Magnesium in PDB 8ez5: Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
All present enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution:
1.10.3.9;
Protein crystallography data
The structure of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution, PDB code: 8ez5
was solved by
A.Bhowmick,
R.Hussein,
I.Bogacz,
P.S.Simon,
M.Ibrahim,
R.Chatterjee,
M.D.Doyle,
M.H.Cheah,
T.Fransson,
P.Chernev,
I.-S.Kim,
H.Makita,
M.Dasgupta,
C.J.Kaminsky,
M.Zhang,
J.Gatcke,
S.Haupt,
I.I.Nangca,
S.M.Keable,
O.Aydin,
K.Tono,
S.Owada,
L.B.Gee,
F.D.Fuller,
A.Batyuk,
R.Alonso-Mori,
J.M.Holton,
D.W.Paley,
N.W.Moriarty,
F.Mamedov,
P.D.Adams,
A.S.Brewster,
H.Dobbek,
N.K.Sauter,
U.Bergmann,
A.Zouni,
J.Messinger,
J.Kern,
J.Yano,
V.K.Yachandra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.65 /
2.09
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.958,
221.646,
307.786,
90,
90,
90
|
R / Rfree (%)
|
18.6 /
23.5
|
Other elements in 8ez5:
The structure of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 1 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg606
b:25.7
occ:1.00
|
MG
|
A:CLA606
|
0.0
|
25.7
|
1.0
|
ND
|
A:CLA606
|
2.0
|
25.8
|
1.0
|
NC
|
A:CLA606
|
2.1
|
23.4
|
1.0
|
NB
|
A:CLA606
|
2.1
|
27.2
|
1.0
|
NA
|
A:CLA606
|
2.2
|
26.6
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
32.6
|
1.0
|
C4D
|
A:CLA606
|
3.0
|
23.6
|
1.0
|
C1C
|
A:CLA606
|
3.1
|
25.8
|
1.0
|
C4B
|
A:CLA606
|
3.1
|
24.7
|
1.0
|
C1B
|
A:CLA606
|
3.1
|
26.8
|
1.0
|
C4C
|
A:CLA606
|
3.1
|
25.8
|
1.0
|
C4A
|
A:CLA606
|
3.1
|
30.4
|
1.0
|
CE1
|
A:HIS198
|
3.1
|
30.5
|
1.0
|
C1D
|
A:CLA606
|
3.1
|
25.8
|
1.0
|
C1A
|
A:CLA606
|
3.2
|
27.8
|
1.0
|
CD2
|
A:HIS198
|
3.3
|
28.7
|
1.0
|
CHC
|
A:CLA606
|
3.4
|
25.2
|
1.0
|
CHB
|
A:CLA606
|
3.5
|
27.2
|
1.0
|
CHD
|
A:CLA606
|
3.5
|
24.0
|
1.0
|
CHA
|
A:CLA606
|
3.5
|
23.2
|
1.0
|
CE
|
A:MET183
|
4.0
|
23.8
|
0.3
|
CE
|
A:MET183
|
4.2
|
22.6
|
0.7
|
C3D
|
A:CLA606
|
4.3
|
22.1
|
1.0
|
ND1
|
A:HIS198
|
4.3
|
31.1
|
1.0
|
C2C
|
A:CLA606
|
4.3
|
25.9
|
1.0
|
C3C
|
A:CLA606
|
4.3
|
25.2
|
1.0
|
C2D
|
A:CLA606
|
4.3
|
25.2
|
1.0
|
C3B
|
A:CLA606
|
4.3
|
27.6
|
1.0
|
C2B
|
A:CLA606
|
4.4
|
27.5
|
1.0
|
CG
|
A:HIS198
|
4.4
|
31.9
|
1.0
|
C3A
|
A:CLA606
|
4.5
|
29.7
|
1.0
|
CAB
|
D:CLA404
|
4.5
|
25.1
|
1.0
|
C2A
|
A:CLA606
|
4.5
|
25.9
|
1.0
|
CBD
|
A:CLA606
|
5.0
|
27.7
|
1.0
|
|
