Magnesium in PDB 5tis: Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
All present enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex:
1.10.3.9;
Protein crystallography data
The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis
was solved by
I.D.Young,
M.Ibrahim,
R.Chatterjee,
S.Gul,
F.Fuller,
S.Koroidov,
A.S.Brewster,
R.Tran,
R.Alonso-Mori,
T.Kroll,
T.Michels-Clark,
H.Laksmono,
R.G.Sierra,
C.A.Stan,
R.Hussein,
M.Zhang,
L.Douthit,
M.Kubin,
C.De Lichtenberg,
L.V.Pham,
H.Nilsson,
M.H.Cheah,
D.Shevela,
C.Saracini,
M.A.Bean,
I.Seuffert,
D.Sokaras,
T.-C.Weng,
E.Pastor,
C.Weninger,
T.Fransson,
L.Lassalle,
P.Braeuer,
P.Aller,
P.T.Docker,
B.Andi,
A.M.Orville,
J.M.Glownia,
S.Nelson,
M.Sikorski,
D.Zhu,
M.S.Hunter,
A.Aquila,
J.E.Koglin,
J.Robinson,
M.Liang,
S.Boutet,
A.Y.Lyubimov,
M.Uervirojnangkoorn,
N.W.Moriarty,
D.Liebschner,
P.V.Afonine,
D.G.Watermann,
G.Evans,
P.Wernet,
H.Dobbek,
W.I.Weis,
A.T.Brunger,
P.H.Zwart,
P.D.Adams,
A.Zouni,
J.Messinger,
U.Bergmann,
N.K.Sauter,
J.Kern,
V.K.Yachandra,
J.Yano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.28 /
2.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.870,
223.140,
310.710,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.3 /
23.1
|
Other elements in 5tis:
The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 1 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg606
b:32.2
occ:1.00
|
MG
|
A:CLA606
|
0.0
|
32.2
|
1.0
|
ND
|
A:CLA606
|
2.0
|
30.6
|
1.0
|
NB
|
A:CLA606
|
2.1
|
34.0
|
1.0
|
NC
|
A:CLA606
|
2.1
|
27.4
|
1.0
|
NA
|
A:CLA606
|
2.1
|
32.2
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
36.6
|
1.0
|
C4D
|
A:CLA606
|
2.9
|
27.4
|
1.0
|
C4A
|
A:CLA606
|
3.1
|
35.9
|
1.0
|
C1B
|
A:CLA606
|
3.1
|
34.4
|
1.0
|
C1C
|
A:CLA606
|
3.1
|
29.5
|
1.0
|
CE1
|
A:HIS198
|
3.1
|
33.2
|
1.0
|
C4B
|
A:CLA606
|
3.1
|
31.3
|
1.0
|
C4C
|
A:CLA606
|
3.1
|
28.6
|
1.0
|
C1A
|
A:CLA606
|
3.1
|
30.4
|
1.0
|
C1D
|
A:CLA606
|
3.2
|
31.2
|
1.0
|
CD2
|
A:HIS198
|
3.3
|
32.6
|
1.0
|
CHB
|
A:CLA606
|
3.4
|
31.5
|
1.0
|
CHC
|
A:CLA606
|
3.4
|
31.3
|
1.0
|
CHA
|
A:CLA606
|
3.5
|
31.0
|
1.0
|
CHD
|
A:CLA606
|
3.5
|
30.9
|
1.0
|
CE
|
A:MET183
|
4.0
|
25.0
|
1.0
|
ND1
|
A:HIS198
|
4.3
|
25.3
|
1.0
|
C3D
|
A:CLA606
|
4.3
|
23.4
|
1.0
|
C2C
|
A:CLA606
|
4.3
|
35.9
|
1.0
|
CAB
|
D:CLA402
|
4.3
|
32.0
|
1.0
|
C2B
|
A:CLA606
|
4.3
|
32.2
|
1.0
|
C3C
|
A:CLA606
|
4.4
|
29.3
|
1.0
|
C3B
|
A:CLA606
|
4.4
|
31.5
|
1.0
|
C2D
|
A:CLA606
|
4.4
|
27.3
|
1.0
|
C3A
|
A:CLA606
|
4.4
|
37.1
|
1.0
|
CG
|
A:HIS198
|
4.4
|
35.4
|
1.0
|
C2A
|
A:CLA606
|
