Magnesium in PDB 6pru: Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus
Protein crystallography data
The structure of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus, PDB code: 6pru
was solved by
E.S.Burgie,
J.A.Clinger,
M.D.Miller,
G.N.Phillips Jr.,
R.D.Vierstra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.12 /
1.54
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
42.590,
61.085,
116.297,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.3 /
20.7
|
Other elements in 6pru:
The structure of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus
(pdb code 6pru). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus, PDB code: 6pru:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6pru
Go back to
Magnesium Binding Sites List in 6pru
Magnesium binding site 1 out
of 4 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:33.3
occ:1.00
|
O
|
A:HOH737
|
2.0
|
28.4
|
0.6
|
O
|
A:GLU581
|
2.1
|
31.8
|
1.0
|
O
|
A:HOH794
|
2.1
|
40.9
|
1.0
|
O
|
A:HOH728
|
2.1
|
40.6
|
1.0
|
OXT
|
A:HIS584
|
2.1
|
43.1
|
1.0
|
O
|
A:HOH711
|
2.1
|
42.0
|
1.0
|
C
|
A:HIS584
|
3.1
|
36.7
|
1.0
|
C
|
A:GLU581
|
3.3
|
23.1
|
1.0
|
O
|
A:HIS584
|
3.5
|
31.8
|
1.0
|
O
|
A:HOH737
|
3.7
|
32.2
|
0.4
|
HA
|
A:GLU581
|
3.8
|
26.9
|
1.0
|
HA
|
A:ARG582
|
3.8
|
29.8
|
1.0
|
HG3
|
A:GLU581
|
4.1
|
35.2
|
1.0
|
H
|
A:HIS584
|
4.1
|
37.4
|
1.0
|
CA
|
A:GLU581
|
4.1
|
22.5
|
1.0
|
HG2
|
A:GLU581
|
4.1
|
35.2
|
1.0
|
O
|
A:HOH823
|
4.1
|
63.3
|
1.0
|
OD2
|
A:ASP543
|
4.2
|
37.2
|
1.0
|
N
|
A:ARG582
|
4.2
|
23.1
|
1.0
|
O
|
A:HOH789
|
4.3
|
40.4
|
0.5
|
OD1
|
A:ASP543
|
4.3
|
45.4
|
1.0
|
CA
|
A:ARG582
|
4.4
|
24.8
|
1.0
|
CA
|
A:HIS584
|
4.4
|
37.9
|
1.0
|
CG
|
A:GLU581
|
4.5
|
29.3
|
1.0
|
N
|
A:HIS584
|
4.5
|
31.1
|
1.0
|
C
|
A:ARG582
|
4.6
|
27.9
|
1.0
|
CG
|
A:ASP543
|
4.7
|
34.9
|
1.0
|
O
|
A:LEU580
|
4.7
|
24.9
|
1.0
|
O
|
A:ARG582
|
4.9
|
27.5
|
1.0
|
CB
|
A:GLU581
|
4.9
|
20.9
|
1.0
|
HA
|
A:HIS584
|
5.0
|
45.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6pru
Go back to
Magnesium Binding Sites List in 6pru
Magnesium binding site 2 out
of 4 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg608
b:35.8
occ:1.00
|
O
|
B:HOH709
|
2.1
|
41.9
|
1.0
|
CL
|
B:CL612
|
2.8
|
81.1
|
1.0
|
HE21
|
B:GLN505
|
3.7
|
60.6
|
1.0
|
OD2
|
B:ASP544
|
4.0
|
29.7
|
0.6
|
OD1
|
B:ASP544
|
4.0
|
33.6
|
0.4
|
OD2
|
B:ASP544
|
4.1
|
30.1
|
0.4
|
O
|
B:HOH814
|
4.1
|
45.8
|
1.0
|
OD1
|
B:ASP544
|
4.2
|
30.8
|
0.6
|
CG
|
B:ASP544
|
4.5
|
35.8
|
0.4
|
NE2
|
B:GLN505
|
4.5
|
50.5
|
1.0
|
CG
|
B:ASP544
|
4.6
|
38.0
|
0.6
|
HG2
|
B:GLN505
|
4.7
|
41.8
|
1.0
|
HE22
|
B:GLN505
|
4.8
|
60.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6pru
Go back to
Magnesium Binding Sites List in 6pru
Magnesium binding site 3 out
of 4 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg609
b:66.3
occ:1.00
|
O
|
B:HOH708
|
2.0
|
65.2
|
1.0
|
O
|
B:HOH702
|
2.2
|
46.6
|
1.0
|
O
|
B:GLU581
|
2.3
|
35.3
|
1.0
|
O
|
B:HOH764
|
2.5
|
49.5
|
1.0
|
O
|
B:HOH841
|
2.7
|
74.6
|
1.0
|
OXT
|
B:HIS584
|
2.7
|
80.5
|
0.5
|
OXT
|
B:HIS584
|
2.8
|
80.3
|
0.5
|
O
|
B:HIS584
|
3.3
|
84.7
|
0.5
|
C
