Magnesium in PDB 6pry: X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis
Protein crystallography data
The structure of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis, PDB code: 6pry
was solved by
E.S.Burgie,
J.A.Clinger,
M.D.Miller,
G.N.Phillips Jr.,
R.D.Vierstra,
A.M.Orville,
J.F.Kern,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.09 /
1.55
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.788,
61.417,
116.484,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.7 /
18.5
|
Other elements in 6pry:
The structure of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis
(pdb code 6pry). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis, PDB code: 6pry:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6pry
Go back to
Magnesium Binding Sites List in 6pry
Magnesium binding site 1 out
of 4 in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:69.4
occ:0.61
|
MG
|
A:MG602
|
0.0
|
69.4
|
0.6
|
O
|
B:HOH714
|
2.0
|
87.4
|
1.0
|
OD2
|
A:ASP439
|
2.3
|
32.0
|
0.3
|
MG
|
A:MG602
|
2.4
|
43.1
|
0.4
|
HG
|
A:SER435
|
2.6
|
0.9
|
0.4
|
HG
|
A:SER435
|
2.6
|
0.7
|
0.7
|
OD2
|
A:ASP439
|
2.6
|
37.5
|
0.7
|
OG
|
A:SER435
|
3.1
|
92.4
|
0.3
|
OG
|
A:SER435
|
3.2
|
94.8
|
0.7
|
OD1
|
A:ASP439
|
3.3
|
38.5
|
0.7
|
CG
|
A:ASP439
|
3.4
|
28.9
|
0.7
|
OD2
|
B:ASP439
|
3.5
|
77.0
|
1.0
|
CG
|
A:ASP439
|
3.5
|
39.4
|
0.3
|
O
|
A:SER435
|
3.8
|
84.5
|
0.3
|
O
|
B:HOH754
|
3.9
|
27.2
|
0.3
|
O
|
A:SER435
|
4.0
|
83.1
|
0.7
|
OD1
|
A:ASP439
|
4.1
|
29.5
|
0.3
|
HG
|
B:SER435
|
4.2
|
0.3
|
1.0
|
C
|
A:SER435
|
4.4
|
76.2
|
0.3
|
CB
|
A:SER435
|
4.4
|
85.5
|
0.3
|
C
|
A:SER435
|
4.4
|
75.9
|
0.7
|
CB
|
A:SER435
|
4.4
|
83.5
|
0.7
|
OG
|
B:SER435
|
4.6
|
0.1
|
1.0
|
HE
|
A:ARG438
|
4.6
|
99.4
|
0.7
|
HB2
|
A:ASP439
|
4.6
|
32.4
|
0.3
|
OE2
|
B:GLU436
|
4.6
|
0.1
|
1.0
|
HE
|
A:ARG438
|
4.6
|
90.9
|
0.3
|
HA
|
A:GLU436
|
4.6
|
67.9
|
0.7
|
CB
|
A:ASP439
|
4.6
|
27.0
|
0.3
|
HG
|
B:LEU583
|
4.6
|
0.1
|
1.0
|
HA
|
A:GLU436
|
4.7
|
67.8
|
0.3
|
CG
|
B:ASP439
|
4.7
|
68.5
|
1.0
|
HB2
|
A:SER435
|
4.7
|
0.2
|
0.7
|
HB2
|
A:SER435
|
4.7
|
0.5
|
0.4
