Iron in PDB 7urh: Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
Enzymatic activity of Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
All present enzymatic activity of Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2:
1.16.3.1;
Protein crystallography data
The structure of Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2, PDB code: 7urh
was solved by
T.R.Malcolm,
M.J.Maher,
S.S.M.Mubarak,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.51 /
1.47
|
Space group
|
I 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
154.84,
154.84,
128.763,
90,
90,
90
|
R / Rfree (%)
|
15.9 /
17.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
(pdb code 7urh). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2, PDB code: 7urh:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 7urh
Go back to
Iron Binding Sites List in 7urh
Iron binding site 1 out
of 6 in the Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
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 Ferritin 2 From Caenorhabditis Elegans, Ftn-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:16.2
occ:0.80
|
OE2
|
A:GLU58
|
2.0
|
17.3
|
1.0
|
OE1
|
A:GLU23
|
2.0
|
16.7
|
1.0
|
O
|
A:HOH447
|
2.2
|
23.6
|
1.0
|
ND1
|
A:HIS61
|
2.2
|
18.4
|
1.0
|
O
|
A:HOH314
|
2.3
|
23.7
|
1.0
|
ND2
|
A:ASN106
|
2.4
|
24.1
|
1.0
|
CD
|
A:GLU58
|
3.0
|
17.6
|
1.0
|
CE1
|
A:HIS61
|
3.0
|
18.2
|
1.0
|
CD
|
A:GLU23
|
3.1
|
16.3
|
1.0
|
CG
|
A:HIS61
|
3.3
|
17.5
|
1.0
|
OE1
|
A:GLU58
|
3.4
|
19.9
|
1.0
|
CG
|
A:ASN106
|
3.5
|
23.7
|
1.0
|
OE2
|
A:GLU23
|
3.5
|
18.1
|
1.0
|
CB
|
A:HIS61
|
3.7
|
16.1
|
1.0
|
OD1
|
A:ASN106
|
3.8
|
26.9
|
1.0
|
NE2
|
A:GLN137
|
4.1
|
23.1
|
1.0
|
O
|
A:HOH434
|
4.2
|
31.1
|
1.0
|
NE2
|
A:HIS61
|
4.2
|
18.7
|
1.0
|
CG
|
A:GLU58
|
4.4
|
16.2
|
1.0
|
CD2
|
A:HIS61
|
4.4
|
18.2
|
1.0
|
O
|
A:HOH457
|
4.4
|
22.9
|
1.0
|
CG
|
A:GLU23
|
4.4
|
15.3
|
1.0
|
O
|
A:HOH490
|
4.6
|
25.7
|
1.0
|
CA
|
A:GLU58
|
4.6
|
15.2
|
1.0
|
CB
|
A:GLU58
|
4.7
|
15.4
|
1.0
|
CB
|
A:ASN106
|
4.7
|
20.3
|
1.0
|
CB
|
A:GLU23
|
4.8
|
14.4
|
1.0
|
CA
|
A:GLU23
|
5.0
|
13.7
|
1.0
|
|
Iron binding site 2 out
of 6 in 7urh
Go back to
Iron Binding Sites List in 7urh
Iron binding site 2 out
of 6 in the Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
