Magnesium in PDB 5kaf: Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution
Enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution
All present enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution:
1.10.3.9;
Protein crystallography data
The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf
was solved by
I.D.Young,
M.Ibrahim,
R.Chatterjee,
S.Gul,
S.Koroidov,
A.S.Brewster,
R.Tran,
R.Alonso-Mori,
F.Fuller,
T.Kroll,
T.Michels-Clark,
H.Laksmono,
R.G.Sierra,
C.A.Stan,
C.Saracini,
M.A.Bean,
I.Seuffert,
D.Sokaras,
T.-C.Weng,
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.Waterman,
G.Evans,
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)
|
43.12 /
3.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.731,
223.815,
330.818,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.4 /
30.3
|
Other elements in 5kaf:
The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 1 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg606
b:34.1
occ:1.00
|
MG
|
A:CLA606
|
0.0
|
34.1
|
1.0
|
ND
|
A:CLA606
|
2.0
|
33.8
|
1.0
|
NB
|
A:CLA606
|
2.0
|
41.3
|
1.0
|
NC
|
A:CLA606
|
2.1
|
38.9
|
1.0
|
NA
|
A:CLA606
|
2.1
|
31.7
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
33.5
|
1.0
|
CE1
|
A:HIS198
|
2.9
|
31.1
|
1.0
|
C4D
|
A:CLA606
|
2.9
|
30.8
|
1.0
|
C1B
|
A:CLA606
|
3.0
|
37.1
|
1.0
|
C4A
|
A:CLA606
|
3.0
|
30.5
|
1.0
|
C1C
|
A:CLA606
|
3.1
|
35.7
|
1.0
|
C4B
|
A:CLA606
|
3.1
|
42.4
|
1.0
|
C4C
|
A:CLA606
|
3.1
|
36.0
|
1.0
|
C1A
|
A:CLA606
|
3.1
|
33.4
|
1.0
|
C1D
|
A:CLA606
|
3.2
|
31.8
|
1.0
|
CD2
|
A:HIS198
|
3.4
|
39.1
|
1.0
|
CHB
|
A:CLA606
|
3.4
|
38.7
|
1.0
|
CHC
|
A:CLA606
|
3.4
|
36.3
|
1.0
|
CHA
|
A:CLA606
|
3.5
|
33.5
|
1.0
|
CHD
|
A:CLA606
|
3.5
|
31.9
|
1.0
|
CE
|
A:MET183
|
4.1
|
19.6
|
1.0
|
ND1
|
A:HIS198
|
4.1
|
34.7
|
1.0
|
C3D
|
A:CLA606
|
4.3
|
30.4
|
1.0
|
C2B
|
A:CLA606
|
4.3
|
33.4
|
1.0
|
C2C
|
A:CLA606
|
4.3
|
32.5
|
1.0
|
CAB
|
D:CLA402
|
4.3
|
41.3
|
1.0
|
C3B
|
A:CLA606
|
4.3
|
40.1
|
1.0
|
C3C
|
A:CLA606
|
4.4
|
35.9
|
1.0
|
C2D
|
A:CLA606
|
4.4
|
31.8
|
1.0
|
CG
|
A:HIS198
|
4.4
|
36.7
|
1.0
|
C3A
|
A:CLA606
|
4.4
|
32.2
|
1.0
|
C2A
|
A:CLA606
|
4.4
|
33.2
|
1.0
|
CBB
|
D:CLA402
|
4.9
|
41.8
|
1.0
|
CBD
|
A:CLA606
|
4.9
|
30.4
|
1.0
|
|
Magnesium binding site 2 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 2 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:37.5
occ:1.00
|
MG
|
A:CLA607
|
0.0
|
37.5
|
1.0
|
ND
|
A:CLA607
|
2.0
|
39.9
|
1.0
|
NB
|
A:CLA607
|
2.0
|
35.3
|
1.0
|
NC
|
A:CLA607
|
2.1
|
40.2
|
1.0
|
NA
|
A:CLA607
|
2.1
|
38.4
|
1.0
|
O
|
A:HOH710
|
2.1
|
40.2
|
1.0
|
C4D
|
A:CLA607
|
2.9
|
37.9
|
1.0
|
C1B
|
A:CLA607
|
3.0
|
38.7
|
1.0
|
C4A
|
A:CLA607
|
3.0
|
37.8
|
1.0
|
C1C
|
A:CLA607
|
3.1
|
34.5
|
1.0
|
C4B
|
A:CLA607