4.4
|
29.2
|
1.0
|
CBB
|
D:CLA402
|
4.9
|
31.1
|
1.0
|
CBD
|
A:CLA606
|
4.9
|
34.5
|
1.0
|
|
Magnesium binding site 2 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 2 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:33.7
occ:1.00
|
MG
|
A:CLA607
|
0.0
|
33.7
|
1.0
|
NB
|
A:CLA607
|
2.0
|
33.1
|
1.0
|
ND
|
A:CLA607
|
2.0
|
36.5
|
1.0
|
NC
|
A:CLA607
|
2.1
|
32.1
|
1.0
|
NA
|
A:CLA607
|
2.1
|
34.8
|
1.0
|
O
|
A:HOH743
|
2.1
|
27.3
|
1.0
|
C4D
|
A:CLA607
|
2.9
|
30.5
|
1.0
|
C1B
|
A:CLA607
|
3.0
|
32.2
|
1.0
|
C4A
|
A:CLA607
|
3.1
|
33.9
|
1.0
|
C1C
|
A:CLA607
|
3.1
|
35.5
|
1.0
|
C4B
|
A:CLA607
|
3.1
|
35.1
|
1.0
|
C4C
|
A:CLA607
|
3.1
|
34.6
|
1.0
|
C1A
|
A:CLA607
|
3.1
|
37.6
|
1.0
|
C1D
|
A:CLA607
|
3.2
|
34.7
|
1.0
|
CHB
|
A:CLA607
|
3.4
|
32.9
|
1.0
|
CHC
|
A:CLA607
|
3.4
|
33.1
|
1.0
|
CHA
|
A:CLA607
|
3.5
|
35.5
|
1.0
|
CHD
|
A:CLA607
|
3.5
|
29.2
|
1.0
|
CBB
|
A:PHO608
|
4.0
|
36.1
|
1.0
|
C3D
|
A:CLA607
|
4.3
|
33.2
|
1.0
|
C2B
|
A:CLA607
|
4.3
|
35.0
|
1.0
|
C2C
|
A:CLA607
|
4.3
|
35.9
|
1.0
|
C3B
|
A:CLA607
|
4.3
|
34.0
|
1.0
|
O
|
D:HOH562
|
4.3
|
36.6
|
1.0
|
C3C
|
A:CLA607
|
4.4
|
30.9
|
1.0
|
C2D
|
A:CLA607
|
4.4
|
33.4
|
1.0
|
C3A
|
A:CLA607
|
4.4
|
36.6
|
1.0
|
C2A
|
A:CLA607
|
4.4
|
32.5
|
1.0
|
CBA
|
A:CLA607
|
4.7
|
35.3
|
1.0
|
CE2
|
A:PHE206
|
4.8
|
29.6
|
1.0
|
CG2
|
D:ILE178
|
4.9
|
35.0
|
1.0
|
CBD
|
A:CLA607
|
4.9
|
33.1
|
1.0
|
|
Magnesium binding site 3 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 3 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg609
b:30.5
occ:1.00
|
MG
|
A:CLA609
|
0.0
|
30.5
|
1.0
|
ND
|
A:CLA609
|
2.0
|
28.0
|
1.0
|
NB
|
A:CLA609
|
2.0
|
30.1
|
1.0
|
NC
|
A:CLA609
|
2.1
|
29.4
|
1.0
|
NA
|
A:CLA609
|
2.1
|
32.4
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
33.4
|
1.0
|
C4D
|
A:CLA609
|
2.9
|
26.6
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
27.7
|
1.0
|
C4A
|
A:CLA609
|
3.0
|
31.4
|
1.0
|
C1B
|
A:CLA609
|
3.0
|
31.1
|
1.0
|
C1C
|
A:CLA609
|
3.1
|
31.5
|
1.0
|
C4B
|
A:CLA609
|
3.1
|
28.3
|
1.0
|
C4C
|
A:CLA609
|
3.1
|
34.7
|
1.0
|
C1A
|
A:CLA609
|
3.1
|
30.6
|
1.0
|
C1D
|
A:CLA609
|
3.2
|
25.7
|
1.0
|
CD2
|
A:HIS118
|
3.4
|
30.2
|
1.0
|
CHB
|
A:CLA609
|
3.4
|
30.2
|
1.0
|
CHC
|
A:CLA609
|
3.4
|
35.1
|
1.0
|
CHA
|
A:CLA609
|
3.5
|
31.8
|
1.0
|
CHD
|
A:CLA609
|
3.5
|
28.0
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
27.3
|
1.0
|
CG1
|
I:VAL8
|
4.3
|
36.1
|
1.0
|
C3D
|
A:CLA609
|
4.3
|
29.7
|
1.0
|
C2B
|
A:CLA609
|
4.3
|
34.3
|
1.0
|
C2C
|
A:CLA609
|
4.3
|
34.8
|
1.0
|
C3B
|
A:CLA609
|
4.3
|
29.5
