Iron in PDB 6wf2: Crystal Structure of Mouse SCD1 with A Diiron Center
Enzymatic activity of Crystal Structure of Mouse SCD1 with A Diiron Center
All present enzymatic activity of Crystal Structure of Mouse SCD1 with A Diiron Center:
1.14.19.1;
Protein crystallography data
The structure of Crystal Structure of Mouse SCD1 with A Diiron Center, PDB code: 6wf2
was solved by
J.Shen,
M.Zhou,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
88.63 /
3.51
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.647,
113.981,
140.971,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.9 /
27.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Mouse SCD1 with A Diiron Center
(pdb code 6wf2). 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 Mouse SCD1 with A Diiron Center, PDB code: 6wf2:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6wf2
Go back to
Iron Binding Sites List in 6wf2
Iron binding site 1 out
of 4 in the Crystal Structure of Mouse SCD1 with A Diiron Center
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 Mouse SCD1 with A Diiron Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:48.9
occ:1.00
|
NE2
|
A:HIS297
|
1.9
|
50.6
|
1.0
|
NE2
|
A:HIS153
|
2.0
|
57.0
|
1.0
|
NE2
|
A:HIS121
|
2.1
|
55.9
|
1.0
|
NE2
|
A:HIS116
|
2.1
|
53.0
|
1.0
|
NE2
|
A:HIS157
|
2.1
|
57.6
|
1.0
|
CE1
|
A:HIS121
|
2.8
|
53.2
|
1.0
|
CE1
|
A:HIS297
|
2.8
|
50.4
|
1.0
|
CE1
|
A:HIS153
|
2.9
|
60.4
|
1.0
|
CD2
|
A:HIS116
|
3.0
|
56.3
|
1.0
|
CE1
|
A:HIS157
|
3.0
|
58.3
|
1.0
|
CD2
|
A:HIS297
|
3.0
|
51.6
|
1.0
|
CD2
|
A:HIS153
|
3.1
|
59.6
|
1.0
|
CD2
|
A:HIS157
|
3.2
|
59.5
|
1.0
|
CD2
|
A:HIS121
|
3.2
|
58.6
|
1.0
|
CE1
|
A:HIS116
|
3.2
|
51.7
|
1.0
|
ND1
|
A:HIS297
|
4.0
|
48.1
|
1.0
|
ND1
|
A:HIS121
|
4.0
|
56.0
|
1.0
|
ND1
|
A:HIS153
|
4.0
|
63.9
|
1.0
|
ND1
|
A:HIS157
|
4.1
|
61.3
|
1.0
|
CG
|
A:HIS297
|
4.1
|
50.3
|
1.0
|
CG
|
A:HIS153
|
4.2
|
63.1
|
1.0
|
CG
|
A:HIS116
|
4.2
|
54.6
|
1.0
|
CG
|
A:HIS157
|
4.2
|
62.2
|
1.0
|
CG
|
A:HIS121
|
4.2
|
59.3
|
1.0
|
ND1
|
A:HIS116
|
4.3
|
53.8
|
1.0
|
C09
|
A:3VV403
|
4.5
|
54.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 6wf2
Go back to
Iron Binding Sites List in 6wf2
Iron binding site 2 out
of 4 in the Crystal Structure of Mouse SCD1 with A Diiron Center
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 Mouse SCD1 with A Diiron Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:49.0
occ:1.00
|
NE2
|
A:HIS294
|
1.7
|
50.5
|
1.0
|
NE2
|
A:HIS156
|
2.1
|
57.8
|
1.0
|
NE2
|
A:HIS265
|
2.1
|
62.1
|
1.0
|
NE2
|
A:HIS298
|
2.3
|
52.1
|
1.0
|
CE1
|
A:HIS294
|
2.6
|
57.7
|
1.0
|
CD2
|
A:HIS294
|
2.8
|
52.7
|
1.0
|
CE1
|
A:HIS156
|
2.8
|
57.8
|
1.0
|
CD2
|
A:HIS298
|
3.0
|
54.5
|
1.0
|
CE1
|
A:HIS265
|
3.1
|
67.0
|
1.0
|
CD2
|
A:HIS265
|
3.1
|
63.9
|
1.0
|
CD2
|
A:HIS156
|
3.3
|
57.1
|
1.0
|
CE1
|
A:HIS298
|
3.4
|
55.3
|
1.0
|
ND1
|
A:HIS294
|
3.7
|
58.1
|
1.0
|
CG
|
A:HIS294
|
3.8
|
56.6
|
1.0
|
ND1
|
A:HIS156
|
4.0
|
56.6
|
1.0
|
ND1
|
A:HIS265
|
4.2
|
72.3
|
1.0
|
CG
|
A:HIS298