Magnesium binding site 2 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 2 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:30.4
occ:1.00
|
MG
|
A:CLA607
|
0.0
|
30.4
|
1.0
|
NB
|
A:CLA607
|
2.0
|
32.0
|
1.0
|
ND
|
A:CLA607
|
2.0
|
31.2
|
1.0
|
NC
|
A:CLA607
|
2.1
|
32.5
|
1.0
|
NA
|
A:CLA607
|
2.1
|
31.1
|
1.0
|
O
|
A:HOH796
|
2.2
|
29.7
|
1.0
|
C4D
|
A:CLA607
|
2.9
|
29.0
|
1.0
|
C1B
|
A:CLA607
|
3.0
|
34.7
|
1.0
|
C1C
|
A:CLA607
|
3.0
|
31.4
|
1.0
|
C4B
|
A:CLA607
|
3.0
|
32.9
|
1.0
|
C4A
|
A:CLA607
|
3.1
|
32.5
|
1.0
|
C4C
|
A:CLA607
|
3.1
|
31.6
|
1.0
|
C1D
|
A:CLA607
|
3.1
|
26.9
|
1.0
|
C1A
|
A:CLA607
|
3.2
|
32.5
|
1.0
|
CHC
|
A:CLA607
|
3.4
|
33.1
|
1.0
|
CHB
|
A:CLA607
|
3.5
|
28.0
|
1.0
|
CHA
|
A:CLA607
|
3.5
|
30.0
|
1.0
|
CHD
|
A:CLA607
|
3.5
|
28.5
|
1.0
|
CBB
|
D:PHO402
|
3.9
|
31.8
|
1.0
|
C3D
|
A:CLA607
|
4.2
|
30.7
|
1.0
|
O
|
D:HOH589
|
4.3
|
33.7
|
1.0
|
C3B
|
A:CLA607
|
4.3
|
31.7
|
1.0
|
C2B
|
A:CLA607
|
4.3
|
32.6
|
1.0
|
C2C
|
A:CLA607
|
4.3
|
31.7
|
1.0
|
C2D
|
A:CLA607
|
4.3
|
28.9
|
1.0
|
C3C
|
A:CLA607
|
4.3
|
33.1
|
1.0
|
C3A
|
A:CLA607
|
4.5
|
29.0
|
1.0
|
C2A
|
A:CLA607
|
4.5
|
29.6
|
1.0
|
CG2
|
D:ILE178
|
4.8
|
28.1
|
1.0
|
CBA
|
A:CLA607
|
4.8
|
29.3
|
1.0
|
CE2
|
A:PHE206
|
4.8
|
31.1
|
1.0
|
CBD
|
A:CLA607
|
4.9
|
31.2
|
1.0
|
|
Magnesium binding site 3 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 3 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg609
b:24.5
occ:1.00
|
MG
|
A:CLA609
|
0.0
|
24.5
|
1.0
|
ND
|
A:CLA609
|
2.0
|
23.0
|
1.0
|
NA
|
A:CLA609
|
2.0
|
25.9
|
1.0
|
NB
|
A:CLA609
|
2.1
|
26.3
|
1.0
|
NC
|
A:CLA609
|
2.1
|
21.5
|
1.0
|
NE2
|
A:HIS118
|
2.3
|
23.1
|
1.0
|
C4D
|
A:CLA609
|
2.9
|
26.4
|
1.0
|
C4A
|
A:CLA609
|
3.0
|
26.3
|
1.0
|
C1B
|
A:CLA609
|
3.0
|
27.5
|
1.0
|
C1A
|
A:CLA609
|
3.1
|
25.3
|
1.0
|
C1C
|
A:CLA609
|
3.1
|
27.3
|
1.0
|
C4B
|
A:CLA609
|
3.1
|
23.7
|
1.0
|
CE1
|
A:HIS118
|
3.1
|
28.8
|
1.0
|
C4C
|
A:CLA609
|
3.2
|
24.4
|
1.0
|
C1D
|
A:CLA609
|
3.2
|
27.0
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
24.4
|
1.0
|
CHA
|
A:CLA609
|
3.4
|
22.9
|
1.0
|
CHB
|
A:CLA609
|
3.4
|
27.6
|
1.0
|
CHC
|
A:CLA609
|
3.5
|
24.8
|
1.0
|
CHD
|
A:CLA609
|
3.6
|
30.6
|
1.0
|
C3D
|
A:CLA609
|
4.2
|
22.4
|
1.0
|
ND1
|
A:HIS118
|
4.3
|
26.9
|
1.0
|
CG1
|
I:VAL8
|
4.3
|
32.1
|
1.0
|
C2B
|
A:CLA609
|
4.3
|
28.2
|
1.0
|
C3A
|
A:CLA609
|
4.3
|
28.1
|
1.0
|
C3B
|
A:CLA609
|
4.3
|
23.7
|
1.0
|
C2D
|
A:CLA609
|
4.4
|
27.9
|
1.0
|
C2C
|
A:CLA609
|
4.4
|
25.1
