Magnesium in PDB 5kai: NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Enzymatic activity of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
All present enzymatic activity of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution:
1.10.3.9;
Protein crystallography data
The structure of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution, PDB code: 5kai
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)
|
43.57 /
2.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.911,
224.268,
330.996,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25 /
30
|
Other elements in 5kai:
The structure of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 1 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg606
b:44.4
occ:1.00
|
MG
|
A:CLA606
|
0.0
|
44.4
|
1.0
|
ND
|
A:CLA606
|
2.0
|
43.5
|
1.0
|
NB
|
A:CLA606
|
2.1
|
47.4
|
1.0
|
NC
|
A:CLA606
|
2.1
|
43.7
|
1.0
|
NA
|
A:CLA606
|
2.1
|
41.4
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
42.4
|
1.0
|
C4D
|
A:CLA606
|
2.9
|
45.0
|
1.0
|
CE1
|
A:HIS198
|
2.9
|
46.3
|
1.0
|
C4A
|
A:CLA606
|
3.0
|
46.6
|
1.0
|
C1B
|
A:CLA606
|
3.0
|
45.3
|
1.0
|
C1C
|
A:CLA606
|
3.1
|
37.4
|
1.0
|
C4B
|
A:CLA606
|
3.1
|
35.6
|
1.0
|
C4C
|
A:CLA606
|
3.1
|
45.9
|
1.0
|
C1A
|
A:CLA606
|
3.1
|
45.0
|
1.0
|
C1D
|
A:CLA606
|
3.2
|
43.6
|
1.0
|
CD2
|
A:HIS198
|
3.4
|
44.8
|
1.0
|
CHB
|
A:CLA606
|
3.4
|
46.9
|
1.0
|
CHC
|
A:CLA606
|
3.5
|
36.7
|
1.0
|
CHA
|
A:CLA606
|
3.5
|
47.5
|
1.0
|
CHD
|
A:CLA606
|
3.5
|
43.6
|
1.0
|
CE
|
A:MET183
|
3.9
|
37.3
|
1.0
|
ND1
|
A:HIS198
|
4.2
|
44.4
|
1.0
|
C3D
|
A:CLA606
|
4.3
|
47.5
|
1.0
|
C2B
|
A:CLA606
|
4.3
|
42.6
|
1.0
|
C2C
|
A:CLA606
|
4.3
|
40.2
|
1.0
|
C3B
|
A:CLA606
|
4.3
|
38.5
|
1.0
|
C2D
|
A:CLA606
|
4.4
|
48.4
|
1.0
|
C3C
|
A:CLA606
|
4.4
|
42.7
|
1.0
|
CG
|
A:HIS198
|
4.4
|
44.1
|
1.0
|
C3A
|
A:CLA606
|
4.4
|
38.3
|
1.0
|
C2A
|
A:CLA606
|
4.4
|
45.2
|
1.0
|
CAB
|
D:CLA403
|
4.5
|
44.3
|
1.0
|
CBD
|
A:CLA606
|
4.9
|
47.0
|
1.0
|
|
Magnesium binding site 2 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 2 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:31.6
occ:1.00
|
MG
|
A:CLA607
|
0.0
|
31.6
|
1.0
|
ND
|
A:CLA607
|
2.0
|
46.7
|
1.0
|
NB
|
A:CLA607
|
2.0
|
42.9
|
1.0
|
NC
|
A:CLA607
|
2.1
|
43.9
|
1.0
|
NA
|
A:CLA607
|
2.1
|
43.0
|
1.0
|
O
|
A:HOH712
|
2.1
|
38.2
|
1.0
|
C4D
|
A:CLA607
|
2.9
|
45.8
|
1.0
|
C1B
|
A:CLA607
|
3.0
|
47.0
|
1.0
|
C4A
|
A:CLA607
|
3.0
|
43.6
|
1.0
|
C1C
|
A:CLA607
|
3.1
|
49.0
|
1.0
|
C4B
|
A:CLA607
|
3.1
|
42.3
|
1.0
|
C4C
|
A:CLA607
|
3.1
|
44.9
|
1.0
|
C1A
|
A:CLA607
|
3.1
|
44.9
|
1.0
|
C1D
|
A:CLA607
|
3.2
|
43.9
|
1.0
|
CHB
|
A:CLA607
|
3.4
|
46.2
|
1.0
|
CHC
|
A:CLA607
|
3.4
|
44.2
|
1.0
|
CHA
|
A:CLA607