|
3.1
|
34.0
|
1.0
|
C4C
|
A:CLA607
|
3.1
|
37.7
|
1.0
|
C1A
|
A:CLA607
|
3.1
|
34.2
|
1.0
|
C1D
|
A:CLA607
|
3.2
|
37.3
|
1.0
|
CHB
|
A:CLA607
|
3.4
|
36.0
|
1.0
|
CHC
|
A:CLA607
|
3.4
|
30.5
|
1.0
|
CHA
|
A:CLA607
|
3.5
|
31.1
|
1.0
|
CHD
|
A:CLA607
|
3.5
|
39.8
|
1.0
|
CBB
|
D:PHO401
|
3.7
|
35.9
|
1.0
|
O
|
D:HOH509
|
4.0
|
33.8
|
1.0
|
C3D
|
A:CLA607
|
4.3
|
33.2
|
1.0
|
C2B
|
A:CLA607
|
4.3
|
41.8
|
1.0
|
C2C
|
A:CLA607
|
4.3
|
37.0
|
1.0
|
C3B
|
A:CLA607
|
4.3
|
43.7
|
1.0
|
C3C
|
A:CLA607
|
4.4
|
38.0
|
1.0
|
C2D
|
A:CLA607
|
4.4
|
35.3
|
1.0
|
C3A
|
A:CLA607
|
4.4
|
36.6
|
1.0
|
C2A
|
A:CLA607
|
4.4
|
35.6
|
1.0
|
CBA
|
A:CLA607
|
4.7
|
29.1
|
1.0
|
CBD
|
A:CLA607
|
4.9
|
31.2
|
1.0
|
CG2
|
D:ILE178
|
4.9
|
39.4
|
1.0
|
CAB
|
D:PHO401
|
5.0
|
33.1
|
1.0
|
CE2
|
A:PHE206
|
5.0
|
37.5
|
1.0
|
|
Magnesium binding site 3 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 3 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg609
b:30.0
occ:1.00
|
MG
|
A:CLA609
|
0.0
|
30.0
|
1.0
|
ND
|
A:CLA609
|
2.0
|
25.5
|
1.0
|
NB
|
A:CLA609
|
2.0
|
27.5
|
1.0
|
NC
|
A:CLA609
|
2.1
|
26.7
|
1.0
|
NA
|
A:CLA609
|
2.1
|
33.4
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
28.6
|
1.0
|
C4D
|
A:CLA609
|
2.9
|
23.9
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
27.4
|
1.0
|
C1B
|
A:CLA609
|
3.0
|
27.4
|
1.0
|
C4A
|
A:CLA609
|
3.0
|
29.4
|
1.0
|
C1C
|
A:CLA609
|
3.1
|
26.6
|
1.0
|
C4B
|
A:CLA609
|
3.1
|
32.8
|
1.0
|
C4C
|
A:CLA609
|
3.1
|
21.8
|
1.0
|
C1A
|
A:CLA609
|
3.1
|
28.0
|
1.0
|
C1D
|
A:CLA609
|
3.2
|
20.8
|
1.0
|
CD2
|
A:HIS118
|
3.4
|
31.6
|
1.0
|
CHB
|
A:CLA609
|
3.4
|
27.0
|
1.0
|
CHC
|
A:CLA609
|
3.4
|
33.5
|
1.0
|
CHA
|
A:CLA609
|
3.5
|
23.2
|
1.0
|
CHD
|
A:CLA609
|
3.5
|
17.5
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
29.3
|
1.0
|
C3D
|
A:CLA609
|
4.3
|
25.4
|
1.0
|
C2B
|
A:CLA609
|
4.3
|
25.5
|
1.0
|
C2C
|
A:CLA609
|
4.3
|
28.1
|
1.0
|
C3B
|
A:CLA609
|
4.3
|
25.1
|
1.0
|
C3C
|
A:CLA609
|
4.3
|
25.8
|
1.0
|
C2D
|
A:CLA609
|
4.4
|
26.5
|
1.0
|
C3A
|
A:CLA609
|
4.4
|
26.4
|
1.0
|
CG2
|
I:VAL12
|
4.4
|
41.7
|
1.0
|
CG
|
A:HIS118
|
4.4
|
34.3
|
1.0
|
C2A
|
A:CLA609
|
4.4
|
26.0
|
1.0
|
CG1
|
I:VAL8
|
4.5
|
24.8
|
1.0
|
CBA
|
A:CLA609
|
4.9
|
31.3
|
1.0
|
CBD
|
A:CLA609
|
4.9
|
25.1
|
1.0
|
|
Magnesium binding site 4 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 4 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg615
b:30.2
occ:1.00
|
MG
|
A:CLA615
|
0.0
|
30.2
|
1.0
|
ND
|
A:CLA615
|
2.0
|
32.8
|
1.0
|
NB
|
A:CLA615
|
2.0
|
33.0
|
1.0
|
NC
|
A:CLA615
|
2.1
|
40.3
|
1.0
|
NA
|
A:CLA615
|
2.1
|
33.3
|
1.0
|
O
|
A:HOH705
|
2.2
|
33.3
|
1.0
|
C4D
|
A:CLA615
|
2.9
|
39.1
|
1.0
|
C1B
|
A:CLA615
|
3.0
|
34.0
|
1.0
|
C4A
|
A:CLA615
|
3.0
|
37.0
|
1.0
|
C1C
|
A:CLA615
