 8dwr
Iron binding site 1 out
of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis
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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:15.0
occ:1.00
|
FE
|
A:HEM801
|
0.0
|
15.0
|
1.0
|
NC
|
A:HEM801
|
2.0
|
11.6
|
1.0
|
NA
|
A:HEM801
|
2.0
|
14.1
|
1.0
|
ND
|
A:HEM801
|
2.1
|
14.6
|
1.0
|
NB
|
A:HEM801
|
2.1
|
12.2
|
1.0
|
NE2
|
A:HIS270
|
2.6
|
14.1
|
1.0
|
O2
|
A:TOX107
|
2.7
|
19.0
|
1.0
|
C4D
|
A:HEM801
|
3.0
|
12.3
|
1.0
|
C1D
|
A:HEM801
|
3.0
|
12.7
|
1.0
|
C1C
|
A:HEM801
|
3.1
|
15.1
|
1.0
|
C1A
|
A:HEM801
|
3.1
|
11.3
|
1.0
|
C4B
|
A:HEM801
|
3.1
|
14.2
|
1.0
|
C4C
|
A:HEM801
|
3.1
|
11.5
|
1.0
|
C4A
|
A:HEM801
|
3.1
|
15.4
|
1.0
|
C1B
|
A:HEM801
|
3.1
|
14.5
|
1.0
|
CD2
|
A:HIS270
|
3.3
|
14.0
|
1.0
|
CHA
|
A:HEM801
|
3.4
|
12.8
|
1.0
|
CHC
|
A:HEM801
|
3.4
|
12.1
|
1.0
|
CHD
|
A:HEM801
|
3.4
|
9.5
|
1.0
|
CHB
|
A:HEM801
|
3.5
|
11.0
|
1.0
|
O1
|
A:TOX107
|
3.5
|
23.5
|
1.0
|
CE1
|
A:HIS270
|
3.7
|
10.5
|
1.0
|
C2D
|
A:HEM801
|
4.2
|
10.6
|
1.0
|
C3D
|
A:HEM801
|
4.2
|
13.7
|
1.0
|
NE1
|
A:TOX107
|
4.3
|
11.8
|
1.0
|
C2A
|
A:HEM801
|
4.3
|
13.5
|
1.0
|
C2C
|
A:HEM801
|
4.3
|
11.5
|
1.0
|
C3C
|
A:HEM801
|
4.3
|
10.1
|
1.0
|
C3B
|
A:HEM801
|
4.3
|
12.0
|
1.0
|
C3A
|
A:HEM801
|
4.3
|
17.5
|
1.0
|
C2B
|
A:HEM801
|
4.3
|
13.9
|
1.0
|
O
|
A:HOH1195
|
4.4
|
18.1
|
1.0
|
CD1
|
A:TOX107
|
4.4
|
11.1
|
1.0
|
CG
|
A:HIS270
|
4.6
|
16.9
|
1.0
|
ND1
|
A:HIS270
|
4.7
|
15.9
|
1.0
|
O
|
A:HOH1404
|
4.9
|
25.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 8dwr
Go back to
Iron Binding Sites List in 8dwr
Iron binding site 2 out
of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis
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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe802
b:16.1
occ:1.00
|
FE
|
B:HEM802
|
0.0
|
16.1
|
1.0
|
NA
|
B:HEM802
|
2.0
|
14.9
|
1.0
|
ND
|
B:HEM802
|
2.0
|
14.5
|
1.0
|
NC
|
B:HEM802
|
2.1
|
14.6
|
1.0
|
NB
|
B:HEM802
|
2.1
|
12.7
|
1.0
|
NE2
|
B:HIS270
|
2.6
|
19.5
|
1.0
|
O2
|
B:TOX107
|
2.7
|
21.5
|
1.0
|
C1D
|
B:HEM802
|
3.0
|
14.1
|
1.0
|
C4D
|
B:HEM802
|
3.1
|
14.4
|
1.0
|
C4B
|
B:HEM802
|
3.1
|
15.8
|
1.0
|
C1A
|
B:HEM802
|
3.1
|
15.0
|
1.0
|
C4C
|
B:HEM802
|
3.1
|
13.7
|
1.0
|
C1B
|
