Iron in PDB 5nj4: From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Protein crystallography data
The structure of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography, PDB code: 5nj4
was solved by
R.Dods,
P.Baath,
G.Branden,
R.Neutze,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.70 /
2.40
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
226.500,
226.500,
113.900,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.1 /
18.6
|
Other elements in 5nj4:
The structure of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
(pdb code 5nj4). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography, PDB code: 5nj4:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 5nj4
Go back to
Iron Binding Sites List in 5nj4
Iron binding site 1 out
of 5 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:80.7
occ:1.00
|
FE
|
C:HEC401
|
0.0
|
80.7
|
1.0
|
NE2
|
C:HIS91
|
2.0
|
78.5
|
1.0
|
NB
|
C:HEC401
|
2.0
|
80.5
|
1.0
|
NA
|
C:HEC401
|
2.1
|
82.1
|
1.0
|
NC
|
C:HEC401
|
2.1
|
78.0
|
1.0
|
ND
|
C:HEC401
|
2.1
|
82.7
|
1.0
|
SD
|
C:MET74
|
2.4
|
76.6
|
1.0
|
CE1
|
C:HIS91
|
3.0
|
78.2
|
1.0
|
CD2
|
C:HIS91
|
3.0
|
79.3
|
1.0
|
C4B
|
C:HEC401
|
3.0
|
78.8
|
1.0
|
C1C
|
C:HEC401
|
3.0
|
75.7
|
1.0
|
C1B
|
C:HEC401
|
3.0
|
82.8
|
1.0
|
C4A
|
C:HEC401
|
3.0
|
86.2
|
1.0
|
C1A
|
C:HEC401
|
3.1
|
84.8
|
1.0
|
C1D
|
C:HEC401
|
3.1
|
85.6
|
1.0
|
C4D
|
C:HEC401
|
3.1
|
82.2
|
1.0
|
C4C
|
C:HEC401
|
3.1
|
76.9
|
1.0
|
CHC
|
C:HEC401
|
3.3
|
78.6
|
1.0
|
CHB
|
C:HEC401
|
3.4
|
85.4
|
1.0
|
CHA
|
C:HEC401
|
3.4
|
88.7
|
1.0
|
CHD
|
C:HEC401
|
3.5
|
79.7
|
1.0
|
CE
|
C:MET74
|
3.6
|
77.0
|
1.0
|
CG
|
C:MET74
|
3.7
|
75.9
|
1.0
|
ND1
|
C:HIS91
|
4.1
|
78.1
|
1.0
|
CG
|
C:HIS91
|
4.1
|
78.6
|
1.0
|
C3B
|
C:HEC401
|
4.2
|
81.3
|
1.0
|
C2B
|
C:HEC401
|
4.3
|
82.6
|
1.0
|
C2C
|
C:HEC401
|
4.3
|
71.1
|
1.0
|
C3A
|
C:HEC401
|
4.3
|
88.8
|
1.0
|
C2A
|
C:HEC401
|
4.3
|
86.6
|
1.0
|
C2D
|
C:HEC401
|
4.3
|
85.9
|
1.0
|
C3D
|
C:HEC401
|
4.3
|
80.5
|
1.0
|
C3C
|
C:HEC401
|
4.3
|
76.5
|
1.0
|
CB
|
C:MET74
|
4.4
|
78.7
|
1.0
|
|
Iron binding site 2 out
of 5 in 5nj4
Go back to
Iron Binding Sites List in 5nj4
Iron binding site 2 out
of 5 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:73.3
occ:1.00
|
FE
|
C:HEC402
|
0.0
|
73.3
|
1.0
|
NE2
|
C:HIS136
|
2.0
|
67.2
|
1.0
|
NB
|
C:HEC402
|
2.0
|
75.7
|
1.0
|
NC
|
C:HEC402
|
2.1
|
76.7
|
1.0
|
ND
|
C:HEC402
|
2.1
|
78.4
|
1.0
|
NA
|
C:HEC402
|
2.1
|
76.0
|
1.0
|
SD
|
C:MET110
|
2.3
|
74.0
|
1.0
|
CE1
|
C:HIS136
|
3.0
|
68.4
|
1.0
|
C4B
|
C:HEC402
|
3.0
|
74.8
|
1.0
|
C1C
|
C:HEC402
|
3.0
|
74.8
|
1.0
|