|
3.1
|
38.4
|
1.0
|
C4B
|
A:CLA615
|
3.1
|
31.6
|
1.0
|
C4C
|
A:CLA615
|
3.1
|
38.8
|
1.0
|
C1A
|
A:CLA615
|
3.1
|
34.8
|
1.0
|
C1D
|
A:CLA615
|
3.2
|
31.1
|
1.0
|
CHB
|
A:CLA615
|
3.4
|
31.9
|
1.0
|
CHC
|
A:CLA615
|
3.4
|
33.5
|
1.0
|
CHA
|
A:CLA615
|
3.5
|
36.6
|
1.0
|
CHD
|
A:CLA615
|
3.5
|
29.0
|
1.0
|
CBB
|
A:PHO608
|
4.1
|
37.7
|
1.0
|
C3D
|
A:CLA615
|
4.3
|
40.3
|
1.0
|
C2C
|
A:CLA615
|
4.3
|
34.0
|
1.0
|
C2B
|
A:CLA615
|
4.3
|
34.9
|
1.0
|
C3B
|
A:CLA615
|
4.3
|
34.7
|
1.0
|
C3C
|
A:CLA615
|
4.3
|
32.0
|
1.0
|
C2D
|
A:CLA615
|
4.4
|
38.6
|
1.0
|
C3A
|
A:CLA615
|
4.4
|
36.7
|
1.0
|
C2A
|
A:CLA615
|
4.4
|
32.4
|
1.0
|
CBA
|
A:CLA615
|
4.6
|
26.1
|
1.0
|
CG2
|
A:THR179
|
4.7
|
27.5
|
1.0
|
CBD
|
A:CLA615
|
4.9
|
29.7
|
1.0
|
|
Magnesium binding site 5 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 5 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:60.2
occ:1.00
|
MG
|
B:CLA601
|
0.0
|
60.2
|
1.0
|
ND
|
B:CLA601
|
2.0
|
60.6
|
1.0
|
NB
|
B:CLA601
|
2.0
|
50.3
|
1.0
|
NC
|
B:CLA601
|
2.1
|
50.1
|
1.0
|
NA
|
B:CLA601
|
2.1
|
56.9
|
1.0
|
O
|
B:HOH710
|
2.2
|
56.0
|
1.0
|
C4D
|
B:CLA601
|
2.9
|
67.0
|
1.0
|
C1B
|
B:CLA601
|
3.0
|
56.6
|
1.0
|
C4A
|
B:CLA601
|
3.0
|
62.0
|
1.0
|
C1C
|
B:CLA601
|
3.1
|
51.1
|
1.0
|
C4B
|
B:CLA601
|
3.1
|
53.8
|
1.0
|
C4C
|
B:CLA601
|
3.1
|
44.8
|
1.0
|
C1A
|
B:CLA601
|
3.1
|
60.0
|
1.0
|
C1D
|
B:CLA601
|
3.2
|
57.6
|
1.0
|
CHB
|
B:CLA601
|
3.4
|
57.9
|
1.0
|
CHC
|
B:CLA601
|
3.4
|
59.1
|
1.0
|
CHA
|
B:CLA601
|
3.5
|
66.5
|
1.0
|
C10
|
B:CLA601
|
3.5
|
49.8
|
1.0
|
CHD
|
B:CLA601
|
3.5
|
55.0
|
1.0
|
C8
|
B:CLA601
|
4.2
|
53.4
|
1.0
|
O
|
B:TRP185
|
4.2
|
61.9
|
1.0
|
C3D
|
B:CLA601
|
4.3
|
64.4
|
1.0
|
C2B
|
B:CLA601
|
4.3
|
61.4
|
1.0
|
C2C
|
B:CLA601
|
4.3
|
44.8
|
1.0
|
C3B
|
B:CLA601
|
4.3
|
57.3
|
1.0
|
C3C
|
B:CLA601
|
4.4
|
46.4
|
1.0
|
C2D
|
B:CLA601
|
4.4
|
59.5
|
1.0
|
C3A
|
B:CLA601
|
4.4
|
58.4
|
1.0
|
C2A
|
B:CLA601
|
4.5
|
65.1
|
1.0
|
C14
|
B:CLA601
|
4.6
|
56.4
|
1.0
|
C12
|
B:CLA601
|
4.7
|
53.3
|
1.0
|
C11
|
B:CLA601
|
4.7
|
56.0
|
1.0
|
CE2
|
B:PHE190
|
4.7
|
39.5
|
1.0
|
CBB
|
B:CLA602
|
4.8
|
43.9
|
1.0
|
CBD
|
B:CLA601
|
4.9
|
67.5
|
1.0
|
CBA
|
B:CLA601
|
5.0
|
77.5
|
1.0
|
|
Magnesium binding site 6 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 6 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:45.5
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
45.5
|
1.0
|
ND
|
B:CLA602
|
2.0
|
45.4
|
1.0
|
NB
|
B:CLA602
|
2.0
|
42.2
|
1.0
|
NC
|
B:CLA602
|
2.1
|
44.2
|
1.0
|
NA
|
B:CLA602
|
2.1
|
41.0
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
40.9
|
1.0
|
CE1
|
B:HIS201
|
2.7
|
38.0
|
1.0
|
C4D
|
B:CLA602
|
2.9
|
39.9
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
38.4
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
