Magnesium in PDB 4tnh: Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution
Enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution
All present enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution:
1.10.3.9;
Protein crystallography data
The structure of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution, PDB code: 4tnh
was solved by
J.Kern,
R.Tran,
R.Alonso-Mori,
S.Koroidov,
N.Echols,
J.Hattne,
M.Ibrahim,
S.Gul,
H.Laksmono,
R.G.Sierra,
R.J.Gildea,
G.Han,
J.Hellmich,
B.Lassalle-Kaiser,
R.Chatterjee,
A.Brewster,
C.A.Stan,
C.Gloeckner,
A.Lampe,
D.Difiore,
D.Milathianaki,
A.R.Fry,
M.M.Seibert,
J.E.Koglin,
E.Gallo,
J.Uhlig,
D.Sokaras,
T.-C.Weng,
P.H.Zwart,
D.E.Skinner,
M.J.Bogan,
M.Messerschmidt,
P.Glatzel,
G.J.Williams,
S.Boutet,
P.D.Adams,
A.Zouni,
J.Messinger,
N.K.Sauter,
U.Bergmann,
J.Yano,
V.K.Yachandra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
72.93 /
4.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
132.885,
229.033,
307.715,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
28.1 /
29.2
|
Other elements in 4tnh:
The structure of Rt Xfel Structure of Photosystem II in the Dark State at 4.9 A Resolution also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 1 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:0.0
occ:1.00
|
MG
|
A:CLA402
|
0.0
|
0.0
|
1.0
|
NB
|
A:CLA402
|
2.0
|
0.6
|
1.0
|
ND
|
A:CLA402
|
2.0
|
0.1
|
1.0
|
NC
|
A:CLA402
|
2.1
|
0.8
|
1.0
|
NA
|
A:CLA402
|
2.1
|
0.4
|
1.0
|
NE2
|
A:HIS198
|
2.9
|
0.9
|
1.0
|
C4D
|
A:CLA402
|
2.9
|
0.4
|
1.0
|
C1B
|
A:CLA402
|
3.0
|
0.9
|
1.0
|
C4A
|
A:CLA402
|
3.0
|
1.0
|
1.0
|
C4B
|
A:CLA402
|
3.1
|
0.5
|
1.0
|
C1C
|
A:CLA402
|
3.1
|
0.7
|
1.0
|
C4C
|
A:CLA402
|
3.1
|
0.9
|
1.0
|
C1A
|
A:CLA402
|
3.2
|
0.3
|
1.0
|
C1D
|
A:CLA402
|
3.2
|
0.9
|
1.0
|
CHB
|
A:CLA402
|
3.4
|
0.9
|
1.0
|
CHC
|
A:CLA402
|
3.4
|
0.1
|
1.0
|
CHA
|
A:CLA402
|
3.5
|
0.2
|
1.0
|
CHD
|
A:CLA402
|
3.5
|
0.9
|
1.0
|
CE1
|
A:HIS198
|
3.6
|
0.4
|
1.0
|
CD2
|
A:HIS198
|
4.0
|
0.0
|
1.0
|
CAB
|
D:CLA404
|
4.1
|
0.3
|
1.0
|
C3D
|
A:CLA402
|
4.3
|
1.0
|
1.0
|
C2B
|
A:CLA402
|
4.3
|
0.2
|
1.0
|
C3B
|
A:CLA402
|
4.3
|
0.0
|
1.0
|
C2C
|
A:CLA402
|
4.3
|
0.5
|
1.0
|
C3C
|
A:CLA402
|
4.4
|
0.8
|
1.0
|
C2D
|
A:CLA402
|
4.4
|
0.8
|
1.0
|
C3A
|
A:CLA402
|
4.4
|
0.6
|
1.0
|
C2A
|
A:CLA402
|
4.5
|
0.8
|
1.0
|
CBB
|
D:CLA404
|
4.7
|
0.0
|
1.0
|
SD
|
A:MET183
|
4.7
|
0.2
|
1.0
|
ND1
|
A:HIS198
|
4.9
|
0.2
|
1.0
|
CBD
|
A:CLA402
|
4.9
|
0.9
|
1.0
|
|
