Iron in PDB 6p5q: X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid
Protein crystallography data
The structure of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid, PDB code: 6p5q
was solved by
L.J.Rajakovich,
A.J.Mitchell,
A.K.Boal,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.08 /
1.86
|
Space group
|
P 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.009,
74.148,
142.563,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.8 /
21.7
|
Iron Binding Sites:
The binding sites of Iron atom in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid
(pdb code 6p5q). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid, PDB code: 6p5q:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6p5q
Go back to
Iron Binding Sites List in 6p5q
Iron binding site 1 out
of 4 in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:20.6
occ:0.55
|
OE1
|
A:GLU159
|
2.0
|
29.3
|
1.0
|
O
|
A:HOH403
|
2.3
|
20.3
|
1.0
|
O
|
A:HOH534
|
2.3
|
29.5
|
1.0
|
ND1
|
A:HIS201
|
2.5
|
44.7
|
1.0
|
CD
|
A:GLU159
|
3.2
|
28.3
|
1.0
|
CE1
|
A:HIS201
|
3.3
|
39.4
|
1.0
|
HE1
|
A:HIS201
|
3.3
|
47.3
|
1.0
|
CG
|
A:HIS201
|
3.6
|
40.2
|
1.0
|
HG2
|
A:GLU159
|
3.6
|
30.6
|
1.0
|
HB3
|
A:GLU159
|
3.7
|
22.3
|
1.0
|
HB3
|
A:HIS201
|
3.7
|
31.9
|
1.0
|
HB2
|
A:HIS201
|
3.8
|
31.9
|
1.0
|
OE2
|
A:GLU101
|
3.9
|
36.0
|
1.0
|
CG
|
A:GLU159
|
3.9
|
25.5
|
1.0
|
CB
|
A:HIS201
|
3.9
|
26.5
|
1.0
|
O
|
A:HOH486
|
4.0
|
24.9
|
1.0
|
HD2
|
A:HIS194
|
4.1
|
21.8
|
1.0
|
OE2
|
A:GLU159
|
4.2
|
24.3
|
1.0
|
O2
|
A:DAO301
|
4.2
|
19.9
|
1.0
|
CB
|
A:GLU159
|
4.3
|
18.5
|
1.0
|
NE2
|
A:HIS201
|
4.5
|
41.3
|
1.0
|
CD2
|
A:HIS201
|
4.6
|
36.1
|
1.0
|
OD2
|
A:ASP199
|
4.8
|
46.2
|
1.0
|
HE2
|
A:PHE68
|
4.8
|
20.8
|
1.0
|
HG3
|
A:GLU159
|
4.8
|
30.6
|
1.0
|
CD2
|
A:HIS194
|
4.8
|
18.2
|
1.0
|
FE
|
A:FE303
|
4.9
|
21.3
|
1.0
|
HB2
|
A:GLU159
|
5.0
|
22.3
|
1.0
|
HE1
|
A:HIS104
|
5.0
|
20.8
|
1.0
|
HA
|
A:GLU159
|
5.0
|
18.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 6p5q
Go back to
Iron Binding Sites List in 6p5q
Iron binding site 2 out
of 4 in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:21.3
occ:0.96
|
O
|
A:HOH401
|
2.1
|
23.6
|
1.0
|
ND1
|
A:HIS104
|
2.2
|
15.1
|
1.0
|
O2
|
A:DAO301
|
2.2
|
19.9
|
1.0
|
NE2
|
A:HIS194
|
2.2
|
18.5
|
1.0
|
OE1
|
A:GLU101
|
2.3
|
22.8
