Iron in PDB 6by0: Crystal Structure of Catalase Hpii From E. Coli in Space Group P1
Enzymatic activity of Crystal Structure of Catalase Hpii From E. Coli in Space Group P1
All present enzymatic activity of Crystal Structure of Catalase Hpii From E. Coli in Space Group P1:
1.11.1.6;
Protein crystallography data
The structure of Crystal Structure of Catalase Hpii From E. Coli in Space Group P1, PDB code: 6by0
was solved by
M.N.Lisa,
A.Buschiazzo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.39 /
2.93
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
69.337,
90.141,
114.764,
107.10,
105.60,
95.98
|
R / Rfree (%)
|
18.3 /
23.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1
(pdb code 6by0). 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 Catalase Hpii From E. Coli in Space Group P1, PDB code: 6by0:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6by0
Go back to
Iron Binding Sites List in 6by0
Iron binding site 1 out
of 4 in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1
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 Catalase Hpii From E. Coli in Space Group P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:13.7
occ:1.00
|
FE
|
A:HEM801
|
0.0
|
13.7
|
1.0
|
NA
|
A:HEM801
|
1.9
|
14.1
|
1.0
|
NC
|
A:HEM801
|
1.9
|
13.6
|
1.0
|
NB
|
A:HEM801
|
2.0
|
14.0
|
1.0
|
ND
|
A:HEM801
|
2.0
|
13.5
|
1.0
|
OH
|
A:TYR415
|
2.1
|
32.6
|
1.0
|
C4A
|
A:HEM801
|
2.9
|
14.4
|
1.0
|
C1B
|
A:HEM801
|
2.9
|
14.7
|
1.0
|
C1A
|
A:HEM801
|
3.0
|
14.1
|
1.0
|
C4C
|
A:HEM801
|
3.0
|
13.5
|
1.0
|
C1C
|
A:HEM801
|
3.0
|
13.8
|
1.0
|
C4B
|
A:HEM801
|
3.0
|
14.5
|
1.0
|
CZ
|
A:TYR415
|
3.0
|
27.4
|
1.0
|
C1D
|
A:HEM801
|
3.1
|
13.6
|
1.0
|
C4D
|
A:HEM801
|
3.1
|
13.6
|
1.0
|
CHB
|
A:HEM801
|
3.2
|
15.1
|
1.0
|
CHC
|
A:HEM801
|
3.4
|
14.8
|
1.0
|
CHD
|
A:HEM801
|
3.4
|
14.0
|
1.0
|
CHA
|
A:HEM801
|
3.5
|
14.2
|
1.0
|
CE2
|
A:TYR415
|
3.7
|
21.9
|
1.0
|
CE1
|
A:TYR415
|
3.9
|
17.8
|
1.0
|
C3A
|
A:HEM801
|
4.1
|
15.0
|
1.0
|
C3C
|
A:HEM801
|
4.2
|
13.9
|
1.0
|
C2A
|
A:HEM801
|
4.2
|
14.8
|
1.0
|
C2C
|
A:HEM801
|
4.2
|
14.2
|
1.0
|
NE
|
A:ARG411
|
4.2
|
19.5
|
1.0
|
C2B
|
A:HEM801
|
4.2
|
15.2
|
1.0
|
NH2
|
A:ARG411
|
4.2
|
15.1
|
1.0
|
C3B
|
A:HEM801
|
4.3
|
15.4
|
1.0
|
C3D
|
A:HEM801
|
4.4
|
13.7
|
1.0
|
C2D
|
A:HEM801
|
4.4
|
13.6
|
1.0
|
CG2
|
A:VAL127
|
4.5
|
17.5
|
1.0
|
CD2
|
A:HIS128
|
4.6
|
12.2
|
1.0
|
CZ
|
A:ARG411
|
4.6
|
26.9
|
1.0
|
NE2
|
A:HIS128
|
4.7
|
11.0
|
1.0
|
CZ
|
A:PHE214
|
4.7
|
12.0
|
1.0
|
CD2
|
A:TYR415
|
4.9
|
21.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 6by0
Go back to
Iron Binding Sites List in 6by0
Iron binding site 2 out