|
1.0
|
C2A
|
A:CLA609
|
4.4
|
30.1
|
1.0
|
C3C
|
A:CLA609
|
4.4
|
28.2
|
1.0
|
CG
|
A:HIS118
|
4.4
|
30.0
|
1.0
|
CG2
|
I:VAL12
|
4.4
|
25.5
|
1.0
|
CBD
|
A:CLA609
|
4.8
|
25.4
|
1.0
|
|
Magnesium binding site 4 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 4 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:37.8
occ:1.00
|
MG
|
B:CLA601
|
0.0
|
37.8
|
1.0
|
ND
|
B:CLA601
|
2.0
|
48.6
|
1.0
|
NB
|
B:CLA601
|
2.0
|
38.5
|
1.0
|
NC
|
B:CLA601
|
2.0
|
43.7
|
1.0
|
O
|
B:HOH735
|
2.1
|
40.7
|
1.0
|
NA
|
B:CLA601
|
2.2
|
49.3
|
1.0
|
C4D
|
B:CLA601
|
2.9
|
53.3
|
1.0
|
C1C
|
B:CLA601
|
3.0
|
39.7
|
1.0
|
C4B
|
B:CLA601
|
3.0
|
48.0
|
1.0
|
C1B
|
B:CLA601
|
3.1
|
45.8
|
1.0
|
C4C
|
B:CLA601
|
3.1
|
44.8
|
1.0
|
C1D
|
B:CLA601
|
3.1
|
51.0
|
1.0
|
C4A
|
B:CLA601
|
3.2
|
45.1
|
1.0
|
C1A
|
B:CLA601
|
3.2
|
48.9
|
1.0
|
CHC
|
B:CLA601
|
3.4
|
44.7
|
1.0
|
CHA
|
B:CLA601
|
3.5
|
47.2
|
1.0
|
CHB
|
B:CLA601
|
3.5
|
48.6
|
1.0
|
CHD
|
B:CLA601
|
3.5
|
45.1
|
1.0
|
C7
|
B:CLA601
|
3.9
|
59.1
|
1.0
|
C9
|
B:CLA601
|
4.0
|
60.6
|
1.0
|
C10
|
B:CLA601
|
4.0
|
57.3
|
1.0
|
C8
|
B:CLA601
|
4.2
|
56.6
|
1.0
|
C3D
|
B:CLA601
|
4.3
|
55.8
|
1.0
|
C2C
|
B:CLA601
|
4.3
|
46.5
|
1.0
|
O
|
B:TRP185
|
4.3
|
39.4
|
1.0
|
C3B
|
B:CLA601
|
4.3
|
45.9
|
1.0
|
C3C
|
B:CLA601
|
4.3
|
47.9
|
1.0
|
C2B
|
B:CLA601
|
4.3
|
41.2
|
1.0
|
C2D
|
B:CLA601
|
4.4
|
55.5
|
1.0
|
C3A
|
B:CLA601
|
4.5
|
53.5
|
1.0
|
C2A
|
B:CLA601
|
4.6
|
59.3
|
1.0
|
CE2
|
B:PHE190
|
4.6
|
43.8
|
1.0
|
C6
|
B:CLA601
|
4.8
|
58.2
|
1.0
|
CBB
|
B:CLA602
|
4.9
|
37.1
|
1.0
|
CBD
|
B:CLA601
|
5.0
|
53.6
|
1.0
|
|
Magnesium binding site 5 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 5 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:31.1
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
31.1
|
1.0
|
ND
|
B:CLA602
|
2.0
|
37.0
|
1.0
|
NB
|
B:CLA602
|
2.1
|
37.0
|
1.0
|
NC
|
B:CLA602
|
2.1
|
33.3
|
1.0
|
NA
|
B:CLA602
|
2.1
|
39.4
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
34.3
|
1.0
|
C4D
|
B:CLA602
|
2.9
|
33.1
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
33.7
|
1.0
|
C4A
|
B:CLA602
|
3.1
|
36.8
|
1.0
|
C1B
|
B:CLA602
|
3.1
|
38.1
|
1.0
|
C1C
|
B:CLA602
|
3.1
|
38.1
|
1.0
|
C4B
|
B:CLA602
|
3.1
|
32.7
|
1.0
|
C4C
|
B:CLA602
|
3.1
|
33.9
|
1.0
|
C1D
|
B:CLA602
|
3.1
|
38.9
|
1.0
|
C1A
|
B:CLA602
|
3.2
|
31.7
|
1.0
|
CG
|
B:HIS201
|
3.3
|
29.5
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