|
1.0
|
C3C
|
A:CLA609
|
4.4
|
33.0
|
1.0
|
C2D
|
A:CLA609
|
4.4
|
32.4
|
1.0
|
C3A
|
A:CLA609
|
4.4
|
31.6
|
1.0
|
CG
|
A:HIS118
|
4.4
|
34.2
|
1.0
|
C2A
|
A:CLA609
|
4.4
|
32.5
|
1.0
|
CG2
|
I:VAL12
|
4.4
|
33.8
|
1.0
|
CBD
|
A:CLA609
|
4.9
|
29.3
|
1.0
|
CBA
|
A:CLA609
|
4.9
|
39.5
|
1.0
|
|
Magnesium binding site 4 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 4 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg613
b:33.0
occ:1.00
|
MG
|
A:CLA613
|
0.0
|
33.0
|
1.0
|
ND
|
A:CLA613
|
2.0
|
36.6
|
1.0
|
NB
|
A:CLA613
|
2.0
|
32.0
|
1.0
|
NC
|
A:CLA613
|
2.1
|
34.6
|
1.0
|
NA
|
A:CLA613
|
2.1
|
32.4
|
1.0
|
O
|
A:HOH732
|
2.2
|
29.8
|
1.0
|
C4D
|
A:CLA613
|
2.9
|
29.9
|
1.0
|
C1B
|
A:CLA613
|
3.0
|
32.9
|
1.0
|
C4A
|
A:CLA613
|
3.0
|
32.1
|
1.0
|
C1C
|
A:CLA613
|
3.1
|
35.6
|
1.0
|
C4B
|
A:CLA613
|
3.1
|
33.2
|
1.0
|
C4C
|
A:CLA613
|
3.1
|
32.3
|
1.0
|
C1A
|
A:CLA613
|
3.1
|
34.6
|
1.0
|
C1D
|
A:CLA613
|
3.2
|
38.3
|
1.0
|
CHB
|
A:CLA613
|
3.4
|
28.2
|
1.0
|
CHC
|
A:CLA613
|
3.4
|
34.5
|
1.0
|
CHA
|
A:CLA613
|
3.5
|
29.5
|
1.0
|
CHD
|
A:CLA613
|
3.5
|
38.7
|
1.0
|
CBB
|
D:PHO401
|
4.0
|
35.9
|
1.0
|
C3D
|
A:CLA613
|
4.3
|
30.1
|
1.0
|
C2B
|
A:CLA613
|
4.3
|
29.7
|
1.0
|
C2C
|
A:CLA613
|
4.3
|
42.5
|
1.0
|
O
|
A:HOH767
|
4.3
|
31.9
|
1.0
|
C3B
|
A:CLA613
|
4.3
|
38.2
|
1.0
|
C3C
|
A:CLA613
|
4.3
|
39.3
|
1.0
|
C2D
|
A:CLA613
|
4.4
|
34.9
|
1.0
|
C3A
|
A:CLA613
|
4.4
|
30.7
|
1.0
|
C2A
|
A:CLA613
|
4.4
|
32.1
|
1.0
|
CBA
|
A:CLA613
|
4.6
|
32.4
|
1.0
|
CG2
|
A:THR179
|
4.7
|
33.4
|
1.0
|
CBD
|
A:CLA613
|
4.9
|
31.1
|
1.0
|
OG1
|
A:THR179
|
5.0
|
25.7
|
1.0
|
|
Magnesium binding site 5 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 5 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:41.7
occ:1.00
|
MG
|
B:CLA601
|
0.0
|
41.7
|
1.0
|
ND
|
B:CLA601
|
2.0
|
50.4
|
1.0
|
NB
|
B:CLA601
|
2.0
|
45.0
|
1.0
|
NC
|
B:CLA601
|
2.1
|
49.6
|
1.0
|
NA
|
B:CLA601
|
2.1
|
48.3
|
1.0
|
O
|
B:HOH733
|
2.1
|
41.8
|
1.0
|
C4D
|
B:CLA601
|
2.9
|
54.2
|
1.0
|
C1B
|
B:CLA601
|
3.0
|
40.7
|
1.0
|
C4A
|
B:CLA601
|
3.0
|
46.7
|
1.0
|
C1C
|
B:CLA601
|
3.1
|
43.8
|
1.0
|
C4B
|
B:CLA601
|
3.1
|
46.3
|
1.0
|
C4C
|
B:CLA601
|
3.1
|
46.1
|
1.0
|
C1A
|
B:CLA601
|
3.1
|
50.9
|
1.0
|
C1D
|
B:CLA601
|
3.2
|
53.5
|
1.0
|
CHB
|
B:CLA601
|
3.4
|
44.5
|
1.0
|
CHC
|
B:CLA601
|
3.4
|
43.2
|
1.0
|
CHA
|
B:CLA601
|
3.5
|
49.8
|
1.0
|
CHD
|
B:CLA601
|
3.5
|
49.5
|
1.0
|
C8
|
B:CLA601
|
3.9
|
64.4
|
1.0
|
C3D
|
B:CLA601
|
4.3
|
54.6
|
1.0
|
C2B
|
B:CLA601
|
4.3
|
40.4
|
1.0
|
C2C
|
B:CLA601
|
4.3
|
45.1
|
1.0
|