of 4 in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1
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 Catalase Hpii From E. Coli in Space Group P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe801
b:14.8
occ:1.00
|
FE
|
B:HEM801
|
0.0
|
14.8
|
1.0
|
NC
|
B:HEM801
|
1.9
|
14.9
|
1.0
|
ND
|
B:HEM801
|
1.9
|
14.8
|
1.0
|
NB
|
B:HEM801
|
1.9
|
14.7
|
1.0
|
NA
|
B:HEM801
|
2.0
|
14.9
|
1.0
|
OH
|
B:TYR415
|
2.1
|
12.5
|
1.0
|
C4D
|
B:HEM801
|
2.9
|
15.0
|
1.0
|
C4C
|
B:HEM801
|
2.9
|
15.0
|
1.0
|
C1C
|
B:HEM801
|
2.9
|
15.0
|
1.0
|
C4B
|
B:HEM801
|
3.0
|
15.2
|
1.0
|
C1B
|
B:HEM801
|
3.0
|
15.1
|
1.0
|
C1D
|
B:HEM801
|
3.0
|
15.1
|
1.0
|
C1A
|
B:HEM801
|
3.0
|
15.0
|
1.0
|
C4A
|
B:HEM801
|
3.1
|
14.9
|
1.0
|
CZ
|
B:TYR415
|
3.1
|
23.9
|
1.0
|
CHC
|
B:HEM801
|
3.3
|
15.8
|
1.0
|
CHA
|
B:HEM801
|
3.3
|
15.4
|
1.0
|
CHD
|
B:HEM801
|
3.4
|
15.6
|
1.0
|
CHB
|
B:HEM801
|
3.4
|
15.4
|
1.0
|
CE2
|
B:TYR415
|
3.8
|
22.2
|
1.0
|
CE1
|
B:TYR415
|
3.9
|
24.6
|
1.0
|
NE
|
B:ARG411
|
4.1
|
19.2
|
1.0
|
C3C
|
B:HEM801
|
4.1
|
15.4
|
1.0
|
C2C
|
B:HEM801
|
4.2
|
15.5
|
1.0
|
C3D
|
B:HEM801
|
4.2
|
15.4
|
1.0
|
NH2
|
B:ARG411
|
4.2
|
23.9
|
1.0
|
C3B
|
B:HEM801
|
4.2
|
15.8
|
1.0
|
C2B
|
B:HEM801
|
4.2
|
15.4
|
1.0
|
C2A
|
B:HEM801
|
4.3
|
15.3
|
1.0
|
C2D
|
B:HEM801
|
4.3
|
15.3
|
1.0
|
C3A
|
B:HEM801
|
4.3
|
15.3
|
1.0
|
CZ
|
B:ARG411
|
4.5
|
30.1
|
1.0
|
CG2
|
B:VAL127
|
4.6
|
14.4
|
1.0
|
CZ
|
B:PHE214
|
4.6
|
24.7
|
1.0
|
NE2
|
B:HIS128
|
4.7
|
27.1
|
1.0
|
CD2
|
B:HIS128
|
4.7
|
27.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 6by0
Go back to
Iron Binding Sites List in 6by0
Iron binding site 3 out
of 4 in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1
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 Catalase Hpii From E. Coli in Space Group P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe801
b:15.7
occ:1.00
|
FE
|
C:HEM801
|
0.0
|
15.7
|
1.0
|
ND
|
C:HEM801
|
1.9
|
15.4
|
1.0
|
NA
|
C:HEM801
|
1.9
|
15.8
|
1.0
|
NC
|
C:HEM801
|
1.9
|
15.6
|
1.0
|
NB
|
C:HEM801
|
2.0
|
15.9
|
1.0
|
OH
|
C:TYR415
|
2.1
|
27.5
|
1.0
|
C4D
|
C:HEM801
|
2.9
|
15.5
|
1.0
|
C1C
|
C:HEM801
|
3.0
|
15.8
|
1.0
|
C1A
|
C:HEM801
|
3.0
|
15.7
|
1.0
|
C1B
|
C:HEM801
|
3.0
|
16.5
|
1.0
|
C4C
|
C:HEM801
|
3.0
|
15.6
|
1.0
|
C4B
|
C:HEM801
|
3.0
|
16.4
|
1.0
|
C1D
|
C:HEM801
|
3.0
|
15.6
|
1.0
|
C4A
|
C:HEM801
|
3.0
|
16.0
|
1.0
|
CZ
|
C:TYR415
|
3.0
|
25.8
|
1.0
|
CHA
|
C:HEM801
|
3.3
|
15.9
|
1.0
|
CHB
|
C:HEM801
|
3.4
|
16.7
|
1.0
|
CHC
|
C:HEM801
|
3.4
|
16.8
|
1.0
|
CHD
|
C:HEM801
|
3.5
|
16.1
|
1.0
|
CE2
|
C:TYR415
|
3.7
|
17.4
|
1.0
|
CE1
|
C:TYR415
|
3.9
|
18.1
|
1.0
|
C2C
|
C:HEM801
|
4.1
|
16.3
|
1.0
|
