Iron in PDB 6fkt: Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp)
Protein crystallography data
The structure of Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fkt
was solved by
V.Pfanzagl,
S.Hofbauer,
G.Mlynek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
75.22 /
1.86
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.160,
91.160,
247.820,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.8 /
20.7
|
Other elements in 6fkt:
The structure of Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp)
(pdb code 6fkt). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp), PDB code: 6fkt:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 6fkt
Go back to
Iron Binding Sites List in 6fkt
Iron binding site 1 out
of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp)
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 A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:25.1
occ:1.00
|
FE
|
A:HEM500
|
0.0
|
25.1
|
1.0
|
NB
|
A:HEM500
|
2.0
|
19.3
|
1.0
|
ND
|
A:HEM500
|
2.0
|
20.0
|
1.0
|
NC
|
A:HEM500
|
2.0
|
22.2
|
1.0
|
NA
|
A:HEM500
|
2.1
|
24.1
|
1.0
|
NE2
|
A:HIS215
|
2.3
|
21.8
|
1.0
|
C1D
|
A:HEM500
|
3.0
|
22.6
|
1.0
|
C1B
|
A:HEM500
|
3.0
|
23.6
|
1.0
|
C4A
|
A:HEM500
|
3.0
|
26.4
|
1.0
|
C4C
|
A:HEM500
|
3.0
|
22.7
|
1.0
|
C4B
|
A:HEM500
|
3.1
|
20.9
|
1.0
|
C1A
|
A:HEM500
|
3.1
|
24.3
|
1.0
|
C1C
|
A:HEM500
|
3.1
|
21.5
|
1.0
|
C4D
|
A:HEM500
|
3.1
|
23.8
|
1.0
|
CD2
|
A:HIS215
|
3.2
|
24.8
|
1.0
|
HD2
|
A:HIS215
|
3.3
|
29.8
|
1.0
|
CE1
|
A:HIS215
|
3.3
|
26.1
|
1.0
|
CHD
|
A:HEM500
|
3.4
|
20.1
|
1.0
|
CHB
|
A:HEM500
|
3.4
|
24.1
|
1.0
|
CHC
|
A:HEM500
|
3.4
|
19.4
|
1.0
|
CHA
|
A:HEM500
|
3.5
|
22.6
|
1.0
|
HE1
|
A:HIS215
|
3.5
|
31.3
|
1.0
|
HG21
|
A:VAL219
|
3.9
|
32.1
|
1.0
|
HE1
|
A:PHE248
|
3.9
|
27.1
|
1.0
|
C3A
|
A:HEM500
|
4.3
|
30.1
|
1.0
|
C2A
|
A:HEM500
|
4.3
|
27.2
|
1.0
|
C2B
|
A:HEM500
|
4.3
|
22.2
|
1.0
|
C2D
|
A:HEM500
|
4.3
|
22.1
|
1.0
|
C3B
|
A:HEM500
|
4.3
|
19.9
|
1.0
|
C3C
|
A:HEM500
|
4.3
|
23.6
|
1.0
|
C3D
|
A:HEM500
|
4.3
|
24.8
|
1.0
|
C2C
|
A:HEM500
|
4.3
|
21.6
|
1.0
|
CG
|
A:HIS215
|
4.4
|
27.1
|
1.0
|
HHD
|
A:HEM500
|
4.4
|
24.1
|
1.0
|
HHB
|
A:HEM500
|
4.4
|
28.9
|
1.0
|
ND1
|
A:HIS215
|
4.4
|
24.6
|
1.0
|
HHC
|
A:HEM500
|
4.4
|
23.2
|
1.0
|
HHA
|
A:HEM500
|
4.4
|
27.2
|
1.0
|
HE1
|
A:MET276
|
4.4
|
31.9
|
1.0
|
HA3
|
A:GLY144
|
4.5
|
66.3
|
1.0
|
HG11
|
A:VAL219
|
4.6
|
31.7
|
1.0
|
CE1
|
A:PHE248
|
4.7
|
22.6
|
1.0
|
CG2
|
A:VAL219
|