|
3.5
|
46.9
|
1.0
|
CHD
|
A:CLA607
|
3.5
|
39.0
|
1.0
|
CBB
|
D:PHO401
|
3.9
|
42.2
|
1.0
|
C3D
|
A:CLA607
|
4.3
|
39.2
|
1.0
|
C2C
|
A:CLA607
|
4.3
|
44.8
|
1.0
|
C2B
|
A:CLA607
|
4.3
|
47.6
|
1.0
|
C3B
|
A:CLA607
|
4.3
|
44.5
|
1.0
|
C3C
|
A:CLA607
|
4.4
|
41.8
|
1.0
|
C2D
|
A:CLA607
|
4.4
|
44.0
|
1.0
|
C3A
|
A:CLA607
|
4.4
|
37.4
|
1.0
|
C2A
|
A:CLA607
|
4.4
|
42.2
|
1.0
|
CBA
|
A:CLA607
|
4.7
|
43.3
|
1.0
|
CG2
|
D:ILE178
|
4.9
|
38.0
|
1.0
|
CE2
|
A:PHE206
|
4.9
|
38.4
|
1.0
|
CBD
|
A:CLA607
|
4.9
|
45.6
|
1.0
|
|
Magnesium binding site 3 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 3 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg609
b:39.8
occ:1.00
|
MG
|
A:CLA609
|
0.0
|
39.8
|
1.0
|
ND
|
A:CLA609
|
2.0
|
47.4
|
1.0
|
NB
|
A:CLA609
|
2.0
|
40.0
|
1.0
|
NC
|
A:CLA609
|
2.1
|
40.5
|
1.0
|
NA
|
A:CLA609
|
2.1
|
42.3
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
44.3
|
1.0
|
C4D
|
A:CLA609
|
2.9
|
43.6
|
1.0
|
C1B
|
A:CLA609
|
3.0
|
40.5
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
41.4
|
1.0
|
C4A
|
A:CLA609
|
3.0
|
42.3
|
1.0
|
C1C
|
A:CLA609
|
3.1
|
42.0
|
1.0
|
C4B
|
A:CLA609
|
3.1
|
34.6
|
1.0
|
C4C
|
A:CLA609
|
3.1
|
45.0
|
1.0
|
C1A
|
A:CLA609
|
3.1
|
39.0
|
1.0
|
C1D
|
A:CLA609
|
3.2
|
41.3
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
42.9
|
1.0
|
CHB
|
A:CLA609
|
3.4
|
37.4
|
1.0
|
CHC
|
A:CLA609
|
3.4
|
36.3
|
1.0
|
CHA
|
A:CLA609
|
3.5
|
38.1
|
1.0
|
CHD
|
A:CLA609
|
3.5
|
39.2
|
1.0
|
CG1
|
I:VAL8
|
4.1
|
43.2
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
35.1
|
1.0
|
C3D
|
A:CLA609
|
4.3
|
43.5
|
1.0
|
C2B
|
A:CLA609
|
4.3
|
43.0
|
1.0
|
C3B
|
A:CLA609
|
4.3
|
40.3
|
1.0
|
C2C
|
A:CLA609
|
4.3
|
41.4
|
1.0
|
C3C
|
A:CLA609
|
4.4
|
44.3
|
1.0
|
C2D
|
A:CLA609
|
4.4
|
42.4
|
1.0
|
CG
|
A:HIS118
|
4.4
|
40.8
|
1.0
|
C3A
|
A:CLA609
|
4.4
|
45.6
|
1.0
|
C2A
|
A:CLA609
|
4.4
|
45.3
|
1.0
|
CG2
|
I:VAL12
|
4.5
|
46.4
|
1.0
|
CBA
|
A:CLA609
|
4.8
|
40.6
|
1.0
|
CBD
|
A:CLA609
|
4.9
|
39.0
|
1.0
|
|
Magnesium binding site 4 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 4 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:61.5
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
61.5
|
1.0
|
ND
|
B:CLA602
|
2.0
|
66.2
|
1.0
|
NB
|
B:CLA602
|
2.0
|
62.2
|
1.0
|
NC
|
B:CLA602
|
2.1
|
57.7
|
1.0
|
NA
|
B:CLA602
|
2.1
|
60.1
|
1.0
|
O
|
B:HOH705
|
2.2
|
57.2
|
1.0
|
C4D
|
B:CLA602
|
2.9
|
68.8
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
60.3
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
64.1
|
1.0
|
C1C
|
B:CLA602
|
3.1
|
58.0
|
1.0
|
C4B
|
B:CLA602
|
3.1
|
65.7
|
1.0
|
C4C
|
B:CLA602
|
3.1
|
59.1
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
65.2
|