C3C
|
C:HEM801
|
4.2
|
16.1
|
1.0
|
C3D
|
C:HEM801
|
4.2
|
15.6
|
1.0
|
C2A
|
C:HEM801
|
4.2
|
16.2
|
1.0
|
NE
|
C:ARG411
|
4.2
|
22.2
|
1.0
|
C3A
|
C:HEM801
|
4.2
|
16.4
|
1.0
|
C2B
|
C:HEM801
|
4.2
|
16.9
|
1.0
|
C3B
|
C:HEM801
|
4.3
|
17.2
|
1.0
|
NH2
|
C:ARG411
|
4.3
|
19.5
|
1.0
|
C2D
|
C:HEM801
|
4.3
|
15.6
|
1.0
|
CG2
|
C:VAL127
|
4.5
|
10.4
|
1.0
|
CZ
|
C:PHE214
|
4.6
|
9.8
|
1.0
|
CD2
|
C:HIS128
|
4.6
|
18.3
|
1.0
|
CZ
|
C:ARG411
|
4.7
|
25.6
|
1.0
|
NE2
|
C:HIS128
|
4.7
|
18.4
|
1.0
|
CD2
|
C:TYR415
|
4.9
|
17.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 6by0
Go back to
Iron Binding Sites List in 6by0
Iron binding site 4 out
of 4 in the Crystal Structure of Catalase Hpii From E. Coli in Space Group P1
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 Catalase Hpii From E. Coli in Space Group P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe801
b:16.8
occ:1.00
|
FE
|
D:HEM801
|
0.0
|
16.8
|
1.0
|
NC
|
D:HEM801
|
1.9
|
16.6
|
1.0
|
ND
|
D:HEM801
|
2.0
|
16.7
|
1.0
|
NA
|
D:HEM801
|
2.0
|
17.2
|
1.0
|
NB
|
D:HEM801
|
2.0
|
16.9
|
1.0
|
OH
|
D:TYR415
|
2.1
|
6.5
|
1.0
|
C4C
|
D:HEM801
|
2.9
|
16.7
|
1.0
|
C1D
|
D:HEM801
|
3.0
|
16.9
|
1.0
|
C1B
|
D:HEM801
|
3.0
|
17.4
|
1.0
|
C1C
|
D:HEM801
|
3.0
|
16.7
|
1.0
|
C4B
|
D:HEM801
|
3.0
|
17.2
|
1.0
|
C4D
|
D:HEM801
|
3.0
|
17.0
|
1.0
|
C4A
|
D:HEM801
|
3.1
|
17.4
|
1.0
|
C1A
|
D:HEM801
|
3.1
|
17.3
|
1.0
|
CZ
|
D:TYR415
|
3.1
|
22.6
|
1.0
|
CHD
|
D:HEM801
|
3.3
|
17.3
|
1.0
|
CHB
|
D:HEM801
|
3.4
|
17.9
|
1.0
|
CHC
|
D:HEM801
|
3.5
|
17.6
|
1.0
|
CHA
|
D:HEM801
|
3.5
|
17.5
|
1.0
|
O
|
D:HOH974
|
3.7
|
7.9
|
1.0
|
CE2
|
D:TYR415
|
3.8
|
25.4
|
1.0
|
CE1
|
D:TYR415
|
4.0
|
26.6
|
1.0
|
C2B
|
D:HEM801
|
4.1
|
17.8
|
1.0
|
NE
|
D:ARG411
|
4.1
|
13.1
|
1.0
|
C3C
|
D:HEM801
|
4.2
|
17.0
|
1.0
|
NH2
|
D:ARG411
|
4.2
|
23.5
|
1.0
|
C2C
|
D:HEM801
|
4.2
|
17.2
|
1.0
|
C3B
|
D:HEM801
|
4.2
|
17.9
|
1.0
|
C2A
|
D:HEM801
|
4.2
|
17.8
|
1.0
|
C3A
|
D:HEM801
|
4.2
|
18.0
|
1.0
|
C3D
|
D:HEM801
|
4.3
|
17.3
|
1.0
|
C2D
|
D:HEM801
|
4.3
|
17.1
|
1.0
|
CZ
|
D:ARG411
|
4.5
|
28.7
|
1.0
|
NE2
|
D:HIS128
|
4.6
|
19.2
|
1.0
|
CD2
|
D:HIS128
|
4.6
|
19.7
|
1.0
|
CG2
|
D:VAL127
|
4.6
|
13.4
|
1.0
|
CZ
|
D:PHE214
|
4.7
|
25.0
|
1.0
|
|
Reference:
A.J.Simpkin,
F.Simkovic,
J.M.H.Thomas,
M.Savko,
A.Lebedev,
V.Uski,
C.Ballard,
M.Wojdyr,
R.Wu,
R.Sanishvili,
Y.Xu,
M.N.Lisa,
A.Buschiazzo,
W.Shepard,
D.J.Rigden,
R.M.Keegan.
Simbad: A Sequence-Independent Molecular-Replacement Pipeline. Acta Crystallogr D Struct V. 74 595 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29968670
DOI: 10.1107/S2059798318005752
Page generated: Tue Aug 6 14:40:49 2024
|