39.5
|
1.0
|
C1C
|
B:CLA602
|
3.1
|
41.9
|
1.0
|
C4B
|
B:CLA602
|
3.1
|
40.5
|
1.0
|
C4C
|
B:CLA602
|
3.1
|
38.6
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
40.1
|
1.0
|
C1D
|
B:CLA602
|
3.2
|
46.4
|
1.0
|
CG
|
B:HIS201
|
3.4
|
36.9
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
37.6
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
44.0
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
38.1
|
1.0
|
CHD
|
B:CLA602
|
3.5
|
35.0
|
1.0
|
NE2
|
B:HIS201
|
3.9
|
37.6
|
1.0
|
CZ
|
H:PHE41
|
4.0
|
51.1
|
1.0
|
CB
|
B:HIS201
|
4.1
|
35.8
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
37.9
|
1.0
|
CD2
|
B:HIS201
|
4.3
|
31.9
|
1.0
|
C2B
|
B:CLA602
|
4.3
|
36.5
|
1.0
|
C2C
|
B:CLA602
|
4.3
|
39.6
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
38.8
|
1.0
|
C3C
|
B:CLA602
|
4.3
|
39.7
|
1.0
|
C2D
|
B:CLA602
|
4.4
|
43.1
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
36.6
|
1.0
|
CE2
|
H:PHE41
|
4.4
|
54.5
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
37.5
|
1.0
|
CA
|
B:HIS201
|
4.8
|
38.1
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
36.5
|
1.0
|
|
Magnesium binding site 7 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 7 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:42.5
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
42.5
|
1.0
|
ND
|
B:CLA603
|
2.0
|
36.4
|
1.0
|
NB
|
B:CLA603
|
2.0
|
36.2
|
1.0
|
NC
|
B:CLA603
|
2.1
|
35.5
|
1.0
|
NA
|
B:CLA603
|
2.1
|
37.5
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
43.6
|
1.0
|
C4D
|
B:CLA603
|
2.9
|
32.1
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
39.4
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
36.0
|
1.0
|
C1C
|
B:CLA603
|
3.1
|
38.9
|
1.0
|
C4B
|
B:CLA603
|
3.1
|
34.7
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
35.7
|
1.0
|
CD2
|
B:HIS202
|
3.1
|
46.2
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
38.4
|
1.0
|
C1D
|
B:CLA603
|
3.2
|
39.2
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
37.7
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
38.2
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
39.8
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
36.1
|
1.0
|
CHD
|
B:CLA603
|
3.5
|
34.3
|
1.0
|
C9
|
B:CLA605
|
4.2
|
41.5
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
39.5
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
36.3
|
1.0
|
CG
|
B:HIS202
|
4.3
|
39.2
|
1.0
|
C2B
|
B:CLA603
|
4.3
|
36.1
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
38.6
|
1.0
|
C2C
|
B:CLA603
|
4.3
|
36.6
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
39.8
|
1.0
|
C2D
|
B:CLA603
|
4.4
|
41.4
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
34.4
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