C3B
|
B:CLA601
|
4.3
|
39.5
|
1.0
|
C3C
|
B:CLA601
|
4.4
|
50.3
|
1.0
|
C2D
|
B:CLA601
|
4.4
|
57.0
|
1.0
|
C11
|
B:CLA601
|
4.4
|
70.1
|
1.0
|
O
|
B:TRP185
|
4.4
|
47.6
|
1.0
|
C3A
|
B:CLA601
|
4.4
|
53.2
|
1.0
|
C7
|
B:CLA601
|
4.4
|
60.3
|
1.0
|
C2A
|
B:CLA601
|
4.5
|
53.8
|
1.0
|
CBB
|
B:CLA602
|
4.7
|
42.0
|
1.0
|
CE2
|
B:PHE190
|
4.7
|
41.0
|
1.0
|
C9
|
B:CLA601
|
4.7
|
65.8
|
1.0
|
C10
|
B:CLA601
|
4.7
|
72.8
|
1.0
|
CBD
|
B:CLA601
|
4.9
|
60.0
|
1.0
|
|
Magnesium binding site 6 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 6 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:38.6
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
38.6
|
1.0
|
ND
|
B:CLA602
|
2.0
|
35.2
|
1.0
|
NB
|
B:CLA602
|
2.0
|
35.8
|
1.0
|
NC
|
B:CLA602
|
2.1
|
34.8
|
1.0
|
NA
|
B:CLA602
|
2.1
|
38.1
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
40.9
|
1.0
|
CE1
|
B:HIS201
|
2.8
|
41.6
|
1.0
|
C4D
|
B:CLA602
|
2.9
|
36.6
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
30.8
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
33.3
|
1.0
|
C1C
|
B:CLA602
|
3.1
|
37.8
|
1.0
|
C4B
|
B:CLA602
|
3.1
|
36.8
|
1.0
|
C4C
|
B:CLA602
|
3.1
|
34.7
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
37.6
|
1.0
|
C1D
|
B:CLA602
|
3.2
|
37.4
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
26.6
|
1.0
|
CG
|
B:HIS201
|
3.4
|
37.7
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
33.3
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
36.4
|
1.0
|
CHD
|
B:CLA602
|
3.5
|
39.5
|
1.0
|
CZ
|
H:PHE41
|
3.9
|
50.0
|
1.0
|
NE2
|
B:HIS201
|
4.0
|
38.6
|
1.0
|
CB
|
B:HIS201
|
4.0
|
34.2
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
33.4
|
1.0
|
C2B
|
B:CLA602
|
4.3
|
31.3
|
1.0
|
C2C
|
B:CLA602
|
4.3
|
34.1
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
35.5
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
32.8
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
26.6
|
1.0
|
C2D
|
B:CLA602
|
4.4
|
30.6
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
41.0
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
37.6
|
1.0
|
CE2
|
H:PHE41
|
4.6
|
49.8
|
1.0
|
CA
|
B:HIS201
|
4.6
|
34.7
|
1.0
|
CE1
|
B:PHE190
|
4.8
|
42.3
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
32.6
|
1.0
|
CE1
|
H:PHE41
|
5.0
|
53.0
|
1.0
|
|
Magnesium binding site 7 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 7 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:38.9
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
38.9
|
1.0
|
ND
|
B:CLA603
|
2.0
|
34.7
|
1.0
|
NB
|
B:CLA603