|
1.0
|
CD
|
A:GLU101
|
3.0
|
28.1
|
1.0
|
CE1
|
A:HIS104
|
3.0
|
17.3
|
1.0
|
OE2
|
A:GLU101
|
3.0
|
36.0
|
1.0
|
CE1
|
A:HIS194
|
3.1
|
20.8
|
1.0
|
HE1
|
A:HIS104
|
3.1
|
20.8
|
1.0
|
C1
|
A:DAO301
|
3.1
|
26.0
|
1.0
|
HE1
|
A:HIS194
|
3.1
|
25.0
|
1.0
|
CG
|
A:HIS104
|
3.2
|
16.6
|
1.0
|
O1
|
A:DAO301
|
3.3
|
22.5
|
1.0
|
CD2
|
A:HIS194
|
3.3
|
18.2
|
1.0
|
HB3
|
A:HIS104
|
3.3
|
22.7
|
1.0
|
HD2
|
A:HIS194
|
3.6
|
21.8
|
1.0
|
CB
|
A:HIS104
|
3.7
|
18.9
|
1.0
|
HB2
|
A:HIS104
|
3.7
|
22.7
|
1.0
|
O
|
A:HOH416
|
3.9
|
31.2
|
1.0
|
O
|
A:HOH403
|
3.9
|
20.3
|
1.0
|
HE1
|
A:TRP190
|
4.1
|
17.1
|
1.0
|
NE2
|
A:HIS104
|
4.2
|
15.6
|
1.0
|
HA
|
A:GLU101
|
4.2
|
27.4
|
1.0
|
ND1
|
A:HIS194
|
4.2
|
16.2
|
1.0
|
CD2
|
A:HIS104
|
4.3
|
21.7
|
1.0
|
CG
|
A:HIS194
|
4.4
|
19.2
|
1.0
|
CG
|
A:GLU101
|
4.4
|
18.3
|
1.0
|
C2
|
A:DAO301
|
4.5
|
19.4
|
1.0
|
NE1
|
A:TRP190
|
4.6
|
14.2
|
1.0
|
HZ2
|
A:TRP190
|
4.6
|
17.1
|
1.0
|
HB3
|
A:GLU101
|
4.6
|
26.1
|
1.0
|
H22
|
A:DAO301
|
4.7
|
23.4
|
1.0
|
H21
|
A:DAO301
|
4.8
|
23.4
|
1.0
|
FE
|
A:FE302
|
4.9
|
20.6
|
0.6
|
HG3
|
A:GLU101
|
4.9
|
22.0
|
1.0
|
HG13
|
A:VAL65
|
4.9
|
19.3
|
1.0
|
HE2
|
A:HIS104
|
4.9
|
18.7
|
1.0
|
CB
|
A:GLU101
|
4.9
|
21.8
|
1.0
|
HG2
|
A:GLU101
|
4.9
|
22.0
|
1.0
|
CA
|
A:GLU101
|
5.0
|
22.8
|
1.0
|
HD1
|
A:HIS194
|
5.0
|
19.5
|
1.0
|
HG12
|
A:VAL100
|
5.0
|
22.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 6p5q
Go back to
Iron Binding Sites List in 6p5q
Iron binding site 3 out
of 4 in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe302
b:53.8
occ:0.90
|
O
|
B:HOH402
|
2.0
|
38.9
|
1.0
|
OE1
|
B:GLU159
|
2.2
|
46.7
|
1.0
|
ND1
|
B:HIS201
|
2.5
|
61.9
|
1.0
|
CD
|
B:GLU159
|
3.2
|
38.8
|
1.0
|
HE1
|
B:HIS201
|
3.2
|
64.5
|
1.0
|
HG2
|
B:GLU159
|
3.3
|
38.6
|
1.0
|
CE1
|
B:HIS201
|
3.3
|
53.7
|
1.0
|
CG
|
B:HIS201
|
3.7
|
59.7
|
1.0
|
CG
|
B:GLU159
|
3.7
|
32.2
|
1.0
|
HD2
|
B:HIS194
|
3.8
|
32.5
|
1.0
|
HB2
|
B:HIS201
|
3.9
|
51.1
|
1.0
|
OE2
|
B:GLU101
|
3.9
|
47.9
|
1.0
|
HB3
|
B:HIS201
|
3.9
|
51.1
|
1.0
|
O1
|
B:DAO301
|
4.0
|
30.2
|
1.0
|
HB3
|
B:GLU159
|
4.0
|
35.1
|
1.0
|
CB
|
B:HIS201
|
4.1
|
42.5
|
1.0
|
OE2
|
B:GLU159
|
4.3
|
29.6
|
1.0
|
CD2
|
B:HIS194
|
4.4
|
27.1
|
1.0
|
NE2
|
B:HIS201
|
4.5
|
61.3
|
1.0
|
CB
|
B:GLU159
|
4.5
|
29.2
|
1.0
|
HG3
|
B:GLU159
|
4.5
|