1.0
|
C1D
|
B:CLA602
|
3.2
|
66.8
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
61.0
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
56.5
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
67.3
|
1.0
|
CHD
|
B:CLA602
|
3.5
|
62.5
|
1.0
|
C12
|
B:CLA602
|
3.9
|
52.5
|
1.0
|
C10
|
B:CLA602
|
4.0
|
58.5
|
1.0
|
C11
|
B:CLA602
|
4.0
|
57.8
|
1.0
|
C8
|
B:CLA602
|
4.0
|
62.4
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
71.1
|
1.0
|
C2B
|
B:CLA602
|
4.3
|
57.5
|
1.0
|
C2C
|
B:CLA602
|
4.3
|
61.7
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
64.9
|
1.0
|
C3C
|
B:CLA602
|
4.3
|
63.8
|
1.0
|
O
|
B:TRP185
|
4.4
|
55.5
|
1.0
|
C2D
|
B:CLA602
|
4.4
|
65.4
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
60.7
|
1.0
|
C2A
|
B:CLA602
|
4.5
|
62.9
|
1.0
|
C9
|
B:CLA602
|
4.6
|
62.5
|
1.0
|
CE2
|
B:PHE190
|
4.8
|
50.5
|
1.0
|
CBB
|
B:CLA603
|
4.8
|
56.8
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
68.7
|
1.0
|
CBA
|
B:CLA602
|
5.0
|
72.3
|
1.0
|
|
Magnesium binding site 5 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 5 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:55.9
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
55.9
|
1.0
|
ND
|
B:CLA603
|
2.0
|
52.0
|
1.0
|
NB
|
B:CLA603
|
2.0
|
51.2
|
1.0
|
NC
|
B:CLA603
|
2.1
|
53.9
|
1.0
|
NA
|
B:CLA603
|
2.1
|
53.4
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
49.5
|
1.0
|
CE1
|
B:HIS201
|
2.7
|
50.4
|
1.0
|
C4D
|
B:CLA603
|
2.9
|
48.8
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
52.7
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
54.5
|
1.0
|
C1C
|
B:CLA603
|
3.1
|
54.6
|
1.0
|
C4B
|
B:CLA603
|
3.1
|
52.6
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
52.2
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
52.0
|
1.0
|
C1D
|
B:CLA603
|
3.2
|
54.3
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
51.4
|
1.0
|
CG
|
B:HIS201
|
3.4
|
46.7
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
55.0
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
48.2
|
1.0
|
CHD
|
B:CLA603
|
3.5
|
55.0
|
1.0
|
CZ
|
H:PHE41
|
3.9
|
59.3
|
1.0
|
NE2
|
B:HIS201
|
3.9
|
46.3
|
1.0
|
CB
|
B:HIS201
|
4.1
|
43.4
|
1.0
|
CE2
|
H:PHE41
|
4.3
|
61.9
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
47.7
|
1.0
|
C2B
|
B:CLA603
|
4.3
|
51.8
|
1.0
|
CD2
|
B:HIS201
|
4.3
|
39.6
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
49.5
|
1.0
|
C2C
|
B:CLA603
|
4.3
|
52.9
|
1.0
|
C3C
|
B:CLA603
|
4.3
|
49.1
|
1.0
|
C2D
|
B:CLA603
|
4.4
|
49.4
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
51.4
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
43.2
|
1.0
|
CA
|
B:HIS201
|
4.8
|
50.4
|
1.0
|
CE1
|
B:PHE190
|
4.8
|
57.0
