Iron in PDB 5vj0: Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus
Protein crystallography data
The structure of Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus, PDB code: 5vj0
was solved by
D.A.Meekins,
P.Li,
B.V.Geisbrecht,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.45 /
1.93
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.870,
74.160,
118.640,
90.00,
108.17,
90.00
|
R / Rfree (%)
|
17.3 /
20.1
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus
(pdb code 5vj0). 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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus, PDB code: 5vj0:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5vj0
Go back to
Iron Binding Sites List in 5vj0
Iron binding site 1 out
of 4 in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus
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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:24.7
occ:1.00
|
FE
|
A:HEM500
|
0.0
|
24.7
|
1.0
|
ND
|
A:HEM500
|
2.0
|
17.7
|
1.0
|
NB
|
A:HEM500
|
2.0
|
21.5
|
1.0
|
NA
|
A:HEM500
|
2.0
|
22.8
|
1.0
|
NC
|
A:HEM500
|
2.0
|
25.1
|
1.0
|
NE2
|
A:HIS215
|
2.2
|
21.3
|
1.0
|
C4B
|
A:HEM500
|
3.0
|
23.6
|
1.0
|
C4D
|
A:HEM500
|
3.0
|
22.6
|
1.0
|
C1A
|
A:HEM500
|
3.0
|
23.5
|
1.0
|
C1C
|
A:HEM500
|
3.1
|
21.2
|
1.0
|
C1D
|
A:HEM500
|
3.1
|
23.6
|
1.0
|
C4C
|
A:HEM500
|
3.1
|
19.8
|
1.0
|
C4A
|
A:HEM500
|
3.1
|
22.7
|
1.0
|
C1B
|
A:HEM500
|
3.1
|
21.0
|
1.0
|
CD2
|
A:HIS215
|
3.2
|
22.9
|
1.0
|
CE1
|
A:HIS215
|
3.2
|
21.0
|
1.0
|
CHC
|
A:HEM500
|
3.4
|
20.2
|
1.0
|
CHA
|
A:HEM500
|
3.4
|
20.2
|
1.0
|
CHD
|
A:HEM500
|
3.4
|
24.1
|
1.0
|
CHB
|
A:HEM500
|
3.5
|
25.1
|
1.0
|
NH1
|
A:ARG232
|
4.2
|
22.0
|
1.0
|
C3B
|
A:HEM500
|
4.2
|
23.1
|
1.0
|
C2A
|
A:HEM500
|
4.3
|
22.6
|
1.0
|
C3D
|
A:HEM500
|
4.3
|
22.9
|
1.0
|
C3C
|
A:HEM500
|
4.3
|
21.1
|
1.0
|
C2B
|
A:HEM500
|
4.3
|
21.0
|
1.0
|
C2D
|
A:HEM500
|
4.3
|
21.9
|
1.0
|
C2C
|
A:HEM500
|
4.3
|
22.7
|
1.0
|
C3A
|
A:HEM500
|
4.3
|
22.3
|
1.0
|
CG
|
A:HIS215
|
4.3
|
24.1
|
1.0
|
ND1
|
A:HIS215
|
4.3
|
21.2
|
1.0
|
CE1
|
A:PHE248
|
4.7
|
18.3
|
1.0
|
CD
|
A:ARG232
|
4.7
|
20.3
|
1.0
|
OD1
|
A:ASP143
|
4.8
|
32.4
|
1.0
|
CE
|
A:MET276
|
4.8
|
21.2
|
1.0
|
CZ
|
A:ARG232
|
4.8
|
22.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 5vj0
Go back to
Iron Binding Sites List in 5vj0
Iron binding site 2 out
of 4 in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus
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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:28.7