32.6
|
1.0
|
CHC
|
B:CLA602
|
3.5
|
34.0
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
34.1
|
1.0
|
CHD
|
B:CLA602
|
3.5
|
37.0
|
1.0
|
CB
|
B:HIS201
|
3.7
|
30.9
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
25.6
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
31.5
|
1.0
|
CA
|
B:HIS201
|
4.3
|
31.2
|
1.0
|
CD2
|
B:HIS201
|
4.3
|
28.4
|
1.0
|
C2D
|
B:CLA602
|
4.4
|
36.5
|
1.0
|
C2B
|
B:CLA602
|
4.4
|
30.7
|
1.0
|
C2C
|
B:CLA602
|
4.4
|
39.5
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
37.4
|
1.0
|
C3B
|
B:CLA602
|
4.4
|
33.7
|
1.0
|
CZ
|
H:PHE41
|
4.4
|
54.0
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
39.0
|
1.0
|
C2A
|
B:CLA602
|
4.5
|
35.4
|
1.0
|
CE1
|
B:PHE190
|
4.8
|
35.6
|
1.0
|
CD1
|
H:ILE45
|
4.9
|
36.3
|
1.0
|
O
|
B:HIS201
|
5.0
|
26.6
|
1.0
|
CBD
|
B:CLA602
|
5.0
|
31.5
|
1.0
|
|
Magnesium binding site 6 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 6 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:32.6
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
32.6
|
1.0
|
NC
|
B:CLA603
|
2.1
|
26.4
|
1.0
|
NB
|
B:CLA603
|
2.1
|
25.0
|
1.0
|
ND
|
B:CLA603
|
2.1
|
30.3
|
1.0
|
NE2
|
B:HIS202
|
2.1
|
29.9
|
1.0
|
NA
|
B:CLA603
|
2.1
|
27.6
|
1.0
|
CD2
|
B:HIS202
|
3.0
|
30.0
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
29.6
|
1.0
|
C1C
|
B:CLA603
|
3.1
|
28.3
|
1.0
|
C1B
|
B:CLA603
|
3.1
|
28.4
|
1.0
|
C4A
|
B:CLA603
|
3.1
|
26.8
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
28.1
|
1.0
|
C4B
|
B:CLA603
|
3.1
|
30.1
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
32.1
|
1.0
|
C1A
|
B:CLA603
|
3.2
|
29.6
|
1.0
|
C1D
|
B:CLA603
|
3.2
|
29.8
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
29.8
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
26.6
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
28.1
|
1.0
|
CHD
|
B:CLA603
|
3.6
|
27.5
|
1.0
|
CG
|
B:HIS202
|
4.2
|
29.8
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
29.2
|
1.0
|
C2C
|
B:CLA603
|
4.3
|
25.5
|
1.0
|
C3C
|
B:CLA603
|
4.3
|
28.0
|
1.0
|
C2B
|
B:CLA603
|
4.3
|
29.2
|
1.0
|
C3D
|
B:CLA603
|
4.4
|
30.1
|
1.0
|
C3B
|
B:CLA603
|
4.4
|
32.4
|
1.0
|
C2D
|
B:CLA603
|
4.4
|
31.9
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
29.4
|
1.0
|
C9
|
B:CLA605
|
4.5
|
39.0
|
1.0
|
C2A
|
B:CLA603
|
4.5
|
31.2
|
1.0
|
C5
|
B:CLA605
|
4.6
|
37.4
|
1.0
|
C6
|
B:CLA605
|
4.8
|
42.4
