Iron in PDB 6rjn: Crystal Structure of A Fungal Catalase at 2.3 Angstroms
Enzymatic activity of Crystal Structure of A Fungal Catalase at 2.3 Angstroms
All present enzymatic activity of Crystal Structure of A Fungal Catalase at 2.3 Angstroms:
1.11.1.6;
Protein crystallography data
The structure of Crystal Structure of A Fungal Catalase at 2.3 Angstroms, PDB code: 6rjn
was solved by
S.Gomez,
S.Navas-Yuste,
A.M.Payne,
W.Rivera,
M.Lopez-Estepa,
C.Brangbour,
D.Fulla,
J.Juanhuix,
F.J.Fernandez,
M.C.Vega,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
54.67 /
2.30
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
165.943,
173.690,
96.490,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.3 /
19.6
|
Other elements in 6rjn:
The structure of Crystal Structure of A Fungal Catalase at 2.3 Angstroms also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms
(pdb code 6rjn). 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 A Fungal Catalase at 2.3 Angstroms, PDB code: 6rjn:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6rjn
Go back to
Iron Binding Sites List in 6rjn
Iron binding site 1 out
of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms
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 Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:28.9
occ:1.00
|
FE
|
A:HEM601
|
0.0
|
28.9
|
1.0
|
ND
|
A:HEM601
|
1.9
|
26.8
|
1.0
|
NA
|
A:HEM601
|
2.0
|
24.6
|
1.0
|
NC
|
A:HEM601
|
2.1
|
32.5
|
1.0
|
NB
|
A:HEM601
|
2.1
|
28.6
|
1.0
|
OH
|
A:TYR349
|
2.2
|
19.6
|
1.0
|
C1D
|
A:HEM601
|
2.9
|
23.9
|
1.0
|
C4D
|
A:HEM601
|
2.9
|
21.3
|
1.0
|
C1A
|
A:HEM601
|
2.9
|
23.4
|
1.0
|
C4C
|
A:HEM601
|
3.0
|
28.1
|
1.0
|
C4A
|
A:HEM601
|
3.0
|
23.1
|
1.0
|
C4B
|
A:HEM601
|
3.1
|
25.6
|
1.0
|
C1B
|
A:HEM601
|
3.1
|
23.3
|
1.0
|
C1C
|
A:HEM601
|
3.1
|
20.3
|
1.0
|
CZ
|
A:TYR349
|
3.1
|
20.5
|
1.0
|
CHD
|
A:HEM601
|
3.3
|
20.9
|
1.0
|
CHA
|
A:HEM601
|
3.3
|
20.0
|
1.0
|
CHB
|
A:HEM601
|
3.4
|
20.9
|
1.0
|
CHC
|
A:HEM601
|
3.5
|
26.5
|
1.0
|
CE2
|
A:TYR349
|
3.8
|
19.0
|
1.0
|
CE1
|
A:TYR349
|
3.9
|
25.8
|
1.0
|
C2D
|
A:HEM601
|
4.1
|
20.8
|
1.0
|
C2A
|
A:HEM601
|
4.1
|
22.4
|
1.0
|
C3D
|
A:HEM601
|
4.1
|
23.1
|
1.0
|
NE
|
A:ARG345
|
4.2
|
18.9
|
1.0
|
C3A
|
A:HEM601
|
4.2
|
22.8
|
1.0
|
C3C
|
A:HEM601
|
4.2
|
27.3
|
1.0
|
C2C
|
A:HEM601
|
4.2
|
30.5
|
1.0
|
C2B
|
A:HEM601
|
4.3
|
24.4
|
1.0
|
C3B
|
A:HEM601
|
4.3
|
24.2
|
1.0
|
O
|
A:HOH865
|
4.4
|
28.6
|
1.0
|
NH2
|
A:ARG345
|
4.4
|
24.0
|
1.0
|
CZ
|
A:PHE152
|
4.6
|
24.5
|
1.0
|
CG2
|
A:VAL65
|
4.6
|
22.9
|
1.0
|
CD2
|
A:HIS66
|
4.7
|
22.3
|
1.0
|
NE2
|
A:HIS66
|
4.7
|
19.5
|
1.0
|
CZ
|
A:ARG345
|
4.7
|
23.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 6rjn
Go back to
Iron Binding Sites List in 6rjn
Iron binding site 2 out
