Iron in PDB 8fty: Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
Protein crystallography data
The structure of Crystal Structure of the Carotenoid Isomerooxygenase, Ninab, PDB code: 8fty
was solved by
P.D.Kiser,
Y.J.Solano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.67 /
1.95
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
349.934,
52.036,
210.036,
90,
98.95,
90
|
R / Rfree (%)
|
21.7 /
24.7
|
Other elements in 8fty:
The structure of Crystal Structure of the Carotenoid Isomerooxygenase, Ninab also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
(pdb code 8fty). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of the Carotenoid Isomerooxygenase, Ninab, PDB code: 8fty:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8fty
Go back to
Iron Binding Sites List in 8fty
Iron binding site 1 out
of 8 in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
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 Carotenoid Isomerooxygenase, Ninab within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe601
b:34.6
occ:1.00
|
NE2
|
A:HIS312
|
2.1
|
28.6
|
1.0
|
NE2
|
A:HIS242
|
2.1
|
33.5
|
1.0
|
O
|
A:HOH740
|
2.2
|
27.8
|
1.0
|
NE2
|
A:HIS184
|
2.2
|
29.8
|
1.0
|
NE2
|
A:HIS501
|
2.2
|
26.8
|
1.0
|
CE1
|
A:HIS312
|
3.0
|
28.9
|
1.0
|
CE1
|
A:HIS242
|
3.1
|
34.1
|
1.0
|
CD2
|
A:HIS312
|
3.1
|
27.8
|
1.0
|
CE1
|
A:HIS184
|
3.1
|
28.7
|
1.0
|
CD2
|
A:HIS501
|
3.1
|
27.0
|
1.0
|
CE1
|
A:HIS501
|
3.1
|
26.6
|
1.0
|
CD2
|
A:HIS242
|
3.1
|
32.4
|
1.0
|
CD2
|
A:HIS184
|
3.2
|
29.5
|
1.0
|
O2
|
A:MPD602
|
3.9
|
50.2
|
1.0
|
ND1
|
A:HIS312
|
4.2
|
28.0
|
1.0
|
ND1
|
A:HIS501
|
4.2
|
26.8
|
1.0
|
CG
|
A:HIS501
|
4.2
|
27.5
|
1.0
|
ND1
|
A:HIS242
|
4.2
|
33.0
|
1.0
|
CG
|
A:HIS312
|
4.2
|
27.9
|
1.0
|
ND1
|
A:HIS184
|
4.2
|
28.8
|
1.0
|
CG2
|
A:ILE138
|
4.2
|
33.5
|
1.0
|
CG
|
A:HIS242
|
4.3
|
32.6
|
1.0
|
CG
|
A:HIS184
|
4.3
|
29.2
|
1.0
|
OG
|
A:SER183
|
5.0
|
34.0
|
1.0
|
|
Iron binding site 2 out
of 8 in 8fty
Go back to
Iron Binding Sites List in 8fty
Iron binding site 2 out
of 8 in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
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 Carotenoid Isomerooxygenase, Ninab within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1000
b:27.1
occ:1.00
|
NE2
|
B:HIS312
|
2.1
|
24.8
|
1.0
|
NE2
|
B:HIS242
|
2.1
|
27.1
|
1.0
|
NE2
|
B:HIS184
|
2.2
|
26.3
|
1.0
|
NE2
|
B:HIS501
|
2.2
|
22.4
|
1.0
|
O
|
B:HOH1130
|
2.3
|
30.9
|
1.0
|
CE1
|
B:HIS312
|
3.0
|
24.9
|
1.0
|
CE1
|
B:HIS242
|
3.1
|
26.7
|
1.0
|
CE1
|
B:HIS184
|
3.1
|
25.6
|
1.0
|
CE1
|
B:HIS501
|
3.1
|
22.2
|
1.0
|
CD2
|
B:HIS312
|
3.1
|
24.7
|
1.0
|
CD2
