Iron in PDB 6w32: Crystal Structure of SFH5
Protein crystallography data
The structure of Crystal Structure of SFH5, PDB code: 6w32
was solved by
G.Gulten,
D.Khan,
A.Aggarwal,
I.Krieger,
J.C.Sacchettini,
V.A.Bankaitis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.32 /
2.90
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
205.343,
205.343,
68.313,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.9 /
30.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of SFH5
(pdb code 6w32). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the
Crystal Structure of SFH5, PDB code: 6w32:
Jump to Iron binding site number:
1;
2;
3;
Iron binding site 1 out
of 3 in 6w32
Go back to
Iron Binding Sites List in 6w32
Iron binding site 1 out
of 3 in the Crystal Structure of SFH5
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 SFH5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe301
b:53.2
occ:1.00
|
FE
|
B:HEM301
|
0.0
|
53.2
|
1.0
|
NB
|
B:HEM301
|
2.0
|
53.6
|
1.0
|
NA
|
B:HEM301
|
2.1
|
48.4
|
1.0
|
ND
|
B:HEM301
|
2.1
|
48.8
|
1.0
|
NC
|
B:HEM301
|
2.1
|
47.6
|
1.0
|
OH
|
B:TYR175
|
2.3
|
48.9
|
1.0
|
C4B
|
B:HEM301
|
3.0
|
54.8
|
1.0
|
C1A
|
B:HEM301
|
3.0
|
50.9
|
1.0
|
C1C
|
B:HEM301
|
3.1
|
50.8
|
1.0
|
C1B
|
B:HEM301
|
3.1
|
47.7
|
1.0
|
C4D
|
B:HEM301
|
3.1
|
44.7
|
1.0
|
C4C
|
B:HEM301
|
3.1
|
48.5
|
1.0
|
C4A
|
B:HEM301
|
3.1
|
46.9
|
1.0
|
C1D
|
B:HEM301
|
3.1
|
47.1
|
1.0
|
CZ
|
B:TYR175
|
3.1
|
49.5
|
1.0
|
CHC
|
B:HEM301
|
3.4
|
48.1
|
1.0
|
CHA
|
B:HEM301
|
3.4
|
52.0
|
1.0
|
CHD
|
B:HEM301
|
3.4
|
43.5
|
1.0
|
CHB
|
B:HEM301
|
3.4
|
50.1
|
1.0
|
CE1
|
B:TYR175
|
3.7
|
48.0
|
1.0
|
CD1
|
B:ILE225
|
4.0
|
51.5
|
1.0
|
OG
|
B:SER191
|
4.0
|
55.9
|
1.0
|
CE2
|
B:TYR175
|
4.1
|
48.1
|
1.0
|
ND1
|
B:HIS173
|
4.2
|
43.1
|
1.0
|
C3B
|
B:HEM301
|
4.3
|
52.8
|
1.0
|
C2B
|
B:HEM301
|
4.3
|
47.6
|
1.0
|
C2A
|
B:HEM301
|
4.3
|
46.5
|
1.0
|
C2C
|
B:HEM301
|
4.3
|
53.5
|
1.0
|
C3C
|
B:HEM301
|
4.3
|
50.1
|
1.0
|
C3D
|
B:HEM301
|
4.3
|
44.3
|
1.0
|
C3A
|
B:HEM301
|
4.3
|
48.6
|
1.0
|
C2D
|
B:HEM301
|
4.3
|
46.3
|
1.0
|
CE1
|
B:HIS173
|
4.7
|
44.3
|
1.0
|
CD1
|
B:TYR175
|
4.8
|
47.6
|
1.0
|
|
Iron binding site 2 out
of 3 in 6w32
Go back to
Iron Binding Sites List in 6w32
Iron binding site 2 out
of 3 in the Crystal Structure of SFH5
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 SFH5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:63.2
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
63.2
|
1.0
|
NB
|
A:HEM301
|
2.1
|
64.4
|
1.0
|
ND
|
A:HEM301
|
2.1
|
61.0
|
1.0
|
NA
|
A:HEM301
|
2.1
|
64.5
|
1.0
|
NC
|
A:HEM301
|
2.1
|
60.1
|
1.0
|
OH
|
A:TYR175
|
2.4
|
55.7
|
1.0
|
C1D
|
A:HEM301
|
3.0
|
59.6
|
1.0
|
C1A
|
A:HEM301
|
3.1
|
69.4
|
1.0
|
C4B
|
A:HEM301
|
3.1
|
67.1
|
1.0
|
C4C
|