C1B
|
C:HEC402
|
3.0
|
73.1
|
1.0
|
CD2
|
C:HIS136
|
3.1
|
67.2
|
1.0
|
C4A
|
C:HEC402
|
3.1
|
72.2
|
1.0
|
C1D
|
C:HEC402
|
3.1
|
79.0
|
1.0
|
C4C
|
C:HEC402
|
3.1
|
71.8
|
1.0
|
C1A
|
C:HEC402
|
3.1
|
77.0
|
1.0
|
C4D
|
C:HEC402
|
3.1
|
83.0
|
1.0
|
CHC
|
C:HEC402
|
3.3
|
76.9
|
1.0
|
CG
|
C:MET110
|
3.4
|
75.0
|
1.0
|
CE
|
C:MET110
|
3.4
|
70.4
|
1.0
|
CHB
|
C:HEC402
|
3.4
|
72.5
|
1.0
|
CHD
|
C:HEC402
|
3.5
|
76.0
|
1.0
|
CHA
|
C:HEC402
|
3.5
|
80.0
|
1.0
|
ND1
|
C:HIS136
|
4.1
|
64.9
|
1.0
|
CG
|
C:HIS136
|
4.2
|
67.7
|
1.0
|
CB
|
C:MET110
|
4.2
|
72.6
|
1.0
|
C3B
|
C:HEC402
|
4.2
|
73.3
|
1.0
|
C2B
|
C:HEC402
|
4.3
|
75.2
|
1.0
|
C2C
|
C:HEC402
|
4.3
|
70.5
|
1.0
|
C3A
|
C:HEC402
|
4.3
|
75.5
|
1.0
|
C2A
|
C:HEC402
|
4.3
|
77.0
|
1.0
|
C2D
|
C:HEC402
|
4.3
|
78.4
|
1.0
|
C3C
|
C:HEC402
|
4.3
|
72.5
|
1.0
|
C3D
|
C:HEC402
|
4.3
|
80.1
|
1.0
|
|
Iron binding site 3 out
of 5 in 5nj4
Go back to
Iron Binding Sites List in 5nj4
Iron binding site 3 out
of 5 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe403
b:63.5
occ:1.00
|
FE
|
C:HEC403
|
0.0
|
63.5
|
1.0
|
NB
|
C:HEC403
|
2.0
|
59.9
|
1.0
|
NE2
|
C:HIS248
|
2.0
|
64.6
|
1.0
|
NC
|
C:HEC403
|
2.1
|
61.6
|
1.0
|
NA
|
C:HEC403
|
2.1
|
63.3
|
1.0
|
ND
|
C:HEC403
|
2.1
|
61.5
|
1.0
|
SD
|
C:MET233
|
2.3
|
64.7
|
1.0
|
C4B
|
C:HEC403
|
3.0
|
61.8
|
1.0
|
CD2
|
C:HIS248
|
3.0
|
62.6
|
1.0
|
C1C
|
C:HEC403
|
3.0
|
60.6
|
1.0
|
CE1
|
C:HIS248
|
3.0
|
64.0
|
1.0
|
C1B
|
C:HEC403
|
3.0
|
62.7
|
1.0
|
C4A
|
C:HEC403
|
3.0
|
62.9
|
1.0
|
C1D
|
C:HEC403
|
3.1
|
64.2
|
1.0
|
C4D
|
C:HEC403
|
3.1
|
62.7
|
1.0
|
C1A
|
C:HEC403
|
3.1
|
63.7
|
1.0
|
C4C
|
C:HEC403
|
3.1
|
63.7
|
1.0
|
CHC
|
C:HEC403
|
3.3
|
60.6
|
1.0
|
CHB
|
C:HEC403
|
3.4
|
63.3
|
1.0
|
CE
|
C:MET233
|
3.4
|
68.6
|
1.0
|
CG
|
C:MET233
|
3.4
|
65.9
|
1.0
|
CHD
|
C:HEC403
|
3.4
|
66.1
|
1.0
|
CHA
|
C:HEC403
|
3.5
|
63.5
|
1.0
|
ND1
|
C:HIS248
|
4.1
|
62.4
|
1.0
|
CG
|
C:HIS248
|
4.1
|
61.6
|
1.0
|
C3B
|
C:HEC403
|
4.2
|
60.3
|
1.0
|
C2B
|
C:HEC403
|
4.2
|
61.4
|
1.0
|
C2C
|
C:HEC403
|
4.3
|
63.8
|
1.0
|
CB
|
C:MET233
|
4.3
|
67.0
|
1.0
|
C2D
|
C:HEC403
|
4.3
|
64.7
|
1.0
|
C3A
|
C:HEC403
|
4.3
|
63.3
|
1.0
|
C3D
|
C:HEC403
|
4.3
|
63.8
|
1.0
|
C2A
|
C:HEC403
|
4.3
|
63.8
|
1.0
|
C3C
|
C:HEC403
|
4.3
|
63.5
|
1.0
|
|
Iron binding site 4 out
of 5 in 5nj4
Go back to
Iron Binding Sites List in 5nj4
Iron binding site 4 out
of 5 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe404
b:67.2
occ:1.00
|
FE
|
C:HEC404
|
0.0
|
67.2
|
1.0
|
NE2
|
C:HIS309
|
2.0
|
60.2
|
1.0
|
NB
|
C:HEC404
|
2.0
|
68.4
|
1.0
|
NE2
|
C:HIS124
|
2.0
|
68.2
|