Magnesium binding site 2 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 2 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:0.9
occ:1.00
|
MG
|
A:CLA403
|
0.0
|
0.9
|
1.0
|
NB
|
A:CLA403
|
2.0
|
0.4
|
1.0
|
ND
|
A:CLA403
|
2.0
|
0.9
|
1.0
|
NC
|
A:CLA403
|
2.1
|
0.5
|
1.0
|
NA
|
A:CLA403
|
2.1
|
0.3
|
1.0
|
C4D
|
A:CLA403
|
2.9
|
0.0
|
1.0
|
C1B
|
A:CLA403
|
3.0
|
0.4
|
1.0
|
C4A
|
A:CLA403
|
3.0
|
0.3
|
1.0
|
C4B
|
A:CLA403
|
3.1
|
0.2
|
1.0
|
C1C
|
A:CLA403
|
3.1
|
0.6
|
1.0
|
C4C
|
A:CLA403
|
3.1
|
0.5
|
1.0
|
C1A
|
A:CLA403
|
3.2
|
0.1
|
1.0
|
C1D
|
A:CLA403
|
3.2
|
0.8
|
1.0
|
CHB
|
A:CLA403
|
3.4
|
1.0
|
1.0
|
CHC
|
A:CLA403
|
3.4
|
0.2
|
1.0
|
CHA
|
A:CLA403
|
3.5
|
0.1
|
1.0
|
CHD
|
A:CLA403
|
3.5
|
0.3
|
1.0
|
CBB
|
D:PHO401
|
4.1
|
0.8
|
1.0
|
C3D
|
A:CLA403
|
4.3
|
0.7
|
1.0
|
C2B
|
A:CLA403
|
4.3
|
0.1
|
1.0
|
C3B
|
A:CLA403
|
4.3
|
0.7
|
1.0
|
O1A
|
A:CLA403
|
4.3
|
0.8
|
1.0
|
C2C
|
A:CLA403
|
4.3
|
0.7
|
1.0
|
C3C
|
A:CLA403
|
4.4
|
0.5
|
1.0
|
C2D
|
A:CLA403
|
4.4
|
0.7
|
1.0
|
C3A
|
A:CLA403
|
4.4
|
0.6
|
1.0
|
C2A
|
A:CLA403
|
4.5
|
0.1
|
1.0
|
C20
|
D:PHO401
|
4.8
|
0.3
|
1.0
|
CG2
|
A:THR179
|
4.8
|
0.1
|
1.0
|
CBD
|
A:CLA403
|
4.9
|
0.7
|
1.0
|
|
Magnesium binding site 3 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 3 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:0.7
occ:1.00
|
MG
|
A:CLA404
|
0.0
|
0.7
|
1.0
|
NB
|
A:CLA404
|
2.0
|
0.3
|
1.0
|
ND
|
A:CLA404
|
2.0
|
0.9
|
1.0
|
NC
|
A:CLA404
|
2.1
|
1.0
|
1.0
|
NA
|
A:CLA404
|
2.1
|
0.3
|
1.0
|
C4D
|
A:CLA404
|
2.9
|
0.6
|
1.0
|
C1B
|
A:CLA404
|
3.0
|
0.6
|
1.0
|
C4A
|
A:CLA404
|
3.1
|
0.7
|
1.0
|
C4B
|
A:CLA404
|
3.1
|
0.3
|
1.0
|
C1C
|
A:CLA404
|
3.1
|
0.9
|
1.0
|
C4C
|
A:CLA404
|
3.2
|
0.9
|
1.0
|
C1A
|
A:CLA404
|
3.2
|
0.9
|
1.0
|
C1D
|
A:CLA404
|
3.2
|
0.8
|
1.0
|
CHB
|
A:CLA404
|
3.4
|
0.8
|
1.0
|
CHC
|
A:CLA404
|
3.4
|
0.6
|
1.0
|
CHA
|
A:CLA404
|
3.5
|
0.1
|
1.0
|
CHD
|
A:CLA404
|
3.5
|
0.6
|
1.0
|
CBB
|
D:PHO402
|
4.0
|
0.1
|
1.0
|
C3D
|
A:CLA404
|
4.3
|
0.8
|
1.0
|
C2B
|
A:CLA404
|
4.3
|
0.7
|
1.0
|
C3B
|
A:CLA404
|
4.3
|
0.0
|
1.0
|
C2C
|
A:CLA404
|
4.3
|
1.0
|
1.0
|
C2D
|
A:CLA404
|
4.4
|
0.9
|
1.0
|
C3C
|
A:CLA404
|
4.4
|
0.3
|
1.0
|
C3A
|
A:CLA404
|
4.4
|
0.1
|
1.0
|
C2A
|
A:CLA404
|
4.5
|
0.9
|
1.0
|
C20
|
D:PHO402
|
4.6
|
0.9
|
1.0
|
CBA
|
A:CLA404
|
4.8
|
1.0
|
1.0
|
CE1
|
A:PHE206
|
4.9
|
0.1
|
1.0
|
CBD
|
A:CLA404
|
4.9
|
0.4
|
1.0
|
CG2
|
D:ILE178
|
5.0
|
1.0
|
1.0
|
|
Magnesium binding site 4 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 4 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:0.2