35.8
|
1.0
|
C6
|
B:CLA605
|
4.5
|
39.0
|
1.0
|
C7
|
B:CLA605
|
4.6
|
31.3
|
1.0
|
CBA
|
B:CLA603
|
4.7
|
37.1
|
1.0
|
C5
|
B:CLA605
|
4.8
|
37.2
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
33.8
|
1.0
|
|
Magnesium binding site 8 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 8 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:46.3
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
46.3
|
1.0
|
ND
|
B:CLA604
|
2.0
|
41.5
|
1.0
|
NB
|
B:CLA604
|
2.0
|
37.3
|
1.0
|
NC
|
B:CLA604
|
2.1
|
28.4
|
1.0
|
NA
|
B:CLA604
|
2.1
|
35.2
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
40.6
|
1.0
|
C4D
|
B:CLA604
|
2.9
|
37.8
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
37.3
|
1.0
|
C4A
|
B:CLA604
|
3.0
|
37.1
|
1.0
|
C1C
|
B:CLA604
|
3.1
|
31.5
|
1.0
|
C4B
|
B:CLA604
|
3.1
|
37.9
|
1.0
|
CD2
|
B:HIS455
|
3.1
|
38.8
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
29.7
|
1.0
|
C1A
|
B:CLA604
|
3.2
|
34.4
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
38.6
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
33.1
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
41.2
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
36.3
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
35.2
|
1.0
|
CHD
|
B:CLA604
|
3.5
|
32.8
|
1.0
|
C14
|
B:CLA612
|
4.2
|
31.9
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
34.9
|
1.0
|
CG
|
B:HIS455
|
4.3
|
35.7
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
28.2
|
1.0
|
C2B
|
B:CLA604
|
4.3
|
33.5
|
1.0
|
C2C
|
B:CLA604
|
4.3
|
36.0
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
34.8
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
36.4
|
1.0
|
C2D
|
B:CLA604
|
4.4
|
34.6
|
1.0
|
C15
|
B:CLA612
|
4.4
|
38.6
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
33.0
|
1.0
|
C2A
|
B:CLA604
|
4.5
|
33.7
|
1.0
|
C13
|
B:CLA612
|
4.6
|
42.6
|
1.0
|
CBD
|
B:CLA604
|
4.9
|
36.9
|
1.0
|
|
Magnesium binding site 9 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 9 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:35.1
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
35.1
|
1.0
|
ND
|
B:CLA605
|
2.0
|
34.2
|
1.0
|
NB
|
B:CLA605
|
2.0
|
34.5
|
1.0
|
NC
|
B:CLA605
|
2.1
|
33.8
|
1.0
|
NA
|
B:CLA605
|
2.1
|
31.2
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
31.6
|
1.0
|
C4D
|
B:CLA605
|
2.9
|
29.3
|
1.0
|
C1B
|
B:CLA605
|
3.0
|
39.3
|
1.0
|
C4A
|
B:CLA605
|
3.1
|
35.2
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
33.6
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
24.9
|
1.0
|
C4B
|
B:CLA605
|
3.1
|
37.1
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
35.4
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
38.4
|
1.0
|
C1D
|
B:CLA605
|
3.2
|
36.9
|
1.0
|
CD2