occ:1.00
|
FE
|
B:HEM500
|
0.0
|
28.7
|
1.0
|
NC
|
B:HEM500
|
2.0
|
23.3
|
1.0
|
NA
|
B:HEM500
|
2.0
|
21.1
|
1.0
|
NB
|
B:HEM500
|
2.1
|
25.5
|
1.0
|
ND
|
B:HEM500
|
2.1
|
25.7
|
1.0
|
NE2
|
B:HIS215
|
2.3
|
24.2
|
1.0
|
C4C
|
B:HEM500
|
3.0
|
28.3
|
1.0
|
C4A
|
B:HEM500
|
3.0
|
25.1
|
1.0
|
C1C
|
B:HEM500
|
3.0
|
28.4
|
1.0
|
C1D
|
B:HEM500
|
3.1
|
27.2
|
1.0
|
C1B
|
B:HEM500
|
3.1
|
26.3
|
1.0
|
C4B
|
B:HEM500
|
3.1
|
28.9
|
1.0
|
C1A
|
B:HEM500
|
3.1
|
24.4
|
1.0
|
C4D
|
B:HEM500
|
3.1
|
26.7
|
1.0
|
CD2
|
B:HIS215
|
3.1
|
24.3
|
1.0
|
O
|
B:HOH614
|
3.2
|
32.8
|
1.0
|
CE1
|
B:HIS215
|
3.3
|
24.6
|
1.0
|
CHD
|
B:HEM500
|
3.4
|
28.5
|
1.0
|
CHB
|
B:HEM500
|
3.4
|
26.7
|
1.0
|
CHC
|
B:HEM500
|
3.4
|
27.8
|
1.0
|
CHA
|
B:HEM500
|
3.5
|
26.3
|
1.0
|
C3C
|
B:HEM500
|
4.2
|
26.6
|
1.0
|
C2C
|
B:HEM500
|
4.2
|
26.0
|
1.0
|
C3A
|
B:HEM500
|
4.3
|
25.6
|
1.0
|
NH1
|
B:ARG232
|
4.3
|
27.8
|
1.0
|
C2A
|
B:HEM500
|
4.3
|
23.7
|
1.0
|
C2D
|
B:HEM500
|
4.3
|
30.1
|
1.0
|
C2B
|
B:HEM500
|
4.3
|
24.3
|
1.0
|
C3B
|
B:HEM500
|
4.3
|
26.9
|
1.0
|
C3D
|
B:HEM500
|
4.3
|
28.6
|
1.0
|
CG
|
B:HIS215
|
4.3
|
26.4
|
1.0
|
ND1
|
B:HIS215
|
4.4
|
28.0
|
1.0
|
CE1
|
B:PHE248
|
4.5
|
27.2
|
1.0
|
CD
|
B:ARG232
|
4.6
|
26.1
|
1.0
|
OD1
|
B:ASP143
|
4.8
|
32.9
|
1.0
|
CZ
|
B:ARG232
|
4.8
|
28.1
|
1.0
|
CE
|
B:MET276
|
4.9
|
26.2
|
1.0
|
NE
|
B:ARG232
|
5.0
|
25.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 5vj0
Go back to
Iron Binding Sites List in 5vj0
Iron binding site 3 out
of 4 in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus
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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:17.2
occ:1.00
|
FE
|
C:HEM500
|
0.0
|
17.2
|
1.0
|
NC
|
C:HEM500
|
2.0
|
17.0
|
1.0
|
ND
|
C:HEM500
|
2.1
|
15.5
|
1.0
|
NA
|
C:HEM500
|
2.1
|
17.5
|
1.0
|
NB
|
C:HEM500
|
2.1
|
15.6
|
1.0
|
NE2
|
C:HIS215
|
2.2
|
14.4
|
1.0
|
C4A
|
C:HEM500
|
3.0
|
17.2
|
1.0
|
C4C
|
C:HEM500
|
3.0
|
17.4
|
1.0
|
C1D
|
C:HEM500
|
3.0
|
15.4
|
1.0
|
C1B
|
C:HEM500
|
3.1
|
16.8
|
1.0
|
C1C
|
C:HEM500
|
3.1
|
18.1
|
1.0
|
C4D
|
C:HEM500
|
3.1
|
17.9
|
1.0
|
C4B
|
C:HEM500
|
3.1
|
17.2
|
1.0
|
C1A
|
C:HEM500
|
3.1
|
16.8
|
1.0
|
CD2
|
C:HIS215
|
3.2
|
15.5
|
1.0
|
CE1
|
C:HIS215
|
3.2
|
15.6
|
1.0
|
CHB
|
C:HEM500
|
3.4
|
18.2
|
1.0
|
CHD
|
C:HEM500
|
3.4
|
16.9
|
1.0
|
CHC
|
C:HEM500
|
3.5
|
16.5
|
1.0
|
CHA
|
C:HEM500
|
3.5
|
16.8
|
1.0
|
NH1
|
C:ARG232
|
4.2
|
16.2
|
1.0
|
C3C
|
C:HEM500