occ:1.00
|
MG
|
A:CLA405
|
0.0
|
0.2
|
1.0
|
NB
|
A:CLA405
|
2.0
|
0.4
|
1.0
|
ND
|
A:CLA405
|
2.0
|
0.1
|
1.0
|
NC
|
A:CLA405
|
2.1
|
0.9
|
1.0
|
NA
|
A:CLA405
|
2.1
|
0.9
|
1.0
|
NE2
|
A:HIS118
|
2.9
|
0.7
|
1.0
|
C4D
|
A:CLA405
|
2.9
|
1.0
|
1.0
|
C1B
|
A:CLA405
|
3.0
|
0.1
|
1.0
|
C4A
|
A:CLA405
|
3.0
|
0.9
|
1.0
|
C4B
|
A:CLA405
|
3.1
|
0.1
|
1.0
|
C1C
|
A:CLA405
|
3.1
|
0.1
|
1.0
|
C4C
|
A:CLA405
|
3.1
|
0.4
|
1.0
|
C1A
|
A:CLA405
|
3.2
|
0.7
|
1.0
|
C1D
|
A:CLA405
|
3.2
|
0.1
|
1.0
|
CHB
|
A:CLA405
|
3.4
|
0.8
|
1.0
|
CHC
|
A:CLA405
|
3.4
|
0.9
|
1.0
|
CHA
|
A:CLA405
|
3.5
|
0.0
|
1.0
|
CHD
|
A:CLA405
|
3.5
|
0.3
|
1.0
|
CE1
|
A:HIS118
|
3.6
|
0.6
|
1.0
|
CD2
|
A:HIS118
|
4.0
|
0.1
|
1.0
|
CG2
|
I:VAL12
|
4.1
|
0.7
|
1.0
|
C3D
|
A:CLA405
|
4.3
|
0.2
|
1.0
|
C2B
|
A:CLA405
|
4.3
|
0.3
|
1.0
|
C3B
|
A:CLA405
|
4.3
|
0.2
|
1.0
|
CG1
|
I:VAL8
|
4.3
|
0.7
|
1.0
|
C2C
|
A:CLA405
|
4.3
|
0.8
|
1.0
|
C2D
|
A:CLA405
|
4.4
|
0.8
|
1.0
|
C3C
|
A:CLA405
|
4.4
|
0.6
|
1.0
|
C3A
|
A:CLA405
|
4.4
|
0.7
|
1.0
|
C2A
|
A:CLA405
|
4.5
|
0.5
|
1.0
|
ND1
|
A:HIS118
|
4.7
|
0.2
|
1.0
|
CBD
|
A:CLA405
|
4.9
|
0.6
|
1.0
|
CBA
|
A:CLA405
|
5.0
|
0.8
|
1.0
|
CG
|
A:HIS118
|
5.0
|
0.4
|
1.0
|
|
Magnesium binding site 5 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 5 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:0.5
occ:1.00
|
MG
|
B:CLA601
|
0.0
|
0.5
|
1.0
|
NB
|
B:CLA601
|
2.0
|
0.3
|
1.0
|
ND
|
B:CLA601
|
2.0
|
0.2
|
1.0
|
NC
|
B:CLA601
|
2.1
|
0.5
|
1.0
|
NA
|
B:CLA601
|
2.1
|
0.0
|
1.0
|
C4D
|
B:CLA601
|
2.9
|
0.4
|
1.0
|
C1B
|
B:CLA601
|
3.0
|
0.2
|
1.0
|
C4A
|
B:CLA601
|
3.1
|
0.6
|
1.0
|
C4B
|
B:CLA601
|
3.1
|
0.5
|
1.0
|
C1C
|
B:CLA601
|
3.1
|
0.6
|
1.0
|
C4C
|
B:CLA601
|
3.2
|
0.3
|
1.0
|
C1A
|
B:CLA601
|
3.2
|
0.3
|
1.0
|
C1D
|
B:CLA601
|
3.2
|
0.8
|
1.0
|
CHB
|
B:CLA601
|
3.4
|
0.2
|
1.0
|
CHC
|
B:CLA601
|
3.4
|
0.2
|
1.0
|
CHA
|
B:CLA601
|
3.5
|
0.0
|
1.0
|
CHD
|
B:CLA601
|
3.5
|
0.3
|
1.0
|
O
|
B:TRP185
|
3.9
|
0.5
|
1.0
|
C3D
|
B:CLA601
|
4.3
|
0.9
|
1.0
|
C2B
|
B:CLA601
|
4.3
|
0.9
|
1.0
|
C3B
|
B:CLA601
|
4.3
|
0.5
|
1.0
|
C2C
|
B:CLA601
|
4.3
|
0.2
|
1.0
|
C2D
|
B:CLA601
|
4.4
|
0.4
|
1.0
|
C3C
|
B:CLA601
|
4.4
|
0.4
|
1.0
|
C3A
|
B:CLA601
|
4.4
|
0.4
|
1.0
|
C2A
|
B:CLA601
|
4.5
|
0.6
|
1.0
|
CE1
|
B:PHE190
|
4.9
|
0.1
|
1.0
|
CBD
|
B:CLA601
|
4.9
|
0.1
|
1.0
|
|
Magnesium binding site 6 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 6 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:0.7
