Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography, PDB code: 5nj4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5nj4
Go back to
Magnesium Binding Sites List in 5nj4
Magnesium binding site 1 out
of 4 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
L:Mg301
b:61.9
occ:1.00
|
MG
|
L:BCB301
|
0.0
|
61.9
|
1.0
|
NA
|
L:BCB301
|
2.0
|
57.8
|
1.0
|
ND
|
L:BCB301
|
2.0
|
56.1
|
1.0
|
NC
|
L:BCB301
|
2.0
|
59.4
|
1.0
|
NB
|
L:BCB301
|
2.1
|
59.4
|
1.0
|
NE2
|
L:HIS173
|
2.4
|
63.3
|
1.0
|
C1A
|
L:BCB301
|
3.0
|
57.9
|
1.0
|
C4A
|
L:BCB301
|
3.0
|
58.3
|
1.0
|
C4D
|
L:BCB301
|
3.0
|
56.1
|
1.0
|
C4B
|
L:BCB301
|
3.1
|
56.4
|
1.0
|
C1D
|
L:BCB301
|
3.1
|
60.2
|
1.0
|
C4C
|
L:BCB301
|
3.1
|
58.4
|
1.0
|
C1B
|
L:BCB301
|
3.1
|
59.1
|
1.0
|
C1C
|
L:BCB301
|
3.1
|
59.1
|
1.0
|
CBB
|
M:BCB403
|
3.3
|
58.9
|
1.0
|
CD2
|
L:HIS173
|
3.4
|
61.5
|
1.0
|
CHB
|
L:BCB301
|
3.4
|
59.1
|
1.0
|
CHA
|
L:BCB301
|
3.4
|
58.6
|
1.0
|
CHC
|
L:BCB301
|
3.4
|
55.1
|
1.0
|
CE1
|
L:HIS173
|
3.4
|
63.2
|
1.0
|
CAB
|
M:BCB403
|
3.4
|
56.1
|
1.0
|
CHD
|
L:BCB301
|
3.5
|
57.9
|
1.0
|
OBB
|
M:BCB403
|
3.6
|
59.3
|
1.0
|
C3B
|
M:BCB403
|
4.2
|
57.0
|
1.0
|
C3D
|
L:BCB301
|
4.3
|
58.4
|
1.0
|
C2D
|
L:BCB301
|
4.3
|
58.6
|
1.0
|
C3A
|
L:BCB301
|
4.3
|
57.4
|
1.0
|
C2A
|
L:BCB301
|
4.3
|
57.8
|
1.0
|
C3C
|
L:BCB301
|
4.3
|
56.8
|
1.0
|
C3B
|
L:BCB301
|
4.4
|
58.0
|
1.0
|
C2B
|
L:BCB301
|
4.4
|
58.9
|
1.0
|
C2C
|
L:BCB301
|
4.5
|
60.8
|
1.0
|
CD1
|
L:TRP167
|
4.5
|
59.6
|
1.0
|
CG
|
L:HIS173
|
4.5
|
63.3
|
1.0
|
ND1
|
L:HIS173
|
4.5
|
60.2
|
1.0
|
NE1
|
L:TRP167
|
4.6
|
59.7
|
1.0
|
CBD
|
L:BCB301
|
4.9
|
59.2
|
1.0
|
C2B
|
M:BCB403
|
4.9
|
55.5
|
1.0
|
C4B
|
M:BCB403
|
5.0
|
54.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5nj4
Go back to
Magnesium Binding Sites List in 5nj4
Magnesium binding site 2 out
of 4 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
L:Mg302
b:63.3
occ:1.00
|
MG
|
L:BCB302
|
0.0
|
63.3
|
1.0
|
ND
|
L:BCB302
|
2.0
|
64.1
|
1.0
|
NA
|
L:BCB302
|
2.0
|
65.8
|
1.0
|
NC
|
L:BCB302
|
2.0
|
64.0
|
1.0
|
NB
|
L:BCB302
|
2.1
|
64.4
|
1.0
|
NE2
|
L:HIS153
|
2.5
|
64.9
|
1.0
|
C1A
|
L:BCB302
|
3.0
|
65.2
|
1.0
|
C4A
|
L:BCB302
|
3.0
|
63.5
|
1.0
|
C4D
|
L:BCB302
|
3.0
|
64.8
|
1.0
|
C4B
|
L:BCB302
|
3.1
|