|
B:HIS584
|
3.4
|
82.5
|
0.5
|
C
|
B:GLU581
|
3.4
|
34.6
|
1.0
|
C
|
B:HIS584
|
3.5
|
82.8
|
0.5
|
OD2
|
B:ASP543
|
3.5
|
35.0
|
0.4
|
HG2
|
B:GLU581
|
3.5
|
57.7
|
1.0
|
OD1
|
B:ASP543
|
3.5
|
37.1
|
0.6
|
O
|
B:HIS584
|
3.6
|
84.9
|
0.5
|
HA
|
B:GLU581
|
3.6
|
35.8
|
1.0
|
OD1
|
B:ASP543
|
3.6
|
25.7
|
0.4
|
HG3
|
B:GLU581
|
3.8
|
57.7
|
1.0
|
CG
|
B:ASP543
|
4.0
|
35.4
|
0.4
|
CA
|
B:GLU581
|
4.0
|
29.8
|
1.0
|
CG
|
B:GLU581
|
4.1
|
48.1
|
1.0
|
HA
|
B:ARG582
|
4.3
|
41.7
|
1.0
|
OD2
|
B:ASP543
|
4.3
|
41.5
|
0.6
|
CG
|
B:ASP543
|
4.3
|
31.5
|
0.6
|
H
|
B:HIS584
|
4.4
|
93.5
|
0.5
|
H
|
B:HIS584
|
4.4
|
93.5
|
0.5
|
N
|
B:ARG582
|
4.5
|
32.6
|
1.0
|
CB
|
B:GLU581
|
4.6
|
39.1
|
1.0
|
CA
|
B:HIS584
|
4.7
|
83.5
|
0.5
|
CA
|
B:HIS584
|
4.8
|
83.4
|
0.5
|
CA
|
B:ARG582
|
4.8
|
34.7
|
1.0
|
N
|
B:HIS584
|
4.9
|
77.9
|
0.5
|
N
|
B:HIS584
|
4.9
|
77.9
|
0.5
|
|
Magnesium binding site 4 out
of 4 in 6pru
Go back to
Magnesium Binding Sites List in 6pru
Magnesium binding site 4 out
of 4 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg610
b:43.6
occ:1.00
|
O
|
B:HOH701
|
1.9
|
30.2
|
0.5
|
O
|
A:HOH829
|
2.0
|
29.8
|
0.5
|
O
|
A:HOH829
|
2.1
|
31.0
|
0.5
|
O
|
B:HOH723
|
2.1
|
29.9
|
0.5
|
O
|
B:HOH701
|
2.2
|
35.4
|
0.5
|
OD2
|
B:ASP439
|
2.5
|
50.5
|
0.5
|
N
|
B:SER435
|
3.3
|
69.0
|
0.5
|
N
|
B:SER435
|
3.4
|
65.5
|
0.5
|
CG
|
B:ASP439
|
3.6
|
35.6
|
0.5
|
HE1
|
A:HIS584
|
3.6
|
51.4
|
1.0
|
HE2
|
B:HIS584
|
3.8
|
0.8
|
0.5
|
N
|
A:SER435
|
3.8
|
48.3
|
0.3
|
OD2
|
B:ASP439
|
3.9
|
32.3
|
0.5
|
HE1
|
B:HIS584
|
3.9
|
0.7
|
0.5
|
OD1
|
B:ASP439
|
4.0
|
35.2
|
0.5
|
OD2
|
A:ASP439
|
4.0
|
28.1
|
0.7
|
OD2
|
A:ASP439
|
4.0
|
29.3
|
0.3
|
O
|
A:SER435
|
4.0
|
42.7
|
0.3
|
O
|
B:HOH723
|
4.1
|
37.5
|
0.5
|
OD1
|
B:ASP439
|
4.2
|
31.2
|
0.5
|
O
|
B:SER435
|
4.2
|
63.2
|
0.5
|
HE2
|
A:HIS584
|
4.4
|
44.5
|
1.0
|
CE1
|
A:HIS584
|
4.4
|
42.8
|
1.0
|
CG
|
B:ASP439
|
4.4
|
36.6
|
0.5
|
CA
|
B:SER435
|
4.5
|
66.5
|
0.5
|
C
|
B:SER435
|
4.5
|
65.3
|
0.5
|
OD1
|
A:ASP439
|
4.5
|
28.2
|
0.7
|
N
|
A:SER435
|
4.6
|
39.5
|
0.7
|
HA
|
A:SER435
|
4.6
|
50.9
|
0.3
|
NE2
|
B:HIS584
|
4.6
|
91.5
|
0.5
|
CA
|
A:SER435
|
4.6
|
42.4
|
0.3
|
CA
|
B:SER435
|
4.7
|
65.5
|
0.5
|
C
|
A:SER435
|
4.7
|
40.1
|
0.3
|
CG
|
A:ASP439
|
4.7
|
27.8
|
0.7
|
CE1
|
B:HIS584
|
4.7
|
90.6
|
0.5
|
NE2
|
A:HIS584
|
4.8
|
37.1
|
1.0
|
HE2
|
B:HIS584
|
4.9
|
0.2
|
0.5
|
CB
|
B:ASP439
|
4.9
|
37.5
|
0.5
|
HB2
|
B:ASP439
|
4.9
|
44.9
|
0.5
|
HA
|
B:SER435
|
5.0
|
79.8
|
0.5
|
HA
|
B:SER435
|
5.0
|
78.6
|
0.5
|
O
|
B:SER435
|
5.0
|
60.6
|
0.5
|
|
Reference:
E.S.Burgie,
J.A.Clinger,
M.D.Miller,
A.S.Brewster,
P.Aller,
A.Butryn,
F.D.Fuller,
S.Gul,
I.D.Young,
C.C.Pham,
I.S.Kim,
A.Bhowmick,
L.J.O'riordan,
K.D.Sutherlin,
J.V.Heinemann,
A.Batyuk,
R.Alonso-Mori,
M.S.Hunter,
J.E.Koglin,
J.Yano,
V.K.Yachandra,
N.K.Sauter,
A.E.Cohen,
J.Kern,
A.M.Orville,
G.N.Phillips Jr.,
R.D.Vierstra.
Photoreversible Interconversion of A Phytochrome Photosensory Module in the Crystalline State. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31852825
DOI: 10.1073/PNAS.1912041116
Page generated: Tue Oct 1 14:16:18 2024
|