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 Ferritin 2 From Caenorhabditis Elegans, Ftn-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:16.7
occ:0.80
|
OE2
|
C:GLU58
|
2.0
|
17.0
|
1.0
|
OE1
|
C:GLU23
|
2.0
|
17.2
|
1.0
|
O
|
C:HOH452
|
2.1
|
24.8
|
1.0
|
ND1
|
C:HIS61
|
2.2
|
19.1
|
1.0
|
O
|
C:HOH305
|
2.3
|
23.5
|
1.0
|
ND2
|
C:ASN106
|
2.5
|
23.0
|
1.0
|
CD
|
C:GLU58
|
3.0
|
17.2
|
1.0
|
CE1
|
C:HIS61
|
3.1
|
19.5
|
1.0
|
CD
|
C:GLU23
|
3.1
|
16.9
|
1.0
|
OE1
|
C:GLU58
|
3.3
|
20.9
|
1.0
|
CG
|
C:HIS61
|
3.3
|
17.4
|
1.0
|
CG
|
C:ASN106
|
3.5
|
22.8
|
1.0
|
OE2
|
C:GLU23
|
3.5
|
19.3
|
1.0
|
CB
|
C:HIS61
|
3.7
|
16.5
|
1.0
|
OD1
|
C:ASN106
|
3.8
|
25.8
|
1.0
|
OE1
|
C:GLN137
|
4.1
|
24.3
|
1.0
|
O
|
C:HOH449
|
4.2
|
33.0
|
1.0
|
NE2
|
C:HIS61
|
4.3
|
18.7
|
1.0
|
CG
|
C:GLU58
|
4.3
|
16.0
|
1.0
|
O
|
C:HOH469
|
4.4
|
23.2
|
1.0
|
CG
|
C:GLU23
|
4.4
|
15.6
|
1.0
|
CD2
|
C:HIS61
|
4.4
|
18.4
|
1.0
|
O
|
C:HOH497
|
4.5
|
26.7
|
1.0
|
CA
|
C:GLU58
|
4.6
|
15.1
|
1.0
|
CB
|
C:GLU58
|
4.7
|
15.1
|
1.0
|
CB
|
C:ASN106
|
4.7
|
20.1
|
1.0
|
CB
|
C:GLU23
|
4.8
|
14.7
|
1.0
|
CA
|
C:GLU23
|
5.0
|
14.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 7urh
Go back to
Iron Binding Sites List in 7urh
Iron binding site 3 out
of 6 in the Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
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 Ferritin 2 From Caenorhabditis Elegans, Ftn-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:16.2
occ:0.80
|
OE2
|
E:GLU58
|
2.0
|
17.0
|
1.0
|
OE1
|
E:GLU23
|
2.1
|
17.0
|
1.0
|
O
|
E:HOH453
|
2.1
|
24.3
|
1.0
|
ND1
|
E:HIS61
|
2.2
|
18.2
|
1.0
|
O
|
E:HOH308
|
2.3
|
23.7
|
1.0
|
ND2
|
E:ASN106
|
2.4
|
23.2
|
1.0
|
CD
|
E:GLU58
|
3.0
|
17.4
|
1.0
|
CD
|
E:GLU23
|
3.1
|
17.1
|
1.0
|
CE1
|
E:HIS61
|
3.1
|
18.6
|
1.0
|
OE1
|
E:GLU58
|
3.3
|
20.2
|
1.0
|
CG
|
E:HIS61
|
3.3
|
17.3
|
1.0
|
CG
|
E:ASN106
|
3.5
|
22.9
|
1.0
|
OE2
|
E:GLU23
|
3.5
|
18.0
|
1.0
|
CB
|
E:HIS61
|
3.7
|
16.5
|
1.0
|
OD1
|
E:ASN106
|
3.8
|
25.7
|
1.0
|
OE1
|
E:GLN137
|
4.1
|
24.6
|
1.0
|
O
|
E:HOH442
|
4.2
|
30.9
|
1.0
|
NE2
|
E:HIS61
|
4.3
|
18.4
|
1.0
|
CG
|
E:GLU58
|
4.4
|
16.2
|
1.0
|
CD2
|
E:HIS61
|
4.4
|
18.7
|
1.0
|
CG
|
E:GLU23
|
4.4
|
15.3
|
1.0
|
O
|
E:HOH464
|
4.4
|
23.2
|
1.0
|
O
|
E:HOH487