|
B:HIS100
|
3.3
|
31.7
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
39.8
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
32.2
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
32.3
|
1.0
|
CHD
|
B:CLA605
|
3.5
|
32.8
|
1.0
|
C2
|
B:CLA604
|
4.0
|
39.1
|
1.0
|
C1
|
B:CLA604
|
4.1
|
36.1
|
1.0
|
ND1
|
B:HIS100
|
4.2
|
26.0
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
35.5
|
1.0
|
C2B
|
B:CLA605
|
4.3
|
30.7
|
1.0
|
C3B
|
B:CLA605
|
4.3
|
32.0
|
1.0
|
C2C
|
B:CLA605
|
4.3
|
35.0
|
1.0
|
C3C
|
B:CLA605
|
4.4
|
43.0
|
1.0
|
C2D
|
B:CLA605
|
4.4
|
41.3
|
1.0
|
CG
|
B:HIS100
|
4.4
|
26.9
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
39.0
|
1.0
|
C2A
|
B:CLA605
|
4.5
|
40.8
|
1.0
|
O1A
|
B:CLA604
|
4.9
|
41.2
|
1.0
|
CBA
|
B:CLA605
|
4.9
|
34.5
|
1.0
|
CBD
|
B:CLA605
|
4.9
|
25.3
|
1.0
|
|
Magnesium binding site 10 out
of 70 in 5kaf
Go back to
Magnesium Binding Sites List in 5kaf
Magnesium binding site 10 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:51.6
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
51.6
|
1.0
|
ND
|
B:CLA606
|
2.0
|
50.1
|
1.0
|
NB
|
B:CLA606
|
2.0
|
43.7
|
1.0
|
NC
|
B:CLA606
|
2.1
|
49.4
|
1.0
|
NA
|
B:CLA606
|
2.1
|
44.2
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
46.4
|
1.0
|
CE1
|
B:HIS157
|
2.5
|
49.2
|
1.0
|
C4D
|
B:CLA606
|
2.9
|
48.4
|
1.0
|
C1B
|
B:CLA606
|
3.0
|
34.7
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
40.4
|
1.0
|
C1C
|
B:CLA606
|
3.1
|
41.3
|
1.0
|
C4B
|
B:CLA606
|
3.1
|
43.6
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
50.5
|
1.0
|
C1A
|
B:CLA606
|
3.2
|
42.7
|
1.0
|
C1D
|
B:CLA606
|
3.2
|
52.4
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
41.7
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
39.6
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
45.6
|
1.0
|
CHD
|
B:CLA606
|
3.5
|
45.7
|
1.0
|
CG
|
B:HIS157
|
3.5
|
44.1
|
1.0
|
C33
|
B:UNL623
|
3.7
|
47.2
|
1.0
|
NE2
|
B:HIS157
|
3.8
|
38.8
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
52.9
|
1.0
|
C34
|
B:UNL623
|
4.3
|
40.0
|
1.0
|
CD2
|
B:HIS157
|
4.3
|
43.2
|
1.0
|
C2B
|
B:CLA606
|
4.3
|
34.0
|
1.0
|
C2C
|
B:CLA606
|
4.3
|
45.9
|
1.0
|
CB
|
B:HIS157
|
4.3
|
40.1
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
32.9
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
44.4
|
1.0
|
C2D
|
B:CLA606
|
4.4
|
52.7
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
45.8
|
1.0
|
C2A
|
B:CLA606
|
4.5
|
40.6
|
1.0
|
C35
|
B:UNL623
|
4.5
|
44.4
|
1.0
|
C32
|
B:UNL623
|
4.8
|
46.4
|
1.0
|
CBA
|
B:CLA606
|
4.9
|
41.0
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
42.4
|
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: Sun Sep 29 18:54:40 2024
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