|
HH21
|
A:ARG438
|
4.7
|
89.7
|
0.3
|
HB2
|
B:SER435
|
4.8
|
0.9
|
1.0
|
CA
|
A:SER435
|
4.8
|
90.8
|
0.3
|
CB
|
A:ASP439
|
4.8
|
34.5
|
0.7
|
HH21
|
A:ARG438
|
4.8
|
92.6
|
0.7
|
CA
|
A:SER435
|
4.9
|
94.5
|
0.7
|
HB3
|
A:ASP439
|
4.9
|
32.4
|
0.3
|
N
|
A:SER435
|
4.9
|
96.3
|
0.3
|
HA
|
B:GLU436
|
4.9
|
0.8
|
1.0
|
O
|
B:LEU583
|
5.0
|
0.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6pry
Go back to
Magnesium Binding Sites List in 6pry
Magnesium binding site 2 out
of 4 in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:43.1
occ:0.39
|
MG
|
A:MG602
|
0.0
|
43.1
|
0.4
|
MG
|
A:MG602
|
2.4
|
69.4
|
0.6
|
HG
|
A:SER435
|
2.5
|
0.9
|
0.4
|
HG
|
A:SER435
|
2.6
|
0.7
|
0.7
|
OG
|
A:SER435
|
2.8
|
92.4
|
0.3
|
HE
|
A:ARG438
|
2.8
|
90.9
|
0.3
|
HE
|
A:ARG438
|
2.8
|
99.4
|
0.7
|
HH21
|
A:ARG438
|
2.8
|
89.7
|
0.3
|
OD2
|
A:ASP439
|
2.9
|
32.0
|
0.3
|
OG
|
A:SER435
|
2.9
|
94.8
|
0.7
|
HH21
|
A:ARG438
|
3.0
|
92.6
|
0.7
|
OD1
|
A:ASP439
|
3.2
|
38.5
|
0.7
|
OD1
|
A:ASP439
|
3.3
|
29.5
|
0.3
|
O
|
B:HIS584
|
3.4
|
0.7
|
1.0
|
NE
|
A:ARG438
|
3.5
|
75.7
|
0.3
|
NH2
|
A:ARG438
|
3.5
|
74.7
|
0.3
|
NE
|
A:ARG438
|
3.5
|
82.8
|
0.7
|
CG
|
A:ASP439
|
3.5
|
39.4
|
0.3
|
NH2
|
A:ARG438
|
3.6
|
77.2
|
0.7
|
O
|
B:HOH714
|
3.8
|
87.4
|
1.0
|
CZ
|
A:ARG438
|
3.9
|
79.2
|
0.3
|
HB2
|
A:SER435
|
3.9
|
0.5
|
0.4
|
HB2
|
A:SER435
|
3.9
|
0.2
|
0.7
|
CB
|
A:SER435
|
3.9
|
85.5
|
0.3
|
CZ
|
A:ARG438
|
4.0
|
85.6
|
0.7
|
CB
|
A:SER435
|
4.0
|
83.5
|
0.7
|
OD2
|
A:ASP439
|
4.1
|
37.5
|
0.7
|
CG
|
A:ASP439
|
4.1
|
28.9
|
0.7
|
HH22
|
A:ARG438
|
4.1
|
89.7
|
0.3
|
O
|
A:SER435
|
4.2
|
84.5
|
0.3
|
HG3
|
A:ARG438
|
4.2
|
55.2
|
0.3
|
HG3
|
A:ARG438
|
4.2
|
46.8
|
0.7
|
O
|
A:SER435
|
4.2
|
83.1
|
0.7
|
HH22
|
A:ARG438
|
4.3
|
92.6
|
0.7
|
O
|
B:LEU583
|
4.3
|
0.4
|
1.0
|
HB3
|
A:SER435
|
4.4
|
0.5
|
0.4
|
C
|
B:HIS584
|
4.5
|
0.6
|
1.0
|
HG2
|
A:ARG438
|
4.5
|
46.8
|
0.7
|
CD
|
A:ARG438
|
4.5
|
46.1
|
0.7
|
CD
|
A:ARG438
|
4.6
|
47.0
|
0.3
|
HB3
|
A:SER435
|
4.6
|
0.2
|
0.7
|
O
|
B:HOH754
|
4.6
|
40.0
|
0.7
|
HG2
|
A:ARG438
|
4.6
|
55.2
|
0.3
|
CG
|
A:ARG438
|