|
B:HIS501
|
3.1
|
23.2
|
1.0
|
CD2
|
B:HIS242
|
3.1
|
25.8
|
1.0
|
CD2
|
B:HIS184
|
3.2
|
25.2
|
1.0
|
O
|
B:HOH1387
|
3.8
|
41.9
|
1.0
|
O2
|
B:MPD1001
|
3.8
|
48.0
|
1.0
|
ND1
|
B:HIS501
|
4.1
|
23.4
|
1.0
|
ND1
|
B:HIS312
|
4.2
|
24.7
|
1.0
|
CG
|
B:HIS501
|
4.2
|
24.2
|
1.0
|
ND1
|
B:HIS242
|
4.2
|
26.6
|
1.0
|
ND1
|
B:HIS184
|
4.2
|
25.2
|
1.0
|
CG
|
B:HIS312
|
4.2
|
24.9
|
1.0
|
CG
|
B:HIS184
|
4.3
|
25.2
|
1.0
|
CG
|
B:HIS242
|
4.3
|
26.1
|
1.0
|
CG2
|
B:ILE138
|
4.3
|
27.8
|
1.0
|
OG
|
B:SER183
|
5.0
|
26.6
|
1.0
|
|
Iron binding site 3 out
of 8 in 8fty
Go back to
Iron Binding Sites List in 8fty
Iron binding site 3 out
of 8 in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
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 Carotenoid Isomerooxygenase, Ninab within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe601
b:25.6
occ:1.00
|
O
|
C:HOH1205
|
1.9
|
21.1
|
1.0
|
NE2
|
C:HIS184
|
2.1
|
21.0
|
1.0
|
NE2
|
C:HIS312
|
2.1
|
25.0
|
1.0
|
NE2
|
C:HIS242
|
2.1
|
28.7
|
1.0
|
NE2
|
C:HIS501
|
2.2
|
22.7
|
1.0
|
CE1
|
C:HIS184
|
3.1
|
20.6
|
1.0
|
CE1
|
C:HIS312
|
3.1
|
23.9
|
1.0
|
CE1
|
C:HIS242
|
3.1
|
29.5
|
1.0
|
CD2
|
C:HIS184
|
3.1
|
21.8
|
1.0
|
CD2
|
C:HIS312
|
3.1
|
23.9
|
1.0
|
CD2
|
C:HIS501
|
3.1
|
22.6
|
1.0
|
CE1
|
C:HIS501
|
3.1
|
22.1
|
1.0
|
CD2
|
C:HIS242
|
3.1
|
28.3
|
1.0
|
O2
|
C:MPD602
|
4.0
|
48.7
|
1.0
|
ND1
|
C:HIS501
|
4.2
|
22.0
|
1.0
|
ND1
|
C:HIS184
|
4.2
|
20.5
|
1.0
|
ND1
|
C:HIS312
|
4.2
|
23.7
|
1.0
|
CG
|
C:HIS501
|
4.2
|
22.9
|
1.0
|
ND1
|
C:HIS242
|
4.2
|
29.5
|
1.0
|
CG
|
C:HIS184
|
4.2
|
21.8
|
1.0
|
CG2
|
C:ILE138
|
4.2
|
24.3
|
1.0
|
CG
|
C:HIS312
|
4.2
|
24.6
|
1.0
|
CG
|
C:HIS242
|
4.3
|
28.4
|
1.0
|
OG
|
C:SER183
|
4.9
|
28.2
|
1.0
|
|
Iron binding site 4 out
of 8 in 8fty
Go back to
Iron Binding Sites List in 8fty
Iron binding site 4 out
of 8 in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
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 Carotenoid Isomerooxygenase, Ninab within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe601
b:31.0
occ:1.00
|
O
|
D:HOH2178
|
2.0
|
29.8
|
1.0
|
NE2
|
D:HIS312
|
2.1
|
27.0
|
1.0
|
NE2
|
D:HIS242
|
2.2
|
34.4
|
1.0
|
NE2
|
D:HIS184
|
2.2
|
23.7
|
1.0
|
NE2
|
D:HIS501
|
2.2
|
28.2
|
1.0
|
CE1
|
D:HIS312
|
3.1
|
27.4
|
1.0
|
CD2
|
D:HIS501
|
3.1
|
27.7
|
1.0
|
CE1
|
D:HIS242
|
3.1
|
33.2
|
1.0
|
CE1
|
D:HIS184
|
3.1
|
24.1
|
1.0
|
CE1
|
D:HIS501
|
3.1
|
26.7
|
1.0
|
CD2
|
D:HIS312
|
3.2
|
27.1
|
1.0
|
CD2
|
D:HIS242
|
3.2
|
34.1
|
1.0
|
CD2
|
D:HIS184
|
3.2
|
24.1
|
1.0
|
O2
|
D:MPD602
|
3.8
|
54.2
|
1.0
|
ND1
|
D:HIS501
|
4.2
|
26.4
|
1.0
|
CG
|
D:HIS501
|