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
25.6
|
1.0
|
CE2
|
B:PHE153
|
4.9
|
32.8
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
28.4
|
1.0
|
CBA
|
B:CLA603
|
5.0
|
30.7
|
1.0
|
CBD
|
B:CLA603
|
5.0
|
29.6
|
1.0
|
|
Magnesium binding site 7 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 7 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:28.2
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
28.2
|
1.0
|
ND
|
B:CLA604
|
2.1
|
29.8
|
1.0
|
NB
|
B:CLA604
|
2.1
|
30.1
|
1.0
|
NA
|
B:CLA604
|
2.1
|
33.3
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
25.0
|
1.0
|
NC
|
B:CLA604
|
2.2
|
28.1
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
28.9
|
1.0
|
C4A
|
B:CLA604
|
3.0
|
31.1
|
1.0
|
C1B
|
B:CLA604
|
3.1
|
30.8
|
1.0
|
CD2
|
B:HIS455
|
3.1
|
27.1
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
28.6
|
1.0
|
C4B
|
B:CLA604
|
3.2
|
30.4
|
1.0
|
C1C
|
B:CLA604
|
3.2
|
28.7
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
26.3
|
1.0
|
C1A
|
B:CLA604
|
3.2
|
33.6
|
1.0
|
C4C
|
B:CLA604
|
3.2
|
27.6
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
29.3
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
32.4
|
1.0
|
CHD
|
B:CLA604
|
3.6
|
25.6
|
1.0
|
CHC
|
B:CLA604
|
3.6
|
30.3
|
1.0
|
C14
|
B:CLA612
|
4.1
|
31.0
|
1.0
|
CG
|
B:HIS455
|
4.3
|
26.8
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
28.2
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
26.8
|
1.0
|
C2B
|
B:CLA604
|
4.3
|
28.4
|
1.0
|
C2D
|
B:CLA604
|
4.4
|
31.5
|
1.0
|
C3B
|
B:CLA604
|
4.4
|
27.4
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
30.9
|
1.0
|
C3C
|
B:CLA604
|
4.5
|
32.8
|
1.0
|
C2C
|
B:CLA604
|
4.5
|
27.7
|
1.0
|
C2A
|
B:CLA604
|
4.5
|
26.6
|
1.0
|
C15
|
B:CLA612
|
4.7
|
39.1
|
1.0
|
C13
|
B:CLA612
|
4.8
|
39.7
|
1.0
|
CE2
|
B:PHE451
|
5.0
|
27.8
|
1.0
|
|
Magnesium binding site 8 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 8 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:27.4
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
27.4
|
1.0
|
ND
|
B:CLA605
|
2.0
|
33.4
|
1.0
|
NC
|
B:CLA605
|
2.0
|
27.5
|
1.0
|
NB
|
B:CLA605
|
2.1
|
25.4
|
1.0
|
NA
|
B:CLA605
|
2.1
|
29.2
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
28.5
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
28.1
|
1.0
|
C1C
|
B:CLA605
|
3.0
|
29.5
|
1.0
|
C4B
|
B:CLA605
|
3.1
|
27.6
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