|
4.2
|
50.5
|
1.0
|
CG
|
A:HIS265
|
4.2
|
66.7
|
1.0
|
CG
|
A:HIS156
|
4.3
|
53.7
|
1.0
|
O
|
A:VAL260
|
4.3
|
63.5
|
1.0
|
ND1
|
A:HIS298
|
4.4
|
54.4
|
1.0
|
OG
|
A:SER278
|
4.6
|
67.6
|
1.0
|
C10
|
A:3VV403
|
4.6
|
57.3
|
1.0
|
OD1
|
A:ASN261
|
4.6
|
59.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 6wf2
Go back to
Iron Binding Sites List in 6wf2
Iron binding site 3 out
of 4 in the Crystal Structure of Mouse SCD1 with A Diiron Center
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 Mouse SCD1 with A Diiron Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:48.8
occ:1.00
|
NE2
|
B:HIS297
|
1.9
|
60.7
|
1.0
|
NE2
|
B:HIS153
|
1.9
|
64.6
|
1.0
|
NE2
|
B:HIS116
|
2.1
|
56.0
|
1.0
|
NE2
|
B:HIS157
|
2.1
|
61.6
|
1.0
|
NE2
|
B:HIS121
|
2.3
|
60.1
|
1.0
|
CE1
|
B:HIS121
|
2.8
|
57.5
|
1.0
|
CD2
|
B:HIS297
|
2.9
|
61.8
|
1.0
|
CD2
|
B:HIS153
|
2.9
|
61.1
|
1.0
|
CE1
|
B:HIS297
|
2.9
|
61.7
|
1.0
|
CE1
|
B:HIS153
|
3.0
|
68.0
|
1.0
|
CE1
|
B:HIS116
|
3.1
|
58.5
|
1.0
|
CD2
|
B:HIS116
|
3.1
|
56.6
|
1.0
|
CD2
|
B:HIS157
|
3.1
|
65.8
|
1.0
|
CE1
|
B:HIS157
|
3.1
|
67.1
|
1.0
|
CD2
|
B:HIS121
|
3.5
|
60.3
|
1.0
|
ND1
|
B:HIS121
|
4.0
|
57.9
|
1.0
|
ND1
|
B:HIS297
|
4.0
|
61.6
|
1.0
|
CG
|
B:HIS297
|
4.0
|
62.2
|
1.0
|
CG
|
B:HIS153
|
4.0
|
65.8
|
1.0
|
ND1
|
B:HIS153
|
4.1
|
69.2
|
1.0
|
ND1
|
B:HIS116
|
4.2
|
57.8
|
1.0
|
CG
|
B:HIS116
|
4.2
|
53.1
|
1.0
|
ND1
|
B:HIS157
|
4.2
|
70.0
|
1.0
|
CG
|
B:HIS157
|
4.3
|
71.5
|
1.0
|
CG
|
B:HIS121
|
4.4
|
57.7
|
1.0
|
C09
|
B:3VV403
|
4.5
|
60.6
|
1.0
|
CE1
|
B:HIS294
|
4.8
|
74.2
|
1.0
|
|
Iron binding site 4 out
of 4 in 6wf2
Go back to
Iron Binding Sites List in 6wf2
Iron binding site 4 out
of 4 in the Crystal Structure of Mouse SCD1 with A Diiron Center
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 Mouse SCD1 with A Diiron Center within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe402
b:55.6
occ:1.00
|
NE2
|
B:HIS294
|
2.0
|
71.4
|
1.0
|
NE2
|
B:HIS156
|
2.0
|
62.2
|
1.0
|
NE2
|
B:HIS265
|
2.1
|
74.6
|
1.0
|
NE2
|
B:HIS298
|
2.2
|
60.4
|
1.0
|
CE1
|
B:HIS265
|
2.6
|
74.8
|
1.0
|
CD2
|
B:HIS294
|
2.7
|
62.0
|
1.0
|
CE1
|
B:HIS156
|
2.9
|
67.7
|
1.0
|
CE1
|
B:HIS298
|
3.1
|
67.8
|
1.0
|
CE1
|
B:HIS294
|
3.1
|
74.2
|
1.0
|
CD2
|
B:HIS156
|
3.2
|
64.2
|
1.0
|
CD2
|
B:HIS265
|
3.2
|
69.9
|
1.0
|
CD2
|
B:HIS298
|
3.2
|
63.6
|
1.0
|
ND1
|
B:HIS265
|
3.6
|
75.9
|
1.0
|
CG
|
B:HIS294
|
3.9
|
61.7
|
1.0
|
CG
|
B:HIS265
|
3.9
|
72.9
|
1.0
|
ND2
|
B:ASN261
|
4.1
|
78.0
|
1.0
|
ND1
|
B:HIS294
|
4.1
|
68.6
|
1.0
|
ND1
|
B:HIS156
|
4.1
|
63.8
|
1.0
|
ND1
|
B:HIS298
|
4.2
|
67.5
|
1.0
|
CG
|
B:HIS156
|
4.2
|
63.6
|
1.0
|
CG
|
B:HIS298
|
4.3
|
64.5
|
1.0
|
O
|
B:VAL260
|
4.3
|
68.5
|
1.0
|
C10
|
B:3VV403
|
4.8
|
60.6
|
1.0
|
|
Reference:
J.Shen,
G.Wu,
A.L.Tsai,
M.Zhou.
Structure and Mechanism of A Unique Diiron Center in Mammalian Stearoyl-Coa Desaturase. J.Mol.Biol. 2020.
ISSN: ESSN 1089-8638
PubMed: 32470559
DOI: 10.1016/J.JMB.2020.05.017
Page generated: Wed Aug 7 13:58:58 2024
|