|
2.0
|
31.2
|
1.0
|
NC
|
B:CLA603
|
2.1
|
30.7
|
1.0
|
NA
|
B:CLA603
|
2.1
|
35.4
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
38.4
|
1.0
|
C4D
|
B:CLA603
|
2.9
|
34.1
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
32.9
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
37.4
|
1.0
|
C1C
|
B:CLA603
|
3.1
|
32.2
|
1.0
|
C4B
|
B:CLA603
|
3.1
|
29.1
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
28.8
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
35.9
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
33.7
|
1.0
|
C1D
|
B:CLA603
|
3.2
|
35.4
|
1.0
|
CD2
|
B:HIS202
|
3.2
|
36.2
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
31.5
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
30.6
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
33.0
|
1.0
|
CHD
|
B:CLA603
|
3.5
|
40.1
|
1.0
|
C6
|
B:CLA605
|
4.1
|
41.1
|
1.0
|
C9
|
B:CLA605
|
4.3
|
44.6
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
28.3
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
34.9
|
1.0
|
CG
|
B:HIS202
|
4.3
|
41.1
|
1.0
|
C2B
|
B:CLA603
|
4.3
|
34.7
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
31.0
|
1.0
|
C2C
|
B:CLA603
|
4.3
|
25.4
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
31.1
|
1.0
|
C2D
|
B:CLA603
|
4.4
|
39.3
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
36.4
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
36.0
|
1.0
|
C4
|
B:CLA605
|
4.8
|
42.3
|
1.0
|
CBA
|
B:CLA603
|
4.9
|
31.3
|
1.0
|
C7
|
B:CLA605
|
4.9
|
42.7
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
39.8
|
1.0
|
|
Magnesium binding site 8 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 8 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:32.9
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
32.9
|
1.0
|
ND
|
B:CLA604
|
2.0
|
28.4
|
1.0
|
NB
|
B:CLA604
|
2.0
|
29.2
|
1.0
|
NC
|
B:CLA604
|
2.1
|
31.0
|
1.0
|
NA
|
B:CLA604
|
2.1
|
27.7
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
33.1
|
1.0
|
C4D
|
B:CLA604
|
2.9
|
31.5
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
31.4
|
1.0
|
C4A
|
B:CLA604
|
3.1
|
33.7
|
1.0
|
C1C
|
B:CLA604
|
3.1
|
31.7
|
1.0
|
C4B
|
B:CLA604
|
3.1
|
32.1
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
29.9
|
1.0
|
CE1
|
B:HIS455
|
3.1
|
34.6
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
33.9
|
1.0
|
C1A
|
B:CLA604
|
3.2
|
31.8
|
1.0
|
CD2
|
B:HIS455
|
3.2
|
31.2
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
29.5
|
1.0
|
CHC
|
B:CLA604
|
3.5
|
35.3
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