4.2
|
28.8
|
1.0
|
ND1
|
D:HIS312
|
4.2
|
27.1
|
1.0
|
ND1
|
D:HIS242
|
4.2
|
33.2
|
1.0
|
CG2
|
D:ILE138
|
4.2
|
29.5
|
1.0
|
ND1
|
D:HIS184
|
4.2
|
24.5
|
1.0
|
CG
|
D:HIS312
|
4.3
|
27.6
|
1.0
|
CG
|
D:HIS242
|
4.3
|
32.6
|
1.0
|
CG
|
D:HIS184
|
4.3
|
25.6
|
1.0
|
C1
|
D:MPD602
|
5.0
|
52.7
|
1.0
|
OG
|
D:SER183
|
5.0
|
31.6
|
1.0
|
|
Iron binding site 5 out
of 8 in 8fty
Go back to
Iron Binding Sites List in 8fty
Iron binding site 5 out
of 8 in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of the Carotenoid Isomerooxygenase, Ninab within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe601
b:27.0
occ:1.00
|
NE2
|
E:HIS312
|
2.1
|
24.3
|
1.0
|
NE2
|
E:HIS501
|
2.2
|
25.5
|
1.0
|
NE2
|
E:HIS184
|
2.2
|
23.5
|
1.0
|
NE2
|
E:HIS242
|
2.2
|
23.3
|
1.0
|
O
|
E:HOH726
|
2.3
|
27.1
|
1.0
|
CD2
|
E:HIS501
|
3.0
|
26.5
|
1.0
|
CE1
|
E:HIS501
|
3.1
|
25.4
|
1.0
|
CE1
|
E:HIS312
|
3.1
|
24.1
|
1.0
|
CE1
|
E:HIS184
|
3.1
|
23.3
|
1.0
|
CE1
|
E:HIS242
|
3.1
|
24.5
|
1.0
|
CD2
|
E:HIS312
|
3.1
|
24.5
|
1.0
|
CD2
|
E:HIS184
|
3.2
|
23.2
|
1.0
|
CD2
|
E:HIS242
|
3.2
|
22.9
|
1.0
|
O
|
E:HOH1003
|
3.9
|
44.4
|
1.0
|
O2
|
E:MPD602
|
4.1
|
42.2
|
1.0
|
ND1
|
E:HIS501
|
4.1
|
25.0
|
1.0
|
CG
|
E:HIS501
|
4.1
|
25.6
|
1.0
|
CG2
|
E:ILE138
|
4.2
|
29.7
|
1.0
|
ND1
|
E:HIS312
|
4.2
|
23.3
|
1.0
|
ND1
|
E:HIS184
|
4.2
|
22.1
|
1.0
|
ND1
|
E:HIS242
|
4.3
|
23.2
|
1.0
|
CG
|
E:HIS312
|
4.3
|
23.8
|
1.0
|
CG
|
E:HIS184
|
4.3
|
22.8
|
1.0
|
CG
|
E:HIS242
|
4.3
|
23.8
|
1.0
|
OG
|
E:SER183
|
5.0
|
28.2
|
1.0
|
|
Iron binding site 6 out
of 8 in 8fty
Go back to
Iron Binding Sites List in 8fty
Iron binding site 6 out
of 8 in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of the Carotenoid Isomerooxygenase, Ninab within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe1000
b:23.2
occ:1.00
|
NE2
|
F:HIS312
|
2.1
|
24.1
|
1.0
|
O
|
F:HOH1220
|
2.1
|
19.9
|
1.0
|
NE2
|
F:HIS184
|
2.1
|
21.0
|
1.0
|
NE2
|
F:HIS242
|
2.1
|
21.0
|
1.0
|
NE2
|
F:HIS501
|
2.2
|
24.7
|
1.0
|
CE1
|
F:HIS312
|
3.0
|
25.4
|
1.0
|
CE1
|
F:HIS184
|
3.1
|
21.2
|
1.0
|
CE1
|
F:HIS242
|
3.1
|
21.5
|
1.0
|
CD2
|
F:HIS501
|
3.1
|
24.4
|
1.0
|
CE1
|
F:HIS501
|
3.1
|
24.3
|
1.0
|
CD2
|
F:HIS312
|
3.1
|
24.0
|
1.0
|
CD2
|
F:HIS184
|
3.1
|
20.9
|
1.0
|
CD2
|
F:HIS242
|
3.2
|
20.8
|
1.0
|
O
|
F:HOH1397
|
3.7
|
33.3
|
1.0
|
ND1
|
F:HIS501
|
4.1
|
23.8
|
1.0
|
O2
|
F:MPD1001
|
4.2
|
46.2
|
1.0
|
CG
|
F:HIS501
|
4.2
|
24.4
|
1.0
|
ND1
|
F:HIS312
|
4.2
|
24.1
|
1.0
|
ND1
|
F:HIS184
|
4.2
|
20.8
|
1.0
|
ND1
|
F:HIS242
|
4.2
|
20.6
|
1.0
|
CG
|
F:HIS312
|
4.2
|
24.4
|
1.0
|
CG2
|
F:ILE138
|
4.2
|
26.3
|
1.0
|
CG
|
F:HIS184
|
4.2
|