4.6
|
39.0
|
0.7
|
CG
|
A:ARG438
|
4.7
|
46.0
|
0.3
|
HD2
|
A:ARG438
|
4.8
|
55.3
|
0.7
|
OXT
|
B:HIS584
|
4.8
|
0.1
|
1.0
|
HD2
|
A:ARG438
|
4.8
|
56.4
|
0.3
|
C
|
B:LEU583
|
4.9
|
92.7
|
1.0
|
OE2
|
B:GLU436
|
4.9
|
0.1
|
1.0
|
HA
|
B:LEU583
|
4.9
|
73.5
|
1.0
|
C
|
A:SER435
|
4.9
|
76.2
|
0.3
|
C
|
A:SER435
|
5.0
|
75.9
|
0.7
|
|
Magnesium binding site 3 out
of 4 in 6pry
Go back to
Magnesium Binding Sites List in 6pry
Magnesium binding site 3 out
of 4 in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:42.8
occ:1.00
|
O
|
B:HOH777
|
2.2
|
35.8
|
0.5
|
NE2
|
B:HIS498
|
2.3
|
25.0
|
1.0
|
O
|
B:HOH779
|
2.6
|
67.6
|
1.0
|
O
|
B:HOH777
|
2.9
|
47.9
|
0.6
|
OE1
|
B:GLU497
|
3.0
|
38.9
|
1.0
|
CE1
|
B:HIS498
|
3.1
|
25.6
|
1.0
|
HE1
|
B:HIS498
|
3.1
|
30.7
|
1.0
|
O
|
B:HOH745
|
3.3
|
32.5
|
0.5
|
CD2
|
B:HIS498
|
3.3
|
23.6
|
1.0
|
O
|
B:HOH719
|
3.6
|
60.4
|
1.0
|
HD2
|
B:HIS498
|
3.6
|
28.3
|
1.0
|
HB3
|
B:GLU497
|
3.8
|
35.7
|
1.0
|
CD
|
B:GLU497
|
4.2
|
50.5
|
1.0
|
ND1
|
B:HIS498
|
4.2
|
21.7
|
1.0
|
O
|
B:HOH745
|
4.3
|
24.3
|
0.5
|
HB2
|
B:GLU497
|
4.3
|
35.7
|
1.0
|
CG
|
B:HIS498
|
4.4
|
22.4
|
1.0
|
CB
|
B:GLU497
|
4.5
|
29.7
|
1.0
|
CG
|
B:GLU497
|
4.9
|
33.4
|
1.0
|
HD1
|
B:HIS498
|
5.0
|
26.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6pry
Go back to
Magnesium Binding Sites List in 6pry
Magnesium binding site 4 out
of 4 in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:71.0
occ:1.00
|
O
|
A:HOH724
|
2.2
|
76.3
|
1.0
|
HD23
|
B:LEU454
|
3.3
|
71.9
|
1.0
|
HE22
|
B:GLN568
|
3.7
|
80.6
|
1.0
|
HD22
|
B:LEU454
|
4.0
|
71.9
|
1.0
|
CD2
|
B:LEU454
|
4.0
|
59.9
|
1.0
|
HA
|
B:LEU454
|
4.0
|
40.4
|
1.0
|
OE1
|
A:GLU571
|
4.2
|
53.9
|
1.0
|
NE2
|
B:GLN568
|
4.4
|
67.2
|
1.0
|
HD21
|
B:LEU454
|
4.4
|
71.9
|
1.0
|
O
|
B:LEU454
|
4.5
|
34.9
|
1.0
|
OE1
|
B:GLN568
|
4.7
|
52.0
|
1.0
|
OD2
|
A:ASP567
|
4.8
|
35.8
|
0.6
|
OD1
|
A:ASP567
|
4.8
|
33.8
|
0.6
|
CD
|
B:GLN568
|
4.9
|
52.4
|
1.0
|
CA
|
B:LEU454
|
4.9
|
33.7
|
1.0
|
HE21
|
B:GLN568
|
4.9
|
80.6
|
1.0
|
|
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 15:18:12 2024
|