of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms
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 Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe602
b:30.8
occ:1.00
|
FE
|
B:HEM602
|
0.0
|
30.8
|
1.0
|
OH
|
B:TYR349
|
1.9
|
18.0
|
1.0
|
ND
|
B:HEM602
|
2.0
|
22.4
|
1.0
|
NB
|
B:HEM602
|
2.0
|
22.9
|
1.0
|
NA
|
B:HEM602
|
2.1
|
17.2
|
1.0
|
NC
|
B:HEM602
|
2.1
|
28.2
|
1.0
|
CZ
|
B:TYR349
|
2.9
|
18.3
|
1.0
|
C4D
|
B:HEM602
|
3.0
|
24.7
|
1.0
|
C4B
|
B:HEM602
|
3.0
|
24.4
|
1.0
|
C1C
|
B:HEM602
|
3.1
|
25.9
|
1.0
|
C1D
|
B:HEM602
|
3.1
|
24.3
|
1.0
|
C1B
|
B:HEM602
|
3.1
|
21.0
|
1.0
|
C1A
|
B:HEM602
|
3.1
|
18.6
|
1.0
|
C4A
|
B:HEM602
|
3.1
|
23.2
|
1.0
|
C4C
|
B:HEM602
|
3.1
|
24.8
|
1.0
|
CHA
|
B:HEM602
|
3.4
|
23.9
|
1.0
|
CHC
|
B:HEM602
|
3.4
|
27.7
|
1.0
|
CHD
|
B:HEM602
|
3.4
|
25.8
|
1.0
|
CHB
|
B:HEM602
|
3.4
|
17.9
|
1.0
|
CE2
|
B:TYR349
|
3.7
|
22.9
|
1.0
|
CE1
|
B:TYR349
|
3.7
|
23.6
|
1.0
|
NE
|
B:ARG345
|
4.1
|
21.5
|
1.0
|
NH2
|
B:ARG345
|
4.2
|
25.6
|
1.0
|
O
|
B:HOH757
|
4.2
|
25.3
|
1.0
|
C3D
|
B:HEM602
|
4.2
|
25.3
|
1.0
|
C3B
|
B:HEM602
|
4.3
|
22.2
|
1.0
|
C2D
|
B:HEM602
|
4.3
|
21.2
|
1.0
|
C2C
|
B:HEM602
|
4.3
|
30.7
|
1.0
|
C2B
|
B:HEM602
|
4.3
|
24.9
|
1.0
|
C3C
|
B:HEM602
|
4.3
|
27.1
|
1.0
|
C3A
|
B:HEM602
|
4.3
|
24.1
|
1.0
|
C2A
|
B:HEM602
|
4.3
|
19.9
|
1.0
|
CZ
|
B:ARG345
|
4.6
|
20.8
|
1.0
|
CG2
|
B:VAL65
|
4.7
|
22.1
|
1.0
|
CD2
|
B:HIS66
|
4.7
|
25.7
|
1.0
|
NE2
|
B:HIS66
|
4.7
|
23.6
|
1.0
|
CZ
|
B:PHE152
|
4.7
|
22.4
|
1.0
|
CD2
|
B:TYR349
|
5.0
|
29.0
|
1.0
|
CD1
|
B:TYR349
|
5.0
|
21.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 6rjn
Go back to
Iron Binding Sites List in 6rjn
Iron binding site 3 out
of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms
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 A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe601
b:34.5
occ:1.00
|
FE
|
C:HEM601
|
0.0
|
34.5
|
1.0
|
OH
|
C:TYR349
|
1.9
|
22.7
|
1.0
|
NA
|
C:HEM601
|
2.0
|
23.2
|
1.0
|
NB
|
C:HEM601
|
2.0
|
20.0
|
1.0
|
ND
|
C:HEM601
|
2.1
|
25.1
|
1.0
|
NC
|
C:HEM601
|
2.2
|
27.9
|
1.0
|
CZ
|
C:TYR349
|
2.9
|
24.3
|
1.0
|
C4A
|
C:HEM601
|
3.0
|
22.2
|
1.0
|
C1B
|
C:HEM601
|
3.0
|
24.4
|
1.0
|
C1D
|
C:HEM601
|
3.1
|
21.9
|
1.0
|
C1A
|
C:HEM601
|
3.1
|
26.0
|
1.0
|
C4C
|
C:HEM601
|
3.1
|
26.8
|
1.0
|
C4D
|
C:HEM601
|
3.1
|
18.9
|
1.0
|
C4B
|
C:HEM601
|
3.1
|
26.3
|
1.0
|
C1C
|
C:HEM601
|
3.2
|
27.9
|
1.0
|
CHB
|
C:HEM601
|
3.3
|
21.2
|
1.0
|
CHD
|
C:HEM601
|
3.4
|
24.6
|
1.0
|
CHA
|
C:HEM601
|
3.5
|
27.5
|
1.0
|
CHC
|
C:HEM601
|
3.6
|
29.2
|
1.0
|
CE1
|
C:TYR349
|
3.7
|
21.0
|
1.0
|
CE2
|
C:TYR349
|
3.8
|
26.7
|
1.0
|
NE
|
C:ARG345
|
4.1
|
23.9
|
1.0
|
C3A
|
C:HEM601
|
4.2
|
22.4
|
1.0
|
C2B
|
C:HEM601
|
4.2
|
28.0
|
1.0
|