38.6
|
1.0
|
HD22
|
B:ASN97
|
4.6
|
66.4
|
1.0
|
FE
|
B:FE303
|
4.6
|
32.7
|
1.0
|
CD2
|
B:HIS201
|
4.7
|
61.5
|
1.0
|
HE1
|
B:HIS104
|
4.7
|
34.7
|
1.0
|
NE2
|
B:HIS194
|
4.8
|
31.9
|
1.0
|
HE2
|
B:PHE68
|
4.8
|
33.0
|
1.0
|
CD
|
B:GLU101
|
5.0
|
38.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 6p5q
Go back to
Iron Binding Sites List in 6p5q
Iron binding site 4 out
of 4 in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe303
b:32.7
occ:0.97
|
O
|
B:HOH401
|
2.1
|
27.3
|
1.0
|
OE1
|
B:GLU101
|
2.2
|
35.8
|
1.0
|
ND1
|
B:HIS104
|
2.2
|
30.7
|
1.0
|
O1
|
B:DAO301
|
2.2
|
30.2
|
1.0
|
NE2
|
B:HIS194
|
2.3
|
31.9
|
1.0
|
CE1
|
B:HIS194
|
3.0
|
33.0
|
1.0
|
HE1
|
B:HIS194
|
3.0
|
39.6
|
1.0
|
CD
|
B:GLU101
|
3.1
|
38.5
|
1.0
|
C1
|
B:DAO301
|
3.1
|
34.6
|
1.0
|
HB3
|
B:HIS104
|
3.2
|
36.2
|
1.0
|
CE1
|
B:HIS104
|
3.2
|
28.9
|
1.0
|
CG
|
B:HIS104
|
3.2
|
29.0
|
1.0
|
O2
|
B:DAO301
|
3.2
|
30.7
|
1.0
|
HE1
|
B:HIS104
|
3.3
|
34.7
|
1.0
|
OE2
|
B:GLU101
|
3.4
|
47.9
|
1.0
|
CD2
|
B:HIS194
|
3.4
|
27.1
|
1.0
|
CB
|
B:HIS104
|
3.5
|
30.1
|
1.0
|
O
|
B:HOH402
|
3.6
|
38.9
|
1.0
|
HB2
|
B:HIS104
|
3.6
|
36.2
|
1.0
|
HD2
|
B:HIS194
|
3.7
|
32.5
|
1.0
|
HE1
|
B:TRP190
|
4.1
|
29.9
|
1.0
|
HA
|
B:GLU101
|
4.2
|
46.3
|
1.0
|
ND1
|
B:HIS194
|
4.2
|
32.1
|
1.0
|
NE2
|
B:HIS104
|
4.3
|
27.5
|
1.0
|
CD2
|
B:HIS104
|
4.4
|
33.5
|
1.0
|
CG
|
B:HIS194
|
4.4
|
31.9
|
1.0
|
HB3
|
B:GLU101
|
4.5
|
40.8
|
1.0
|
CG
|
B:GLU101
|
4.5
|
26.8
|
1.0
|
C2
|
B:DAO301
|
4.6
|
29.2
|
1.0
|
NE1
|
B:TRP190
|
4.6
|
24.9
|
1.0
|
FE
|
B:FE302
|
4.6
|
53.8
|
0.9
|
HZ2
|
B:TRP190
|
4.7
|
29.9
|
1.0
|
H21
|
B:DAO301
|
4.8
|
35.1
|
1.0
|
HG13
|
B:VAL65
|
4.8
|
30.9
|
1.0
|
H22
|
B:DAO301
|
4.9
|
35.1
|
1.0
|
CB
|
B:GLU101
|
4.9
|
34.0
|
1.0
|
HG3
|
B:GLU101
|
4.9
|
32.1
|
1.0
|
HD1
|
B:HIS194
|
5.0
|
38.6
|
1.0
|
HG12
|
B:VAL100
|
5.0
|
48.9
|
1.0
|
CA
|
B:GLU101
|
5.0
|
38.5
|
1.0
|
|
Reference:
B.Zhang,
L.J.Rajakovich,
D.Van Cura,
E.J.Blaesi,
A.J.Mitchell,
C.R.Tysoe,
X.Zhu,
B.R.Streit,
Z.Rui,
W.Zhang,
A.K.Boal,
C.Krebs,
J.M.Bollinger Jr..
Substrate-Triggered Formation of A Peroxo-FE2(III/III) Intermediate During Fatty Acid Decarboxylation By Unda. J.Am.Chem.Soc. V. 141 14510 2019.
ISSN: ESSN 1520-5126
PubMed: 31487162
DOI: 10.1021/JACS.9B06093
Page generated: Wed Aug 7 05:38:21 2024
|