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
49.2
|
1.0
|
|
Magnesium binding site 6 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 6 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:49.3
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
49.3
|
1.0
|
ND
|
B:CLA604
|
2.0
|
48.7
|
1.0
|
NB
|
B:CLA604
|
2.0
|
42.1
|
1.0
|
NC
|
B:CLA604
|
2.1
|
35.8
|
1.0
|
NA
|
B:CLA604
|
2.1
|
41.5
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
40.4
|
1.0
|
C4D
|
B:CLA604
|
2.9
|
44.1
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
41.4
|
1.0
|
C4A
|
B:CLA604
|
3.0
|
40.9
|
1.0
|
C1C
|
B:CLA604
|
3.1
|
39.8
|
1.0
|
C4B
|
B:CLA604
|
3.1
|
40.9
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
36.0
|
1.0
|
C1A
|
B:CLA604
|
3.1
|
45.1
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
39.3
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
42.5
|
1.0
|
CD2
|
B:HIS202
|
3.2
|
46.2
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
41.9
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
38.5
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
44.1
|
1.0
|
CHD
|
B:CLA604
|
3.5
|
40.7
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
43.9
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
37.1
|
1.0
|
C9
|
B:CLA606
|
4.3
|
46.4
|
1.0
|
C2B
|
B:CLA604
|
4.3
|
39.2
|
1.0
|
C2C
|
B:CLA604
|
4.3
|
41.7
|
1.0
|
CG
|
B:HIS202
|
4.3
|
46.6
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
46.7
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
37.4
|
1.0
|
C2D
|
B:CLA604
|
4.4
|
43.8
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
41.9
|
1.0
|
C2A
|
B:CLA604
|
4.4
|
44.2
|
1.0
|
C5
|
B:CLA606
|
4.6
|
37.3
|
1.0
|
C4
|
B:CLA606
|
4.8
|
46.9
|
1.0
|
C6
|
B:CLA606
|
4.8
|
43.4
|
1.0
|
CBA
|
B:CLA604
|
4.9
|
43.9
|
1.0
|
CBD
|
B:CLA604
|
4.9
|
43.0
|
1.0
|
C3
|
B:CLA606
|
5.0
|
43.3
|
1.0
|
|
Magnesium binding site 7 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 7 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:49.1
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
49.1
|
1.0
|
ND
|
B:CLA605
|
2.0
|
47.8
|
1.0
|
NB
|
B:CLA605
|
2.0
|
44.8
|
1.0
|
NC
|
B:CLA605
|
2.1
|
42.2
|
1.0
|
NA
|
B:CLA605
|
2.1
|
48.3
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
43.9
|
1.0
|
C4D
|
B:CLA605
|
2.9
|
44.2
|
1.0
|
CE1
|
B:HIS455
|
3.0
|
47.6
|
1.0
|
C4A
|
B:CLA605
|
3.0
|
48.9
|
1.0
|
C1B
|
B:CLA605
|
3.1
|
48.1
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
41.8
|
1.0
|
C4B
|
B:CLA605
|
3.1
|
41.2
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
40.9
|
1.0
|
C1D
|
B:CLA605
|
3.2
|
51.4
|
1.0
|
C1A
|
B:CLA605
|
3.2
|
47.4
|
1.0
|
CD2
|
B:HIS455
|
3.3
|
43.2
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