60.2
|
1.0
|
C1D
|
L:BCB302
|
3.1
|
64.7
|
1.0
|
C1C
|
L:BCB302
|
3.1
|
59.8
|
1.0
|
C4C
|
L:BCB302
|
3.1
|
63.1
|
1.0
|
C1B
|
L:BCB302
|
3.1
|
60.4
|
1.0
|
CD2
|
L:HIS153
|
3.4
|
66.5
|
1.0
|
CHB
|
L:BCB302
|
3.4
|
63.4
|
1.0
|
CHC
|
L:BCB302
|
3.4
|
60.1
|
1.0
|
CHA
|
L:BCB302
|
3.4
|
63.1
|
1.0
|
CHD
|
L:BCB302
|
3.5
|
63.3
|
1.0
|
CE1
|
L:HIS153
|
3.5
|
65.0
|
1.0
|
CBB
|
L:BPB303
|
4.0
|
66.5
|
1.0
|
C3D
|
L:BCB302
|
4.3
|
65.4
|
1.0
|
C2D
|
L:BCB302
|
4.3
|
62.5
|
1.0
|
C3C
|
L:BCB302
|
4.3
|
63.9
|
1.0
|
CE2
|
M:TYR208
|
4.3
|
63.5
|
1.0
|
C2A
|
L:BCB302
|
4.4
|
65.5
|
1.0
|
C3A
|
L:BCB302
|
4.4
|
66.0
|
1.0
|
C3B
|
L:BCB302
|
4.4
|
62.2
|
1.0
|
C2B
|
L:BCB302
|
4.4
|
62.2
|
1.0
|
C2C
|
L:BCB302
|
4.4
|
62.8
|
1.0
|
CG
|
L:HIS153
|
4.6
|
63.3
|
1.0
|
ND1
|
L:HIS153
|
4.6
|
63.1
|
1.0
|
CBA
|
L:BCB302
|
4.8
|
64.2
|
1.0
|
CBD
|
L:BCB302
|
4.9
|
64.0
|
1.0
|
CD2
|
M:TYR208
|
4.9
|
58.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5nj4
Go back to
Magnesium Binding Sites List in 5nj4
Magnesium binding site 3 out
of 4 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
M:Mg402
b:69.2
occ:1.00
|
MG
|
M:BCB402
|
0.0
|
69.2
|
1.0
|
NA
|
M:BCB402
|
2.0
|
69.2
|
1.0
|
ND
|
M:BCB402
|
2.0
|
65.2
|
1.0
|
NB
|
M:BCB402
|
2.0
|
70.3
|
1.0
|
NC
|
M:BCB402
|
2.0
|
72.1
|
1.0
|
NE2
|
M:HIS180
|
2.4
|
63.4
|
1.0
|
C1A
|
M:BCB402
|
3.0
|
65.5
|
1.0
|
C4D
|
M:BCB402
|
3.0
|
64.1
|
1.0
|
C4A
|
M:BCB402
|
3.0
|
69.7
|
1.0
|
C4B
|
M:BCB402
|
3.0
|
69.5
|
1.0
|
C1B
|
M:BCB402
|
3.1
|
69.8
|
1.0
|
C4C
|
M:BCB402
|
3.1
|
67.3
|
1.0
|
C1D
|
M:BCB402
|
3.1
|
69.7
|
1.0
|
C1C
|
M:BCB402
|
3.1
|
64.8
|
1.0
|
CD2
|
M:HIS180
|
3.3
|
64.2
|
1.0
|
CE1
|
M:HIS180
|
3.4
|
64.8
|
1.0
|
CHC
|
M:BCB402
|
3.4
|
69.5
|
1.0
|
CHA
|
M:BCB402
|
3.4
|
66.0
|
1.0
|
CHB
|
M:BCB402
|
3.4
|
67.8
|
1.0
|
CHD
|
M:BCB402
|
3.5
|
68.0
|
1.0
|
OBB
|
M:BPB404
|
4.2
|
84.0
|
1.0
|
C3D
|
M:BCB402
|
4.3
|
66.5
|
1.0
|
C2D
|
M:BCB402
|
4.3
|
67.7
|
1.0
|
C2A
|
M:BCB402
|
4.3
|
68.3
|
1.0
|
C3B
|
M:BCB402
|
4.3
|
72.2
|
1.0
|
C3C
|
M:BCB402
|
4.3
|
66.3
|
1.0
|
C3A
|
M:BCB402
|
4.4
|
68.4
|
1.0
|
C2B
|
M:BCB402
|
4.4
|
70.1
|
1.0
|
C2C
|
M:BCB402
|
4.4
|
63.9
|
1.0
|
CG
|
M:HIS180
|
4.5
|
63.6
|
1.0
|
ND1
|
M:HIS180
|
4.5
|
62.6
|
1.0
|
CE2
|
L:PHE181