C2A
|
C:HEM601
|
4.3
|
21.2
|
1.0
|
O
|
C:HOH777
|
4.3
|
28.0
|
1.0
|
C3B
|
C:HEM601
|
4.3
|
25.1
|
1.0
|
NH2
|
C:ARG345
|
4.3
|
25.8
|
1.0
|
C2D
|
C:HEM601
|
4.3
|
22.9
|
1.0
|
C3C
|
C:HEM601
|
4.3
|
29.4
|
1.0
|
C3D
|
C:HEM601
|
4.3
|
17.9
|
1.0
|
C2C
|
C:HEM601
|
4.3
|
27.5
|
1.0
|
CZ
|
C:ARG345
|
4.6
|
19.2
|
1.0
|
CG2
|
C:VAL65
|
4.6
|
24.8
|
1.0
|
CZ
|
C:PHE152
|
4.6
|
26.9
|
1.0
|
CD2
|
C:HIS66
|
4.7
|
25.4
|
1.0
|
NE2
|
C:HIS66
|
4.8
|
22.4
|
1.0
|
CD1
|
C:TYR349
|
4.9
|
29.9
|
1.0
|
CD
|
C:ARG345
|
5.0
|
24.9
|
1.0
|
CD2
|
C:TYR349
|
5.0
|
25.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 6rjn
Go back to
Iron Binding Sites List in 6rjn
Iron binding site 4 out
of 4 in the Crystal Structure of A Fungal Catalase at 2.3 Angstroms
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 A Fungal Catalase at 2.3 Angstroms within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe604
b:32.7
occ:1.00
|
FE
|
D:HEM604
|
0.0
|
32.7
|
1.0
|
OH
|
D:TYR349
|
1.8
|
21.7
|
1.0
|
NA
|
D:HEM604
|
2.0
|
22.6
|
1.0
|
ND
|
D:HEM604
|
2.0
|
25.8
|
1.0
|
NC
|
D:HEM604
|
2.1
|
34.0
|
1.0
|
NB
|
D:HEM604
|
2.1
|
29.5
|
1.0
|
CZ
|
D:TYR349
|
2.9
|
21.1
|
1.0
|
C1D
|
D:HEM604
|
3.0
|
26.4
|
1.0
|
C4C
|
D:HEM604
|
3.0
|
28.9
|
1.0
|
C4A
|
D:HEM604
|
3.0
|
24.1
|
1.0
|
C1A
|
D:HEM604
|
3.1
|
19.0
|
1.0
|
C4D
|
D:HEM604
|
3.1
|
23.0
|
1.0
|
C1C
|
D:HEM604
|
3.1
|
23.8
|
1.0
|
C1B
|
D:HEM604
|
3.1
|
24.5
|
1.0
|
C4B
|
D:HEM604
|
3.2
|
26.1
|
1.0
|
CHD
|
D:HEM604
|
3.3
|
24.7
|
1.0
|
CHB
|
D:HEM604
|
3.4
|
16.6
|
1.0
|
CHA
|
D:HEM604
|
3.5
|
20.8
|
1.0
|
CHC
|
D:HEM604
|
3.5
|
23.3
|
1.0
|
CE1
|
D:TYR349
|
3.7
|
19.9
|
1.0
|
CE2
|
D:TYR349
|
3.8
|
19.9
|
1.0
|
NE
|
D:ARG345
|
4.0
|
29.3
|
1.0
|
NH2
|
D:ARG345
|
4.2
|
24.0
|
1.0
|
C3A
|
D:HEM604
|
4.2
|
24.5
|
1.0
|
C2D
|
D:HEM604
|
4.2
|
24.6
|
1.0
|
C3C
|
D:HEM604
|
4.2
|
28.5
|
1.0
|
C2A
|
D:HEM604
|
4.3
|
24.5
|
1.0
|
O
|
D:HOH820
|
4.3
|
32.4
|
1.0
|
C2C
|
D:HEM604
|
4.3
|
27.3
|
1.0
|
C3D
|
D:HEM604
|
4.3
|
24.0
|
1.0
|
C3B
|
D:HEM604
|
4.4
|
23.9
|
1.0
|
C2B
|
D:HEM604
|
4.4
|
20.8
|
1.0
|
CZ
|
D:ARG345
|
4.5
|
26.4
|
1.0
|
CZ
|
D:PHE152
|
4.6
|
27.5
|
1.0
|
NE2
|
D:HIS66
|
4.6
|
28.8
|
1.0
|
CD2
|
D:HIS66
|
4.7
|
29.0
|
1.0
|
CG2
|
D:VAL65
|
4.8
|
19.3
|
1.0
|
CD1
|
D:TYR349
|
4.9
|
17.2
|
1.0
|
CD
|
D:ARG345
|
4.9
|
26.0
|
1.0
|
|
Reference:
S.Gomez,
S.Navas-Yuste,
A.M.Payne,
W.Rivera,
M.Lopez-Estepa,
C.Brangbour,
D.Fulla,
J.Juanhuix,
F.J.Fernandez,
M.C.Vega.
Peroxisomal Catalases From the Yeasts Pichia Pastoris and Kluyveromyces Lactis As Models For Oxidative Damage in Higher Eukaryotes. Free Radic. Biol. Med. V. 141 279 2019.
ISSN: ISSN 1873-4596
PubMed: 31238127
DOI: 10.1016/J.FREERADBIOMED.2019.06.025
Page generated: Wed Aug 7 08:44:13 2024
|