1.0
|
NC
|
C:HEC404
|
2.1
|
69.1
|
1.0
|
NA
|
C:HEC404
|
2.1
|
70.7
|
1.0
|
ND
|
C:HEC404
|
2.1
|
70.9
|
1.0
|
CE1
|
C:HIS309
|
2.9
|
61.6
|
1.0
|
CE1
|
C:HIS124
|
2.9
|
68.4
|
1.0
|
C1C
|
C:HEC404
|
3.0
|
68.6
|
1.0
|
C4B
|
C:HEC404
|
3.0
|
66.7
|
1.0
|
C1B
|
C:HEC404
|
3.1
|
66.7
|
1.0
|
C4A
|
C:HEC404
|
3.1
|
66.7
|
1.0
|
C1D
|
C:HEC404
|
3.1
|
71.7
|
1.0
|
C4C
|
C:HEC404
|
3.1
|
66.1
|
1.0
|
CD2
|
C:HIS309
|
3.1
|
61.4
|
1.0
|
C1A
|
C:HEC404
|
3.1
|
69.2
|
1.0
|
CD2
|
C:HIS124
|
3.1
|
69.6
|
1.0
|
C4D
|
C:HEC404
|
3.1
|
72.7
|
1.0
|
CHC
|
C:HEC404
|
3.3
|
69.8
|
1.0
|
CHB
|
C:HEC404
|
3.4
|
68.3
|
1.0
|
CHD
|
C:HEC404
|
3.4
|
69.2
|
1.0
|
CHA
|
C:HEC404
|
3.5
|
68.0
|
1.0
|
ND1
|
C:HIS309
|
4.0
|
61.3
|
1.0
|
ND1
|
C:HIS124
|
4.1
|
67.8
|
1.0
|
CG
|
C:HIS309
|
4.2
|
61.9
|
1.0
|
CG
|
C:HIS124
|
4.2
|
67.1
|
1.0
|
C3B
|
C:HEC404
|
4.2
|
65.4
|
1.0
|
C2C
|
C:HEC404
|
4.3
|
65.0
|
1.0
|
C2B
|
C:HEC404
|
4.3
|
67.2
|
1.0
|
C3A
|
C:HEC404
|
4.3
|
66.6
|
1.0
|
C2D
|
C:HEC404
|
4.3
|
73.6
|
1.0
|
C3C
|
C:HEC404
|
4.3
|
66.7
|
1.0
|
C2A
|
C:HEC404
|
4.3
|
65.9
|
1.0
|
C3D
|
C:HEC404
|
4.3
|
74.0
|
1.0
|
CG
|
C:PRO315
|
5.0
|
65.8
|
1.0
|
|
Iron binding site 5 out
of 5 in 5nj4
Go back to
Iron Binding Sites List in 5nj4
Iron binding site 5 out
of 5 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Fe306
b:68.1
occ:1.00
|
NE2
|
L:HIS190
|
2.1
|
65.5
|
1.0
|
OE2
|
M:GLU232
|
2.1
|
62.0
|
1.0
|
NE2
|
M:HIS217
|
2.2
|
64.3
|
1.0
|
NE2
|
L:HIS230
|
2.3
|
75.1
|
1.0
|
NE2
|
M:HIS264
|
2.4
|
66.1
|
1.0
|
OE1
|
M:GLU232
|
2.4
|
64.2
|
1.0
|
CD
|
M:GLU232
|
2.6
|
62.6
|
1.0
|
CE1
|
L:HIS190
|
3.0
|
66.7
|
1.0
|
CE1
|
M:HIS217
|
3.1
|
65.0
|
1.0
|
CE1
|
L:HIS230
|
3.2
|
73.7
|
1.0
|
CD2
|
L:HIS190
|
3.2
|
63.6
|
1.0
|
CD2
|
M:HIS217
|
3.3
|
60.4
|
1.0
|
CD2
|
L:HIS230
|
3.3
|
73.1
|
1.0
|
CE1
|
M:HIS264
|
3.3
|
67.7
|
1.0
|
CD2
|
M:HIS264
|
3.4
|
64.9
|
1.0
|
CG
|
M:GLU232
|
4.1
|
65.6
|
1.0
|
ND1
|
L:HIS190
|
4.2
|
62.6
|
1.0
|
CG
|
L:HIS190
|
4.3
|
60.0
|
1.0
|
ND1
|
M:HIS217
|
4.3
|
63.6
|
1.0
|
ND1
|
L:HIS230
|
4.3
|
75.3
|
1.0
|
CG
|
M:HIS217
|
4.4
|
64.4
|
1.0
|
CG
|
L:HIS230
|
4.4
|
73.0
|
1.0
|
ND1
|
M:HIS264
|
4.5
|
69.8
|
1.0
|
CG
|
M:HIS264
|
4.5
|
66.1
|
1.0
|
CG1
|
M:ILE221
|
4.5
|
72.7
|
1.0
|
CG1
|
L:ILE194
|
4.6
|
76.7
|
1.0
|
|
Reference:
R.Dods,
P.Bath,
D.Arnlund,
K.R.Beyerlein,
G.Nelson,
M.Liang,
R.Harimoorthy,
P.Berntsen,
E.Malmerberg,
L.Johansson,
R.Andersson,
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ISSN: ISSN 1878-4186
PubMed: 28781082
DOI: 10.1016/J.STR.2017.07.002
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