|
4.5
|
26.4
|
1.0
|
CA
|
E:GLU58
|
4.6
|
15.2
|
1.0
|
CB
|
E:GLU58
|
4.7
|
15.4
|
1.0
|
CB
|
E:ASN106
|
4.7
|
19.5
|
1.0
|
CB
|
E:GLU23
|
4.8
|
14.4
|
1.0
|
CA
|
E:GLU23
|
5.0
|
13.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 7urh
Go back to
Iron Binding Sites List in 7urh
Iron binding site 4 out
of 6 in the Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
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 Ferritin 2 From Caenorhabditis Elegans, Ftn-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:17.9
occ:0.80
|
OE1
|
G:GLU23
|
2.0
|
17.5
|
1.0
|
OE2
|
G:GLU58
|
2.0
|
16.8
|
1.0
|
O
|
G:HOH444
|
2.1
|
23.1
|
1.0
|
ND1
|
G:HIS61
|
2.2
|
20.0
|
1.0
|
O
|
G:HOH309
|
2.3
|
23.9
|
1.0
|
ND2
|
G:ASN106
|
2.5
|
23.4
|
1.0
|
CD
|
G:GLU58
|
3.0
|
18.1
|
1.0
|
CD
|
G:GLU23
|
3.1
|
17.0
|
1.0
|
CE1
|
G:HIS61
|
3.1
|
20.4
|
1.0
|
OE1
|
G:GLU58
|
3.3
|
21.0
|
1.0
|
CG
|
G:HIS61
|
3.3
|
18.7
|
1.0
|
OE2
|
G:GLU23
|
3.5
|
19.4
|
1.0
|
CG
|
G:ASN106
|
3.5
|
22.9
|
1.0
|
CB
|
G:HIS61
|
3.7
|
17.8
|
1.0
|
OD1
|
G:ASN106
|
3.9
|
27.4
|
1.0
|
OE1
|
G:GLN137
|
4.1
|
24.3
|
1.0
|
O
|
G:HOH445
|
4.2
|
30.9
|
1.0
|
NE2
|
G:HIS61
|
4.3
|
19.8
|
1.0
|
CG
|
G:GLU58
|
4.4
|
16.6
|
1.0
|
CG
|
G:GLU23
|
4.4
|
15.8
|
1.0
|
O
|
G:HOH453
|
4.4
|
23.9
|
1.0
|
CD2
|
G:HIS61
|
4.4
|
19.9
|
1.0
|
O
|
G:HOH478
|
4.5
|
25.5
|
1.0
|
CA
|
G:GLU58
|
4.7
|
16.1
|
1.0
|
CB
|
G:GLU58
|
4.8
|
15.8
|
1.0
|
CB
|
G:ASN106
|
4.8
|
19.7
|
1.0
|
CB
|
G:GLU23
|
4.8
|
14.8
|
1.0
|
CA
|
G:GLU23
|
5.0
|
14.2
|
1.0
|
|
Iron binding site 5 out
of 6 in 7urh
Go back to
Iron Binding Sites List in 7urh
Iron binding site 5 out
of 6 in the Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
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 Ferritin 2 From Caenorhabditis Elegans, Ftn-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe201
b:16.8
occ:0.80
|
OE2
|
I:GLU58
|
2.0
|
17.2
|
1.0
|
OE1
|
I:GLU23
|
2.1
|
18.5
|
1.0
|
O
|
I:HOH443
|
2.1
|
22.3
|
1.0
|
ND1
|
I:HIS61
|
2.2
|
19.2
|
1.0
|
O
|
I:HOH309
|
2.4
|
22.9
|
1.0
|
ND2
|
I:ASN106
|
2.4
|
21.7
|
1.0
|
CD
|
I:GLU58
|
3.0
|
17.9
|
1.0
|
CE1
|
I:HIS61
|
3.0
|
19.3
|
1.0
|
CD
|
I:GLU23
|
3.1
|
18.3
|
1.0
|
OE1
|
I:GLU58
|
3.3
|
20.5
|
1.0
|
CG
|
I:HIS61
|
3.3
|
17.9
|
1.0
|
CG
|
I:ASN106
|
3.5