B:HEM802
|
3.1
|
14.5
|
1.0
|
C4A
|
B:HEM802
|
3.1
|
15.5
|
1.0
|
C1C
|
B:HEM802
|
3.1
|
13.8
|
1.0
|
CD2
|
B:HIS270
|
3.3
|
13.8
|
1.0
|
CHD
|
B:HEM802
|
3.4
|
13.2
|
1.0
|
CHA
|
B:HEM802
|
3.4
|
14.0
|
1.0
|
CHC
|
B:HEM802
|
3.4
|
14.4
|
1.0
|
CHB
|
B:HEM802
|
3.4
|
15.7
|
1.0
|
O1
|
B:TOX107
|
3.5
|
25.7
|
1.0
|
CE1
|
B:HIS270
|
3.7
|
15.0
|
1.0
|
C2D
|
B:HEM802
|
4.2
|
13.2
|
1.0
|
C3D
|
B:HEM802
|
4.2
|
11.8
|
1.0
|
C3B
|
B:HEM802
|
4.3
|
17.8
|
1.0
|
C2B
|
B:HEM802
|
4.3
|
16.3
|
1.0
|
NE1
|
B:TOX107
|
4.3
|
17.2
|
1.0
|
C2A
|
B:HEM802
|
4.3
|
15.7
|
1.0
|
C3A
|
B:HEM802
|
4.3
|
17.3
|
1.0
|
C3C
|
B:HEM802
|
4.3
|
13.9
|
1.0
|
C2C
|
B:HEM802
|
4.3
|
13.5
|
1.0
|
CD1
|
B:TOX107
|
4.5
|
14.8
|
1.0
|
CG
|
B:HIS270
|
4.6
|
15.9
|
1.0
|
O
|
B:HOH1349
|
4.7
|
26.8
|
1.0
|
ND1
|
B:HIS270
|
4.7
|
17.4
|
1.0
|
O
|
B:HOH1219
|
4.9
|
19.3
|
1.0
|
|
Iron binding site 3 out
of 4 in 8dwr
Go back to
Iron Binding Sites List in 8dwr
Iron binding site 3 out
of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis
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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe801
b:20.7
occ:1.00
|
FE
|
C:HEM801
|
0.0
|
20.7
|
1.0
|
ND
|
C:HEM801
|
2.0
|
17.6
|
1.0
|
NC
|
C:HEM801
|
2.0
|
15.6
|
1.0
|
NA
|
C:HEM801
|
2.0
|
18.0
|
1.0
|
NB
|
C:HEM801
|
2.1
|
17.9
|
1.0
|
NE2
|
C:HIS270
|
2.6
|
23.4
|
1.0
|
O2
|
C:TOX107
|
2.7
|
21.3
|
1.0
|
C1D
|
C:HEM801
|
3.0
|
17.2
|
1.0
|
C4D
|
C:HEM801
|
3.0
|
20.9
|
1.0
|
C4C
|
C:HEM801
|
3.1
|
13.0
|
1.0
|
C1A
|
C:HEM801
|
3.1
|
18.8
|
1.0
|
C4B
|
C:HEM801
|
3.1
|
20.6
|
1.0
|
C1C
|
C:HEM801
|
3.1
|
21.0
|
1.0
|
C4A
|
C:HEM801
|
3.1
|
17.6
|
1.0
|
C1B
|
C:HEM801
|
3.1
|
16.4
|
1.0
|
CD2
|
C:HIS270
|
3.3
|
19.5
|
1.0
|
CHD
|
C:HEM801
|
3.4
|
16.5
|
1.0
|
CHA
|
C:HEM801
|
3.4
|
20.4
|
1.0
|
CHC
|
C:HEM801
|
3.4
|
18.8
|
1.0
|
CHB
|
C:HEM801
|
3.5
|
17.2
|
1.0
|
O1
|
C:TOX107
|
3.5
|
25.4
|
1.0
|
CE1
|
C:HIS270
|
3.7
|
21.0
|
1.0
|
NE1
|
C:TOX107
|
4.2
|
18.1
|
1.0
|
C2D
|
C:HEM801
|
4.2
|
18.5
|
1.0
|
C3D
|
C:HEM801
|
4.2
|
18.3
|
1.0
|
C2C
|
C:HEM801
|
4.3
|
15.8
|
1.0
|
C3C
|
C:HEM801
|
4.3
|
18.6
|
1.0
|
C2A
|
C:HEM801
|
4.3
|
17.1
|
1.0
|
C3B
|
C:HEM801
|
4.3
|
19.5
|
1.0
|
C2B
|
C:HEM801
|
4.3
|
19.3
|
1.0
|
C3A
|
C:HEM801