47.8
|
1.0
|
CHC
|
B:CLA605
|
3.5
|
44.3
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
49.0
|
1.0
|
CHD
|
B:CLA605
|
3.5
|
43.0
|
1.0
|
C14
|
B:CLA613
|
4.0
|
45.4
|
1.0
|
ND1
|
B:HIS455
|
4.2
|
39.3
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
48.5
|
1.0
|
C2C
|
B:CLA605
|
4.3
|
43.8
|
1.0
|
CG
|
B:HIS455
|
4.3
|
40.9
|
1.0
|
C2B
|
B:CLA605
|
4.3
|
46.4
|
1.0
|
C3B
|
B:CLA605
|
4.4
|
43.4
|
1.0
|
C3C
|
B:CLA605
|
4.4
|
41.0
|
1.0
|
C2D
|
B:CLA605
|
4.4
|
49.8
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
49.2
|
1.0
|
C2A
|
B:CLA605
|
4.5
|
43.7
|
1.0
|
C15
|
B:CLA613
|
4.6
|
43.0
|
1.0
|
C13
|
B:CLA613
|
4.7
|
37.7
|
1.0
|
CBD
|
B:CLA605
|
5.0
|
47.8
|
1.0
|
|
Magnesium binding site 8 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 8 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:43.2
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
43.2
|
1.0
|
ND
|
B:CLA606
|
2.0
|
45.2
|
1.0
|
NB
|
B:CLA606
|
2.0
|
43.8
|
1.0
|
NC
|
B:CLA606
|
2.1
|
46.2
|
1.0
|
NA
|
B:CLA606
|
2.1
|
42.8
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
47.2
|
1.0
|
C4D
|
B:CLA606
|
2.9
|
45.0
|
1.0
|
CE1
|
B:HIS100
|
3.0
|
41.8
|
1.0
|
C1B
|
B:CLA606
|
3.0
|
41.4
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
42.5
|
1.0
|
C1C
|
B:CLA606
|
3.1
|
45.1
|
1.0
|
C4B
|
B:CLA606
|
3.1
|
43.5
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
43.0
|
1.0
|
C1A
|
B:CLA606
|
3.1
|
45.7
|
1.0
|
C1D
|
B:CLA606
|
3.2
|
47.1
|
1.0
|
CD2
|
B:HIS100
|
3.4
|
45.3
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
46.0
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
45.9
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
44.0
|
1.0
|
CHD
|
B:CLA606
|
3.5
|
39.2
|
1.0
|
C2
|
B:CLA605
|
4.2
|
45.4
|
1.0
|
ND1
|
B:HIS100
|
4.2
|
36.6
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
45.7
|
1.0
|
C2B
|
B:CLA606
|
4.3
|
41.3
|
1.0
|
C2C
|
B:CLA606
|
4.3
|
45.3
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
40.4
|
1.0
|
C3C
|
B:CLA606
|
4.3
|
48.0
|
1.0
|
C2D
|
B:CLA606
|
4.4
|
45.0
|
1.0
|
CG
|
B:HIS100
|
4.4
|
40.2
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
37.9
|
1.0
|
C2A
|
B:CLA606
|
4.5
|
45.7
|
1.0
|
C1
|
B:CLA605
|
4.7
|
50.5
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
40.4
|
1.0
|
O2A
|
B:CLA605
|
4.9
|
44.4
|
1.0
|
CBA
|
B:CLA606
|
5.0
|
50.9
|
1.0
|
|
Magnesium binding site 9 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 9 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:54.5
occ:1.00
|
MG
|
B:CLA607
|
0.0
|
54.5
|
1.0
|
ND
|
B:CLA607
|
2.0
|
50.5
|
1.0
|
NB
|
B:CLA607
|
2.0
|
55.1
|
1.0
|
NC
|
B:CLA607
|
2.1
|
58.6
|
1.0
|
NA
|
B:CLA607
|
2.1
|
51.3