|
4.7
|
65.3
|
1.0
|
CBA
|
M:BCB402
|
4.8
|
76.9
|
1.0
|
CBD
|
M:BCB402
|
4.9
|
68.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5nj4
Go back to
Magnesium Binding Sites List in 5nj4
Magnesium binding site 4 out
of 4 in the From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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
|
M:Mg403
b:61.1
occ:1.00
|
MG
|
M:BCB403
|
0.0
|
61.1
|
1.0
|
NC
|
M:BCB403
|
2.0
|
57.8
|
1.0
|
ND
|
M:BCB403
|
2.0
|
57.5
|
1.0
|
NA
|
M:BCB403
|
2.0
|
61.9
|
1.0
|
NB
|
M:BCB403
|
2.0
|
55.1
|
1.0
|
NE2
|
M:HIS200
|
2.4
|
65.2
|
1.0
|
C1A
|
M:BCB403
|
3.0
|
60.7
|
1.0
|
C4D
|
M:BCB403
|
3.0
|
59.5
|
1.0
|
C4A
|
M:BCB403
|
3.0
|
58.6
|
1.0
|
C4B
|
M:BCB403
|
3.0
|
54.0
|
1.0
|
C4C
|
M:BCB403
|
3.1
|
57.6
|
1.0
|
C1C
|
M:BCB403
|
3.1
|
54.7
|
1.0
|
C1D
|
M:BCB403
|
3.1
|
62.9
|
1.0
|
C1B
|
M:BCB403
|
3.1
|
54.1
|
1.0
|
CBB
|
L:BCB301
|
3.3
|
60.6
|
1.0
|
CE1
|
M:HIS200
|
3.3
|
67.8
|
1.0
|
CD2
|
M:HIS200
|
3.4
|
64.5
|
1.0
|
CHC
|
M:BCB403
|
3.4
|
54.3
|
1.0
|
CHA
|
M:BCB403
|
3.4
|
59.9
|
1.0
|
CHB
|
M:BCB403
|
3.4
|
55.8
|
1.0
|
CAB
|
L:BCB301
|
3.5
|
58.7
|
1.0
|
CHD
|
M:BCB403
|
3.5
|
61.1
|
1.0
|
OBB
|
L:BCB301
|
3.7
|
62.0
|
1.0
|
C3B
|
L:BCB301
|
4.2
|
58.0
|
1.0
|
C3C
|
M:BCB403
|
4.3
|
59.9
|
1.0
|
C3D
|
M:BCB403
|
4.3
|
60.9
|
1.0
|
C2D
|
M:BCB403
|
4.3
|
60.2
|
1.0
|
C3A
|
M:BCB403
|
4.3
|
62.1
|
1.0
|
C3B
|
M:BCB403
|
4.4
|
57.0
|
1.0
|
C2A
|
M:BCB403
|
4.4
|
63.4
|
1.0
|
C2B
|
M:BCB403
|
4.4
|
55.5
|
1.0
|
C2C
|
M:BCB403
|
4.4
|
59.7
|
1.0
|
ND1
|
M:HIS200
|
4.5
|
61.0
|
1.0
|
CG
|
M:HIS200
|
4.5
|
61.5
|
1.0
|
CBD
|
M:BCB403
|
4.9
|
64.8
|
1.0
|
C4B
|
L:BCB301
|
5.0
|
56.4
|
1.0
|
C2B
|
L:BCB301
|
5.0
|
58.9
|
1.0
|
CMC
|
M:BCB403
|
5.0
|
61.9
|
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,
R.Bosman,
S.Carbajo,
E.Claesson,
C.E.Conrad,
P.Dahl,
G.Hammarin,
M.S.Hunter,
C.Li,
S.Lisova,
D.Milathianaki,
J.Robinson,
C.Safari,
A.Sharma,
G.Williams,
C.Wickstrand,
O.Yefanov,
J.Davidsson,
D.P.Deponte,
A.Barty,
G.Branden,
R.Neutze.
From Macrocrystals to Microcrystals: A Strategy For Membrane Protein Serial Crystallography. Structure V. 25 1461 2017.
ISSN: ISSN 1878-4186
PubMed: 28781082
DOI: 10.1016/J.STR.2017.07.002
Page generated: Sun Sep 29 23:18:36 2024
|