4.8
|
26.7
|
1.0
|
|
Iron binding site 2 out
of 2 in 6fkt
Go back to
Iron Binding Sites List in 6fkt
Iron binding site 2 out
of 2 in the Crystal Structure of A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp)
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 A Dye-Decolorizing Peroxidase R232A Variant From Klebsiella Pneumoniae (Kpdyp) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:23.7
occ:1.00
|
FE
|
B:HEM401
|
0.0
|
23.7
|
1.0
|
NA
|
B:HEM401
|
2.0
|
25.2
|
1.0
|
NB
|
B:HEM401
|
2.0
|
25.5
|
1.0
|
NC
|
B:HEM401
|
2.1
|
22.0
|
1.0
|
ND
|
B:HEM401
|
2.1
|
24.5
|
1.0
|
NE2
|
B:HIS215
|
2.3
|
26.4
|
1.0
|
C4A
|
B:HEM401
|
3.0
|
26.0
|
1.0
|
C1B
|
B:HEM401
|
3.0
|
28.8
|
1.0
|
C1A
|
B:HEM401
|
3.0
|
25.7
|
1.0
|
C4B
|
B:HEM401
|
3.1
|
27.0
|
1.0
|
C4C
|
B:HEM401
|
3.1
|
22.4
|
1.0
|
C1C
|
B:HEM401
|
3.1
|
22.5
|
1.0
|
C4D
|
B:HEM401
|
3.1
|
27.8
|
1.0
|
C1D
|
B:HEM401
|
3.1
|
24.9
|
1.0
|
CD2
|
B:HIS215
|
3.2
|
27.8
|
1.0
|
HD2
|
B:HIS215
|
3.3
|
33.3
|
1.0
|
CE1
|
B:HIS215
|
3.3
|
26.6
|
1.0
|
CHB
|
B:HEM401
|
3.4
|
28.3
|
1.0
|
CHC
|
B:HEM401
|
3.4
|
22.0
|
1.0
|
CHA
|
B:HEM401
|
3.4
|
28.7
|
1.0
|
CHD
|
B:HEM401
|
3.5
|
24.9
|
1.0
|
HE1
|
B:HIS215
|
3.5
|
31.9
|
1.0
|
HE1
|
B:PHE248
|
3.7
|
32.7
|
1.0
|
HG21
|
B:VAL219
|
3.8
|
34.6
|
1.0
|
O
|
B:HOH521
|
4.1
|
39.7
|
1.0
|
C3A
|
B:HEM401
|
4.2
|
27.4
|
1.0
|
C2A
|
B:HEM401
|
4.2
|
29.7
|
1.0
|
C2B
|
B:HEM401
|
4.3
|
35.5
|
1.0
|
C3B
|
B:HEM401
|
4.3
|
34.0
|
1.0
|
C3C
|
B:HEM401
|
4.3
|
22.6
|
1.0
|
C2C
|
B:HEM401
|
4.3
|
23.9
|
1.0
|
C3D
|
B:HEM401
|
4.3
|
27.1
|
1.0
|
C2D
|
B:HEM401
|
4.3
|
28.7
|
1.0
|
CG
|
B:HIS215
|
4.3
|
23.7
|
1.0
|
HHB
|
B:HEM401
|
4.4
|
34.0
|
1.0
|
ND1
|
B:HIS215
|
4.4
|
26.9
|
1.0
|
HHA
|
B:HEM401
|
4.4
|
34.5
|
1.0
|
HHC
|
B:HEM401
|
4.4
|
26.4
|
1.0
|
HHD
|
B:HEM401
|
4.4
|
29.9
|
1.0
|
HA3
|
B:GLY144
|
4.5
|
41.8
|
1.0
|
CE1
|
B:PHE248
|
4.5
|
27.2
|
1.0
|
HG11
|
B:VAL219
|
4.6
|
37.2
|
1.0
|
HE1
|
B:MET276
|
4.6
|
42.1
|
1.0
|
CG2
|
B:VAL219
|
4.8
|
28.9
|
1.0
|
HD1
|
B:PHE248
|
5.0
|
27.0
|
1.0
|
|
Reference:
V.Pfanzagl,
K.Nys,
M.Bellei,
H.Michlits,
G.Mlynek,
G.Battistuzzi,
K.Djinovic-Carugo,
S.Van Doorslaer,
P.G.Furtmuller,
S.Hofbauer,
C.Obinger.
Roles of Distal Aspartate and Arginine of B-Class Dye-Decolorizing Peroxidase in Heterolytic Hydrogen Peroxide Cleavage. J. Biol. Chem. V. 293 14823 2018.
ISSN: ESSN 1083-351X
PubMed: 30072383
DOI: 10.1074/JBC.RA118.004773
Page generated: Sun Dec 13 16:26:04 2020
|