|
22.1
|
1.0
|
OE2
|
I:GLU23
|
3.5
|
20.4
|
1.0
|
CB
|
I:HIS61
|
3.7
|
17.0
|
1.0
|
OD1
|
I:ASN106
|
3.8
|
24.8
|
1.0
|
OE1
|
I:GLN137
|
4.1
|
24.8
|
1.0
|
NE2
|
I:HIS61
|
4.2
|
18.9
|
1.0
|
O
|
I:HOH441
|
4.3
|
29.3
|
1.0
|
CG
|
I:GLU58
|
4.4
|
16.7
|
1.0
|
CD2
|
I:HIS61
|
4.4
|
19.0
|
1.0
|
CG
|
I:GLU23
|
4.4
|
16.7
|
1.0
|
O
|
I:HOH460
|
4.4
|
24.9
|
1.0
|
O
|
I:HOH488
|
4.5
|
26.4
|
1.0
|
CA
|
I:GLU58
|
4.6
|
15.2
|
1.0
|
CB
|
I:GLU58
|
4.7
|
15.7
|
1.0
|
CB
|
I:ASN106
|
4.7
|
18.9
|
1.0
|
CB
|
I:GLU23
|
4.8
|
15.2
|
1.0
|
CA
|
I:GLU23
|
5.0
|
14.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 7urh
Go back to
Iron Binding Sites List in 7urh
Iron binding site 6 out
of 6 in the Crystal Structure of Ferritin 2 From Caenorhabditis Elegans, Ftn-2
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 Ferritin 2 From Caenorhabditis Elegans, Ftn-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Fe201
b:16.4
occ:0.80
|
OE1
|
K:GLU23
|
2.0
|
17.7
|
1.0
|
OE2
|
K:GLU58
|
2.0
|
18.0
|
1.0
|
O
|
K:HOH448
|
2.1
|
23.2
|
1.0
|
ND1
|
K:HIS61
|
2.2
|
18.4
|
1.0
|
O
|
K:HOH309
|
2.4
|
24.0
|
1.0
|
ND2
|
K:ASN106
|
2.4
|
23.9
|
1.0
|
CD
|
K:GLU58
|
3.0
|
18.1
|
1.0
|
CE1
|
K:HIS61
|
3.1
|
19.1
|
1.0
|
CD
|
K:GLU23
|
3.1
|
17.8
|
1.0
|
CG
|
K:HIS61
|
3.3
|
17.9
|
1.0
|
OE1
|
K:GLU58
|
3.3
|
21.0
|
1.0
|
CG
|
K:ASN106
|
3.5
|
23.9
|
1.0
|
OE2
|
K:GLU23
|
3.5
|
19.1
|
1.0
|
CB
|
K:HIS61
|
3.7
|
16.7
|
1.0
|
OD1
|
K:ASN106
|
3.8
|
27.5
|
1.0
|
OE1
|
K:GLN137
|
4.1
|
25.8
|
1.0
|
NE2
|
K:HIS61
|
4.3
|
18.9
|
1.0
|
O
|
K:HOH457
|
4.3
|
30.4
|
1.0
|
CG
|
K:GLU58
|
4.4
|
17.0
|
1.0
|
CD2
|
K:HIS61
|
4.4
|
19.4
|
1.0
|
CG
|
K:GLU23
|
4.4
|
16.6
|
1.0
|
O
|
K:HOH465
|
4.4
|
23.9
|
1.0
|
O
|
K:HOH484
|
4.5
|
28.4
|
1.0
|
CA
|
K:GLU58
|
4.6
|
15.5
|
1.0
|
CB
|
K:GLU58
|
4.7
|
15.8
|
1.0
|
CB
|
K:ASN106
|
4.7
|
20.9
|
1.0
|
CB
|
K:GLU23
|
4.8
|
15.6
|
1.0
|
CA
|
K:GLU23
|
5.0
|
15.0
|
1.0
|
|
Reference:
S.S.M.Mubarak,
T.R.Malcolm,
H.G.Brown,
E.Hanssen,
M.J.Maher,
G.Mccoll,
G.N.L.Jameson.
Biochemical Characterization of Caenorhabditis Elegans Ferritins. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37014173
DOI: 10.1021/ACS.BIOCHEM.3C00005
Page generated: Fri Aug 9 02:53:35 2024
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