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
54.6
|
1.0
|
CE1
|
B:HIS157
|
2.5
|
55.1
|
1.0
|
C4D
|
B:CLA607
|
2.9
|
49.4
|
1.0
|
C1B
|
B:CLA607
|
3.0
|
53.4
|
1.0
|
C4A
|
B:CLA607
|
3.1
|
49.5
|
1.0
|
C1C
|
B:CLA607
|
3.1
|
53.7
|
1.0
|
C4B
|
B:CLA607
|
3.1
|
50.1
|
1.0
|
C4C
|
B:CLA607
|
3.1
|
50.5
|
1.0
|
C1D
|
B:CLA607
|
3.2
|
51.6
|
1.0
|
C1A
|
B:CLA607
|
3.2
|
51.0
|
1.0
|
CHB
|
B:CLA607
|
3.4
|
47.9
|
1.0
|
CHC
|
B:CLA607
|
3.5
|
48.5
|
1.0
|
CHA
|
B:CLA607
|
3.5
|
50.9
|
1.0
|
CG
|
B:HIS157
|
3.5
|
54.0
|
1.0
|
CHD
|
B:CLA607
|
3.5
|
52.0
|
1.0
|
C5
|
B:UNL601
|
3.6
|
49.8
|
1.0
|
NE2
|
B:HIS157
|
3.8
|
47.6
|
1.0
|
C4
|
B:UNL601
|
4.0
|
49.9
|
1.0
|
C6
|
B:UNL601
|
4.1
|
49.3
|
1.0
|
C3D
|
B:CLA607
|
4.3
|
47.9
|
1.0
|
CD2
|
B:HIS157
|
4.3
|
43.2
|
1.0
|
CB
|
B:HIS157
|
4.3
|
47.2
|
1.0
|
C2B
|
B:CLA607
|
4.3
|
50.9
|
1.0
|
C2C
|
B:CLA607
|
4.3
|
52.5
|
1.0
|
C3B
|
B:CLA607
|
4.3
|
52.0
|
1.0
|
C3C
|
B:CLA607
|
4.4
|
49.4
|
1.0
|
C2D
|
B:CLA607
|
4.4
|
49.3
|
1.0
|
C3A
|
B:CLA607
|
4.4
|
51.0
|
1.0
|
C2A
|
B:CLA607
|
4.5
|
47.5
|
1.0
|
C7
|
B:UNL601
|
4.5
|
50.1
|
1.0
|
CBD
|
B:CLA607
|
4.9
|
48.1
|
1.0
|
CBA
|
B:CLA607
|
5.0
|
47.0
|
1.0
|
|
Magnesium binding site 10 out
of 70 in 5kai
Go back to
Magnesium Binding Sites List in 5kai
Magnesium binding site 10 out
of 70 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg608
b:40.4
occ:1.00
|
MG
|
B:CLA608
|
0.0
|
40.4
|
1.0
|
ND
|
B:CLA608
|
2.0
|
42.3
|
1.0
|
NB
|
B:CLA608
|
2.0
|
35.3
|
1.0
|
NC
|
B:CLA608
|
2.1
|
40.0
|
1.0
|
NA
|
B:CLA608
|
2.1
|
42.9
|
1.0
|
O
|
B:HOH704
|
2.1
|
32.2
|
1.0
|
C4D
|
B:CLA608
|
2.9
|
45.5
|
1.0
|
C1B
|
B:CLA608
|
3.0
|
36.4
|
1.0
|
C4A
|
B:CLA608
|
3.0
|
40.9
|
1.0
|
C1C
|
B:CLA608
|
3.1
|
35.0
|
1.0
|
C4B
|
B:CLA608
|
3.1
|
35.5
|
1.0
|
C4C
|
B:CLA608
|
3.1
|
42.6
|
1.0
|
C1A
|
B:CLA608
|
3.1
|
44.5
|
1.0
|
C1D
|
B:CLA608
|
3.2
|
47.3
|
1.0
|
CHB
|
B:CLA608
|
3.4
|
34.5
|
1.0
|
CHC
|
B:CLA608
|
3.4
|
34.3
|
1.0
|
CHA
|
B:CLA608
|
3.5
|
44.3
|
1.0
|
C12
|
M:LMG101
|
3.5
|
42.9
|
1.0
|
CHD
|
B:CLA608
|
3.5
|
43.4
|
1.0
|
C14
|
M:LMG101
|
4.0
|
41.5
|
1.0
|
C3D
|
B:CLA608
|
4.3
|
50.2
|
1.0
|
C2B
|
B:CLA608
|
4.3
|
35.6
|
1.0
|
C2C
|
B:CLA608
|
4.3
|
30.8
|
1.0
|
C3B
|
B:CLA608
|
4.3
|
38.4
|
1.0
|
C3C
|
B:CLA608
|
4.4
|
36.9
|
1.0
|
C2D
|
B:CLA608
|
4.4
|
49.9
|
1.0
|
C3A
|
B:CLA608
|
4.4
|
44.1
|
1.0
|
C13
|
M:LMG101
|
4.4
|
50.0
|
1.0
|
C2A
|
B:CLA608
|
4.4
|
44.5
|
1.0
|
CE
|
B:MET37
|
4.5
|
45.6
|
1.0
|
C11
|
M:LMG101
|
4.6
|
48.3
|
1.0
|
SD
|
B:MET37
|
4.7
|
44.2
|
1.0
|
CBA
|
B:CLA608
|
4.8
|
48.9
|
1.0
|
CD2
|
B:PHE61
|
4.9
|
43.7
|
1.0
|
CBD
|
B:CLA608
|
4.9
|
47.3
|
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 18:55:01 2024
|