28.1
|
1.0
|
C1B
|
B:CLA605
|
3.1
|
27.6
|
1.0
|
C4A
|
B:CLA605
|
3.1
|
32.1
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
30.1
|
1.0
|
C1A
|
B:CLA605
|
3.2
|
31.6
|
1.0
|
C1D
|
B:CLA605
|
3.2
|
29.1
|
1.0
|
CD2
|
B:HIS100
|
3.2
|
29.6
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
31.1
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
34.0
|
1.0
|
CHB
|
B:CLA605
|
3.5
|
31.9
|
1.0
|
CHD
|
B:CLA605
|
3.5
|
29.6
|
1.0
|
C2
|
B:CLA604
|
4.2
|
37.2
|
1.0
|
ND1
|
B:HIS100
|
4.3
|
27.1
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
31.5
|
1.0
|
C2C
|
B:CLA605
|
4.3
|
27.5
|
1.0
|
C3C
|
B:CLA605
|
4.3
|
31.5
|
1.0
|
CG
|
B:HIS100
|
4.3
|
28.6
|
1.0
|
C1
|
B:CLA604
|
4.3
|
34.7
|
1.0
|
C3B
|
B:CLA605
|
4.4
|
33.4
|
1.0
|
C2D
|
B:CLA605
|
4.4
|
33.9
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
32.6
|
1.0
|
C3A
|
B:CLA605
|
4.5
|
28.3
|
1.0
|
C2A
|
B:CLA605
|
4.5
|
30.0
|
1.0
|
CBD
|
B:CLA605
|
4.9
|
30.4
|
1.0
|
CBA
|
B:CLA605
|
5.0
|
27.5
|
1.0
|
|
Magnesium binding site 9 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 9 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:32.5
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
32.5
|
1.0
|
NB
|
B:CLA606
|
2.0
|
32.7
|
1.0
|
ND
|
B:CLA606
|
2.1
|
37.6
|
1.0
|
NC
|
B:CLA606
|
2.1
|
32.8
|
1.0
|
NA
|
B:CLA606
|
2.2
|
32.8
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
31.7
|
1.0
|
CE1
|
B:HIS157
|
2.9
|
30.8
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
36.9
|
1.0
|
C1B
|
B:CLA606
|
3.0
|
31.1
|
1.0
|
C4B
|
B:CLA606
|
3.1
|
35.9
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
36.3
|
1.0
|
C1C
|
B:CLA606
|
3.1
|
36.4
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
33.4
|
1.0
|
C1D
|
B:CLA606
|
3.2
|
36.4
|
1.0
|
C1A
|
B:CLA606
|
3.2
|
36.5
|
1.0
|
CG
|
B:HIS157
|
3.4
|
29.4
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
33.5
|
1.0
|
CHC
|
B:CLA606
|
3.5
|
35.8
|
1.0
|
CHD
|
B:CLA606
|
3.6
|
31.6
|
1.0
|
CHA
|
B:CLA606
|
3.6
|
38.4
|
1.0
|
C8
|
B:STE620
|
3.7
|
40.9
|
1.0
|
CB
|
B:HIS157
|
3.9
|
34.2
|
1.0
|
NE2
|
B:HIS157
|
4.1
|
29.3
|
1.0
|
C6
|
B:STE620
|
4.3
|
39.8
|
1.0
|
C2B
|
B:CLA606
|
4.3
|
36.8
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
31.6
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
39.7
|
1.0
|
CD2
|
B:HIS157
|
4.4
|
28.9
|
1.0
|
C7
|
B:STE620
|
4.4
|
40.9
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