|
4.3
|
18.8
|
1.0
|
CD1
|
C:TOX107
|
4.4
|
16.7
|
1.0
|
O
|
C:HOH1192
|
4.5
|
26.8
|
1.0
|
CG
|
C:HIS270
|
4.5
|
23.4
|
1.0
|
ND1
|
C:HIS270
|
4.7
|
22.8
|
1.0
|
CH2
|
C:TRP321
|
5.0
|
19.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 8dwr
Go back to
Iron Binding Sites List in 8dwr
Iron binding site 4 out
of 4 in the Crystal Structure of the L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis
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 L333V Variant of Catalase-Peroxidase From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe801
b:21.6
occ:1.00
|
FE
|
D:HEM801
|
0.0
|
21.6
|
1.0
|
NC
|
D:HEM801
|
2.0
|
22.3
|
1.0
|
ND
|
D:HEM801
|
2.0
|
16.7
|
1.0
|
NA
|
D:HEM801
|
2.0
|
21.5
|
1.0
|
NB
|
D:HEM801
|
2.1
|
15.8
|
1.0
|
NE2
|
D:HIS270
|
2.6
|
25.4
|
1.0
|
O2
|
D:TOX107
|
2.7
|
26.2
|
1.0
|
C1D
|
D:HEM801
|
3.0
|
16.5
|
1.0
|
C4C
|
D:HEM801
|
3.0
|
18.4
|
1.0
|
C4D
|
D:HEM801
|
3.1
|
21.8
|
1.0
|
C1C
|
D:HEM801
|
3.1
|
18.4
|
1.0
|
C4A
|
D:HEM801
|
3.1
|
18.4
|
1.0
|
C4B
|
D:HEM801
|
3.1
|
21.7
|
1.0
|
C1B
|
D:HEM801
|
3.1
|
21.9
|
1.0
|
C1A
|
D:HEM801
|
3.1
|
19.7
|
1.0
|
CD2
|
D:HIS270
|
3.3
|
20.2
|
1.0
|
CHD
|
D:HEM801
|
3.4
|
18.2
|
1.0
|
O1
|
D:TOX107
|
3.4
|
32.0
|
1.0
|
CHA
|
D:HEM801
|
3.4
|
20.4
|
1.0
|
CHC
|
D:HEM801
|
3.4
|
22.3
|
1.0
|
CHB
|
D:HEM801
|
3.4
|
21.1
|
1.0
|
CE1
|
D:HIS270
|
3.7
|
22.5
|
1.0
|
NE1
|
D:TOX107
|
4.1
|
23.8
|
1.0
|
C2D
|
D:HEM801
|
4.2
|
20.1
|
1.0
|
C3D
|
D:HEM801
|
4.2
|
16.3
|
1.0
|
C3C
|
D:HEM801
|
4.3
|
19.2
|
1.0
|
C2C
|
D:HEM801
|
4.3
|
17.6
|
1.0
|
C2B
|
D:HEM801
|
4.3
|
20.7
|
1.0
|
C3B
|
D:HEM801
|
4.3
|
18.4
|
1.0
|
C2A
|
D:HEM801
|
4.3
|
20.9
|
1.0
|
C3A
|
D:HEM801
|
4.3
|
20.3
|
1.0
|
CD1
|
D:TOX107
|
4.3
|
19.3
|
1.0
|
CG
|
D:HIS270
|
4.6
|
20.8
|
1.0
|
ND1
|
D:HIS270
|
4.7
|
27.6
|
1.0
|
O
|
D:HOH1256
|
4.7
|
32.7
|
1.0
|
O
|
D:HOH1137
|
4.7
|
25.2
|
1.0
|
CH2
|
D:TRP321
|
5.0
|
23.4
|
1.0
|
|
Reference:
B.Uribe-Vazquez,
A.Diaz-Vilchis,
A.Avila-Linares,
G.Saab-Rincon,
Y.Marin-Tovar,
H.Flores-Soto,
N.Pastor-Colon,
E.Rudino-Pinera,
X.Soberon.
Crystal Structure and Biochemical Characterization of the Mycobacterium Tuberculosis Katg-L333V From A Clinical Isolate To Be Published.
Page generated: Sat Aug 10 00:35:45 2024
|