A:HEM301
|
3.1
|
59.2
|
1.0
|
C4D
|
A:HEM301
|
3.1
|
62.2
|
1.0
|
C4A
|
A:HEM301
|
3.1
|
60.8
|
1.0
|
C1C
|
A:HEM301
|
3.1
|
62.1
|
1.0
|
C1B
|
A:HEM301
|
3.1
|
68.2
|
1.0
|
CHD
|
A:HEM301
|
3.4
|
61.1
|
1.0
|
CZ
|
A:TYR175
|
3.4
|
59.3
|
1.0
|
CHA
|
A:HEM301
|
3.4
|
61.5
|
1.0
|
CHC
|
A:HEM301
|
3.4
|
66.0
|
1.0
|
CHB
|
A:HEM301
|
3.5
|
66.1
|
1.0
|
CE1
|
A:TYR175
|
4.0
|
60.3
|
1.0
|
CD1
|
A:ILE225
|
4.2
|
68.0
|
1.0
|
C2D
|
A:HEM301
|
4.3
|
58.2
|
1.0
|
CE2
|
A:TYR175
|
4.3
|
57.4
|
1.0
|
C3B
|
A:HEM301
|
4.3
|
68.1
|
1.0
|
C2A
|
A:HEM301
|
4.3
|
72.3
|
1.0
|
C3D
|
A:HEM301
|
4.3
|
61.8
|
1.0
|
C3A
|
A:HEM301
|
4.3
|
64.5
|
1.0
|
C3C
|
A:HEM301
|
4.3
|
58.0
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
68.1
|
1.0
|
C2C
|
A:HEM301
|
4.3
|
62.7
|
1.0
|
ND1
|
A:HIS173
|
4.4
|
60.1
|
1.0
|
CE1
|
A:HIS173
|
4.6
|
57.9
|
1.0
|
CB
|
A:SER191
|
4.9
|
64.5
|
1.0
|
|
Iron binding site 3 out
of 3 in 6w32
Go back to
Iron Binding Sites List in 6w32
Iron binding site 3 out
of 3 in the Crystal Structure of SFH5
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 SFH5 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:67.3
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
67.3
|
1.0
|
NB
|
C:HEM301
|
2.0
|
55.4
|
1.0
|
NA
|
C:HEM301
|
2.0
|
63.5
|
1.0
|
ND
|
C:HEM301
|
2.1
|
60.8
|
1.0
|
NC
|
C:HEM301
|
2.1
|
53.7
|
1.0
|
OH
|
C:TYR175
|
2.5
|
62.1
|
1.0
|
C1A
|
C:HEM301
|
3.0
|
68.0
|
1.0
|
C4B
|
C:HEM301
|
3.0
|
56.3
|
1.0
|
C1D
|
C:HEM301
|
3.0
|
65.1
|
1.0
|
C4C
|
C:HEM301
|
3.0
|
58.3
|
1.0
|
C4D
|
C:HEM301
|
3.1
|
64.8
|
1.0
|
C1C
|
C:HEM301
|
3.1
|
59.7
|
1.0
|
C4A
|
C:HEM301
|
3.1
|
58.9
|
1.0
|
C1B
|
C:HEM301
|
3.1
|
61.4
|
1.0
|
CHD
|
C:HEM301
|
3.4
|
64.3
|
1.0
|
CHA
|
C:HEM301
|
3.4
|
69.3
|
1.0
|
CZ
|
C:TYR175
|
3.4
|
60.2
|
1.0
|
CHC
|
C:HEM301
|
3.4
|
60.9
|
1.0
|
CHB
|
C:HEM301
|
3.5
|
60.2
|
1.0
|
CE1
|
C:TYR175
|
3.8
|
55.7
|
1.0
|
C3B
|
C:HEM301
|
4.3
|
57.9
|
1.0
|
C2A
|
C:HEM301
|
4.3
|
68.8
|
1.0
|
C3C
|
C:HEM301
|
4.3
|
57.5
|
1.0
|
C3D
|
C:HEM301
|
4.3
|
64.8
|
1.0
|
C3A
|
C:HEM301
|
4.3
|
64.4
|
1.0
|
C2D
|
C:HEM301
|
4.3
|
61.5
|
1.0
|
C2B
|
C:HEM301
|
4.3
|
61.2
|
1.0
|
C2C
|
C:HEM301
|
4.3
|
59.9
|
1.0
|
ND1
|
C:HIS173
|
4.3
|
71.3
|
1.0
|
CE2
|
C:TYR175
|
4.4
|
61.6
|
1.0
|
CD1
|
C:ILE225
|
4.7
|
78.2
|
1.0
|
CE1
|
C:HIS173
|
4.7
|
67.3
|
1.0
|
CB
|
C:SER191
|
5.0
|
63.0
|
1.0
|
|
Reference:
D.Khan,
D.Lee,
G.Gulten,
A.Aggarwal,
J.Wofford,
I.Krieger,
A.Tripathi,
J.W.Patrick,
D.M.Eckert,
A.Laganowsky,
J.Sacchettini,
P.Lindahl,
V.A.Bankaitis.
A SEC14-Like Phosphatidylinositol Transfer Protein Paralog Defines A Novel Class of Heme-Binding Proteins. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 32780017
DOI: 10.7554/ELIFE.57081
Page generated: Wed Aug 7 13:51:54 2024
|