33.6
|
1.0
|
CHD
|
B:CLA604
|
3.5
|
32.1
|
1.0
|
C14
|
B:CLA612
|
3.8
|
36.8
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
25.6
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
34.0
|
1.0
|
CG
|
B:HIS455
|
4.3
|
30.3
|
1.0
|
C2B
|
B:CLA604
|
4.3
|
28.6
|
1.0
|
C2C
|
B:CLA604
|
4.3
|
35.1
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
32.3
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
30.7
|
1.0
|
C2D
|
B:CLA604
|
4.4
|
33.9
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
31.5
|
1.0
|
C2A
|
B:CLA604
|
4.5
|
31.0
|
1.0
|
C15
|
B:CLA612
|
4.6
|
37.4
|
1.0
|
C13
|
B:CLA612
|
4.7
|
41.1
|
1.0
|
CBD
|
B:CLA604
|
5.0
|
31.8
|
1.0
|
|
Magnesium binding site 9 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 9 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:34.5
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
34.5
|
1.0
|
ND
|
B:CLA605
|
2.0
|
32.5
|
1.0
|
NB
|
B:CLA605
|
2.0
|
32.5
|
1.0
|
NC
|
B:CLA605
|
2.1
|
35.2
|
1.0
|
NA
|
B:CLA605
|
2.1
|
32.0
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
31.1
|
1.0
|
C4D
|
B:CLA605
|
2.9
|
27.2
|
1.0
|
C1B
|
B:CLA605
|
3.0
|
29.2
|
1.0
|
C4A
|
B:CLA605
|
3.0
|
31.1
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
38.2
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
33.8
|
1.0
|
C4B
|
B:CLA605
|
3.1
|
30.8
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
35.8
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
30.6
|
1.0
|
C1D
|
B:CLA605
|
3.2
|
26.6
|
1.0
|
CD2
|
B:HIS100
|
3.3
|
36.2
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
31.3
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
38.5
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
33.6
|
1.0
|
CHD
|
B:CLA605
|
3.5
|
33.5
|
1.0
|
ND1
|
B:HIS100
|
4.2
|
31.7
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
29.9
|
1.0
|
C2B
|
B:CLA605
|
4.3
|
34.7
|
1.0
|
C2C
|
B:CLA605
|
4.3
|
36.8
|
1.0
|
C3B
|
B:CLA605
|
4.3
|
32.5
|
1.0
|
C3C
|
B:CLA605
|
4.4
|
35.4
|
1.0
|
C2D
|
B:CLA605
|
4.4
|
30.3
|
1.0
|
CG
|
B:HIS100
|
4.4
|
33.3
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
26.1
|
1.0
|
C2A
|
B:CLA605
|
4.4
|
31.9
|
1.0
|
C2
|
B:CLA604
|
4.5
|
43.6
|
1.0
|
CBA
|
B:CLA605
|
4.9
|
29.7
|
1.0
|
CBD
|
B:CLA605
|
4.9
|
30.5
|
1.0
|
O1A
|
B:CLA604
|
5.0
|
33.9
|
1.0
|
O2A
|
B:CLA604
|
5.0
|
40.6
|
1.0
|
|
Magnesium binding site 10 out
of 70 in 5tis
Go back to
Magnesium Binding Sites List in 5tis
Magnesium binding site 10 out
of 70 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:36.6