35.0
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
36.0
|
1.0
|
C2D
|
B:CLA606
|
4.4
|
38.9
|
1.0
|
C3A
|
B:CLA606
|
4.5
|
33.3
|
1.0
|
C2A
|
B:CLA606
|
4.6
|
33.3
|
1.0
|
CD
|
B:PRO164
|
5.0
|
32.9
|
1.0
|
CA
|
B:HIS157
|
5.0
|
29.4
|
1.0
|
|
Magnesium binding site 10 out
of 70 in 8ez5
Go back to
Magnesium Binding Sites List in 8ez5
Magnesium binding site 10 out
of 70 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:26.1
occ:1.00
|
MG
|
B:CLA607
|
0.0
|
26.1
|
1.0
|
NB
|
B:CLA607
|
1.9
|
22.4
|
1.0
|
ND
|
B:CLA607
|
2.1
|
26.6
|
1.0
|
NC
|
B:CLA607
|
2.1
|
20.3
|
1.0
|
NA
|
B:CLA607
|
2.1
|
22.5
|
1.0
|
O
|
B:HOH848
|
2.2
|
28.9
|
1.0
|
C1B
|
B:CLA607
|
3.0
|
25.8
|
1.0
|
C4D
|
B:CLA607
|
3.0
|
24.9
|
1.0
|
C4B
|
B:CLA607
|
3.0
|
24.9
|
1.0
|
C1C
|
B:CLA607
|
3.1
|
25.6
|
1.0
|
C4A
|
B:CLA607
|
3.1
|
24.4
|
1.0
|
C4C
|
B:CLA607
|
3.2
|
27.1
|
1.0
|
C1A
|
B:CLA607
|
3.2
|
23.6
|
1.0
|
C1D
|
B:CLA607
|
3.2
|
27.8
|
1.0
|
CHC
|
B:CLA607
|
3.4
|
20.6
|
1.0
|
CHB
|
B:CLA607
|
3.4
|
24.6
|
1.0
|
CHA
|
B:CLA607
|
3.5
|
26.5
|
1.0
|
CHD
|
B:CLA607
|
3.6
|
29.8
|
1.0
|
C14
|
M:LMG101
|
3.7
|
31.6
|
1.0
|
O
|
B:HOH726
|
4.2
|
32.0
|
1.0
|
C2B
|
B:CLA607
|
4.2
|
27.1
|
1.0
|
C3B
|
B:CLA607
|
4.2
|
25.5
|
1.0
|
C12
|
M:LMG101
|
4.3
|
39.7
|
1.0
|
C13
|
M:LMG101
|
4.3
|
35.2
|
1.0
|
C3D
|
B:CLA607
|
4.3
|
32.1
|
1.0
|
C2C
|
B:CLA607
|
4.3
|
23.7
|
1.0
|
C3C
|
B:CLA607
|
4.4
|
22.1
|
1.0
|
C2D
|
B:CLA607
|
4.4
|
28.6
|
1.0
|
SD
|
B:MET37
|
4.4
|
27.5
|
1.0
|
C3A
|
B:CLA607
|
4.4
|
27.2
|
1.0
|
C2A
|
B:CLA607
|
4.5
|
30.7
|
1.0
|
CD2
|
B:PHE61
|
4.6
|
25.4
|
1.0
|
CBA
|
B:CLA607
|
4.8
|
26.9
|
1.0
|
CE
|
B:MET37
|
4.9
|
24.3
|
1.0
|
CB
|
B:PHE61
|
4.9
|
24.8
|
1.0
|
C15
|
M:LMG101
|
4.9
|
41.4
|
1.0
|
CG
|
B:PHE61
|
4.9
|
28.5
|
1.0
|
CBD
|
B:CLA607
|
5.0
|
30.8
|
1.0
|
|
Reference:
A.Bhowmick,
R.Hussein,
I.Bogacz,
P.S.Simon,
M.Ibrahim,
R.Chatterjee,
M.D.Doyle,
M.H.Cheah,
T.Fransson,
P.Chernev,
I.-S.Kim,
H.Makita,
M.Dasgupta,
C.J.Kaminsky,
M.Zhang,
J.Gatcke,
S.Haupt,
I.I.Nangca,
S.M.Keable,
O.Aydin,
K.Tono,
S.Owada,
L.B.Gee,
F.D.Fuller,
A.Batyuk,
R.Alonso-Mori,
J.M.Holton,
D.W.Paley,
N.W.Moriarty,
F.Mamedov,
P.D.Adams,
A.S.Brewster,
H.Dobbek,
N.K.Sauter,
U.Bergmann,
A.Zouni,
J.Messinger,
J.Kern,
J.Yano,
V.K.Yachandra.
Structural Evidence For Intermediates During O2 Formation in Photosystem II To Be Published.
Page generated: Fri Oct 4 01:24:15 2024
|