|
4.3
|
16.5
|
1.0
|
C3A
|
C:HEM500
|
4.3
|
18.1
|
1.0
|
C2C
|
C:HEM500
|
4.3
|
17.7
|
1.0
|
C2D
|
C:HEM500
|
4.3
|
17.7
|
1.0
|
C2A
|
C:HEM500
|
4.3
|
17.1
|
1.0
|
C2B
|
C:HEM500
|
4.3
|
18.7
|
1.0
|
C3D
|
C:HEM500
|
4.3
|
18.4
|
1.0
|
ND1
|
C:HIS215
|
4.3
|
15.3
|
1.0
|
C3B
|
C:HEM500
|
4.3
|
18.4
|
1.0
|
CG
|
C:HIS215
|
4.3
|
16.5
|
1.0
|
O
|
C:HOH765
|
4.5
|
22.4
|
1.0
|
CD
|
C:ARG232
|
4.7
|
15.2
|
1.0
|
CE1
|
C:PHE248
|
4.7
|
15.9
|
1.0
|
CE
|
C:MET276
|
4.7
|
19.6
|
1.0
|
CZ
|
C:ARG232
|
4.9
|
16.3
|
1.0
|
|
Iron binding site 4 out
of 4 in 5vj0
Go back to
Iron Binding Sites List in 5vj0
Iron binding site 4 out
of 4 in the Crystal Structure of Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus
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 Heme-Containing Dyp Type Peroxidase From Enterobacter Lignolyticus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe500
b:28.6
occ:1.00
|
FE
|
D:HEM500
|
0.0
|
28.6
|
1.0
|
NC
|
D:HEM500
|
2.0
|
23.8
|
1.0
|
NA
|
D:HEM500
|
2.0
|
26.9
|
1.0
|
ND
|
D:HEM500
|
2.0
|
25.6
|
1.0
|
NB
|
D:HEM500
|
2.1
|
26.5
|
1.0
|
NE2
|
D:HIS215
|
2.3
|
21.1
|
1.0
|
C4C
|
D:HEM500
|
3.0
|
26.5
|
1.0
|
C4A
|
D:HEM500
|
3.0
|
26.8
|
1.0
|
C1D
|
D:HEM500
|
3.0
|
24.6
|
1.0
|
C1A
|
D:HEM500
|
3.1
|
29.4
|
1.0
|
C1C
|
D:HEM500
|
3.1
|
25.5
|
1.0
|
C1B
|
D:HEM500
|
3.1
|
26.2
|
1.0
|
C4D
|
D:HEM500
|
3.1
|
26.5
|
1.0
|
CD2
|
D:HIS215
|
3.1
|
26.0
|
1.0
|
C4B
|
D:HEM500
|
3.1
|
21.5
|
1.0
|
CHD
|
D:HEM500
|
3.4
|
25.8
|
1.0
|
CHB
|
D:HEM500
|
3.4
|
28.1
|
1.0
|
CE1
|
D:HIS215
|
3.4
|
26.0
|
1.0
|
CHA
|
D:HEM500
|
3.5
|
27.5
|
1.0
|
CHC
|
D:HEM500
|
3.5
|
23.4
|
1.0
|
NH1
|
D:ARG232
|
4.1
|
28.6
|
1.0
|
C3A
|
D:HEM500
|
4.2
|
28.0
|
1.0
|
C3C
|
D:HEM500
|
4.2
|
25.6
|
1.0
|
C2A
|
D:HEM500
|
4.2
|
29.1
|
1.0
|
C2C
|
D:HEM500
|
4.3
|
22.8
|
1.0
|
C2D
|
D:HEM500
|
4.3
|
27.0
|
1.0
|
C3D
|
D:HEM500
|
4.3
|
27.2
|
1.0
|
C2B
|
D:HEM500
|
4.3
|
24.2
|
1.0
|
C3B
|
D:HEM500
|
4.3
|
25.4
|
1.0
|
CG
|
D:HIS215
|
4.3
|
26.2
|
1.0
|
ND1
|
D:HIS215
|
4.4
|
26.0
|
1.0
|
CE2
|
D:PHE248
|
4.7
|
21.6
|
1.0
|
CD
|
D:ARG232
|
4.8
|
25.7
|
1.0
|
OD1
|
D:ASP143
|
4.9
|
35.1
|
1.0
|
CZ
|
D:ARG232
|
4.9
|
30.4
|
1.0
|
|
Reference:
R.Shrestha,
G.Huang,
D.A.Meekins,
B.V.Geisbrecht,
P.Li.
Mechanistic Insights Into Dye-Decolorizing Peroxidase Revealed By Solvent Isotope and Viscosity Effects. Acs Catal V. 7 6352 2017.
ISSN: ESSN 2155-5435
PubMed: 29308295
DOI: 10.1021/ACSCATAL.7B01861
Page generated: Tue Aug 6 10:26:27 2024
|