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
36.6
|
1.0
|
ND
|
B:CLA606
|
2.0
|
34.7
|
1.0
|
NB
|
B:CLA606
|
2.1
|
35.4
|
1.0
|
NC
|
B:CLA606
|
2.1
|
36.6
|
1.0
|
NA
|
B:CLA606
|
2.1
|
31.6
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
39.6
|
1.0
|
CE1
|
B:HIS157
|
2.5
|
40.3
|
1.0
|
C4D
|
B:CLA606
|
2.9
|
36.4
|
1.0
|
C1B
|
B:CLA606
|
3.1
|
33.0
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
35.2
|
1.0
|
C1C
|
B:CLA606
|
3.1
|
33.0
|
1.0
|
C4B
|
B:CLA606
|
3.1
|
38.1
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
35.2
|
1.0
|
C1A
|
B:CLA606
|
3.2
|
36.3
|
1.0
|
C1D
|
B:CLA606
|
3.2
|
35.8
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
36.9
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
32.9
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
36.5
|
1.0
|
CG
|
B:HIS157
|
3.5
|
31.8
|
1.0
|
CHD
|
B:CLA606
|
3.5
|
33.7
|
1.0
|
C8
|
B:UNL622
|
3.6
|
41.9
|
1.0
|
NE2
|
B:HIS157
|
3.8
|
35.8
|
1.0
|
C9
|
B:UNL622
|
3.9
|
42.8
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
46.0
|
1.0
|
CB
|
B:HIS157
|
4.3
|
32.8
|
1.0
|
CD2
|
B:HIS157
|
4.3
|
31.4
|
1.0
|
C2C
|
B:CLA606
|
4.3
|
38.4
|
1.0
|
C2B
|
B:CLA606
|
4.3
|
35.6
|
1.0
|
C3C
|
B:CLA606
|
4.3
|
41.7
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
30.2
|
1.0
|
C2D
|
B:CLA606
|
4.4
|
38.1
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
34.4
|
1.0
|
C7
|
B:UNL622
|
4.4
|
55.0
|
1.0
|
C2A
|
B:CLA606
|
4.5
|
32.0
|
1.0
|
C6
|
B:UNL622
|
4.6
|
43.9
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
37.0
|
1.0
|
|
Reference:
I.D.Young,
M.Ibrahim,
R.Chatterjee,
S.Gul,
F.D.Fuller,
S.Koroidov,
A.S.Brewster,
R.Tran,
R.Alonso-Mori,
T.Kroll,
T.Michels-Clark,
H.Laksmono,
R.G.Sierra,
C.A.Stan,
R.Hussein,
M.Zhang,
L.Douthit,
M.Kubin,
C.De Lichtenberg,
L.Vo Pham,
H.Nilsson,
M.H.Cheah,
D.Shevela,
C.Saracini,
M.A.Bean,
I.Seuffert,
D.Sokaras,
T.C.Weng,
E.Pastor,
C.Weninger,
T.Fransson,
L.Lassalle,
P.Brauer,
P.Aller,
P.T.Docker,
B.Andi,
A.M.Orville,
J.M.Glownia,
S.Nelson,
M.Sikorski,
D.Zhu,
M.S.Hunter,
T.J.Lane,
A.Aquila,
J.E.Koglin,
J.Robinson,
M.Liang,
S.Boutet,
A.Y.Lyubimov,
M.Uervirojnangkoorn,
N.W.Moriarty,
D.Liebschner,
P.V.Afonine,
D.G.Waterman,
G.Evans,
P.Wernet,
H.Dobbek,
W.I.Weis,
A.T.Brunger,
P.H.Zwart,
P.D.Adams,
A.Zouni,
J.Messinger,
U.Bergmann,
N.K.Sauter,
J.Kern,
V.K.Yachandra,
J.Yano.
Structure of Photosystem II and Substrate Binding at Room Temperature. Nature V. 540 453 2016.
ISSN: ESSN 1476-4687
PubMed: 27871088
DOI: 10.1038/NATURE20161
Page generated: Mon Sep 30 04:52:01 2024
|