20.3
|
1.0
|
CG
|
F:HIS242
|
4.3
|
20.9
|
1.0
|
OG
|
F:SER183
|
5.0
|
25.6
|
1.0
|
|
Iron binding site 7 out
of 8 in 8fty
Go back to
Iron Binding Sites List in 8fty
Iron binding site 7 out
of 8 in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of the Carotenoid Isomerooxygenase, Ninab within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe601
b:24.6
occ:1.00
|
O
|
G:HOH808
|
2.0
|
17.1
|
1.0
|
NE2
|
G:HIS312
|
2.1
|
25.6
|
1.0
|
NE2
|
G:HIS242
|
2.1
|
26.7
|
1.0
|
NE2
|
G:HIS184
|
2.2
|
20.8
|
1.0
|
NE2
|
G:HIS501
|
2.2
|
26.9
|
1.0
|
CE1
|
G:HIS312
|
3.0
|
25.4
|
1.0
|
CE1
|
G:HIS242
|
3.0
|
27.6
|
1.0
|
CD2
|
G:HIS242
|
3.1
|
26.9
|
1.0
|
CD2
|
G:HIS312
|
3.1
|
25.1
|
1.0
|
CD2
|
G:HIS501
|
3.1
|
24.9
|
1.0
|
CE1
|
G:HIS184
|
3.1
|
21.6
|
1.0
|
CE1
|
G:HIS501
|
3.1
|
25.5
|
1.0
|
CD2
|
G:HIS184
|
3.2
|
20.8
|
1.0
|
O2
|
G:MPD602
|
4.0
|
50.2
|
1.0
|
ND1
|
G:HIS312
|
4.2
|
24.7
|
1.0
|
ND1
|
G:HIS242
|
4.2
|
25.9
|
1.0
|
ND1
|
G:HIS501
|
4.2
|
25.0
|
1.0
|
CG
|
G:HIS501
|
4.2
|
25.8
|
1.0
|
CG
|
G:HIS242
|
4.2
|
26.4
|
1.0
|
CG
|
G:HIS312
|
4.2
|
24.3
|
1.0
|
CG2
|
G:ILE138
|
4.2
|
29.7
|
1.0
|
ND1
|
G:HIS184
|
4.3
|
20.9
|
1.0
|
CG
|
G:HIS184
|
4.3
|
21.2
|
1.0
|
OG
|
G:SER183
|
5.0
|
28.0
|
1.0
|
|
Iron binding site 8 out
of 8 in 8fty
Go back to
Iron Binding Sites List in 8fty
Iron binding site 8 out
of 8 in the Crystal Structure of the Carotenoid Isomerooxygenase, Ninab
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of the Carotenoid Isomerooxygenase, Ninab within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe1000
b:28.4
occ:1.00
|
O
|
H:HOH1110
|
2.0
|
29.7
|
1.0
|
NE2
|
H:HIS312
|
2.1
|
26.7
|
1.0
|
NE2
|
H:HIS242
|
2.1
|
28.5
|
1.0
|
NE2
|
H:HIS184
|
2.2
|
26.7
|
1.0
|
NE2
|
H:HIS501
|
2.3
|
27.1
|
1.0
|
CE1
|
H:HIS312
|
3.0
|
27.0
|
1.0
|
CE1
|
H:HIS242
|
3.1
|
29.3
|
1.0
|
CD2
|
H:HIS312
|
3.1
|
27.0
|
1.0
|
CD2
|
H:HIS242
|
3.1
|
28.2
|
1.0
|
CE1
|
H:HIS184
|
3.1
|
26.6
|
1.0
|
CD2
|
H:HIS501
|
3.1
|
27.9
|
1.0
|
CE1
|
H:HIS501
|
3.1
|
26.6
|
1.0
|
CD2
|
H:HIS184
|
3.2
|
25.0
|
1.0
|
O2
|
H:MPD1001
|
3.7
|
51.1
|
1.0
|
ND1
|
H:HIS312
|
4.1
|
26.9
|
1.0
|
ND1
|
H:HIS242
|
4.2
|
29.1
|
1.0
|
ND1
|
H:HIS501
|
4.2
|
26.7
|
1.0
|
CG
|
H:HIS312
|
4.2
|
27.1
|
1.0
|
CG
|
H:HIS501
|
4.2
|
28.9
|
1.0
|
CG
|
H:HIS242
|
4.2
|
28.9
|
1.0
|
ND1
|
H:HIS184
|
4.2
|
27.1
|
1.0
|
CG
|
H:HIS184
|
4.3
|
26.3
|
1.0
|
CG2
|
H:ILE138
|
4.3
|
31.8
|
1.0
|
C2
|
H:MPD1001
|
4.9
|
48.5
|
1.0
|
OG
|
H:SER183
|
5.0
|
28.6
|
1.0
|
|
Reference:
Y.J.Solano,
P.D.Kiser.
Structure of the Carotenoid Isomerooxygenase To Be Published.
Page generated: Sat Aug 10 04:31:00 2024
|