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
0.7
|
1.0
|
NB
|
B:CLA602
|
2.0
|
0.4
|
1.0
|
ND
|
B:CLA602
|
2.0
|
0.3
|
1.0
|
NC
|
B:CLA602
|
2.1
|
0.7
|
1.0
|
NA
|
B:CLA602
|
2.1
|
0.4
|
1.0
|
C4D
|
B:CLA602
|
2.9
|
0.1
|
1.0
|
NE2
|
B:HIS202
|
3.0
|
0.3
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
0.3
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
0.0
|
1.0
|
C4B
|
B:CLA602
|
3.1
|
0.3
|
1.0
|
C1C
|
B:CLA602
|
3.1
|
0.7
|
1.0
|
C4C
|
B:CLA602
|
3.2
|
0.1
|
1.0
|
C1D
|
B:CLA602
|
3.2
|
0.5
|
1.0
|
C1A
|
B:CLA602
|
3.2
|
0.5
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
0.1
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
0.7
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
0.0
|
1.0
|
CHD
|
B:CLA602
|
3.5
|
0.2
|
1.0
|
CD2
|
B:HIS202
|
3.8
|
0.7
|
1.0
|
CE1
|
B:HIS202
|
3.9
|
0.0
|
1.0
|
C7
|
B:CLA604
|
3.9
|
0.7
|
1.0
|
C5
|
B:CLA604
|
4.0
|
0.8
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
0.6
|
1.0
|
C2B
|
B:CLA602
|
4.3
|
1.0
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
0.9
|
1.0
|
C2C
|
B:CLA602
|
4.3
|
0.5
|
1.0
|
C2D
|
B:CLA602
|
4.4
|
0.2
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
0.9
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
0.7
|
1.0
|
C2A
|
B:CLA602
|
4.5
|
0.8
|
1.0
|
C6
|
B:CLA604
|
4.6
|
0.6
|
1.0
|
CE1
|
B:HIS201
|
4.6
|
0.1
|
1.0
|
O2A
|
B:CLA602
|
4.9
|
0.1
|
1.0
|
CG
|
B:HIS202
|
4.9
|
0.5
|
1.0
|
ND1
|
B:HIS202
|
4.9
|
0.2
|
1.0
|
CBA
|
B:CLA602
|
4.9
|
0.1
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
0.4
|
1.0
|
|
Magnesium binding site 7 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 7 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:0.6
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
0.6
|
1.0
|
NB
|
B:CLA603
|
2.0
|
0.8
|
1.0
|
ND
|
B:CLA603
|
2.0
|
0.3
|
1.0
|
NA
|
B:CLA603
|
2.1
|
0.6
|
1.0
|
NC
|
B:CLA603
|
2.1
|
1.0
|
1.0
|
NE2
|
B:HIS455
|
2.9
|
0.8
|
1.0
|
C4D
|
B:CLA603
|
2.9
|
0.3
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
1.0
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
0.7
|
1.0
|
C4B
|
B:CLA603
|
3.1
|
0.6
|
1.0
|
C1C
|
B:CLA603
|
3.1
|
0.1
|
1.0
|
C4C
|
B:CLA603
|
3.2
|
0.1
|
1.0
|
C1D
|
B:CLA603
|
3.2
|
0.5
|
1.0
|
C1A
|
B:CLA603
|
3.2
|
0.1
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
0.5
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
0.7
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
0.4
|
1.0
|
CHD
|
B:CLA603
|
3.5
|
0.8
|
1.0
|
CD2
|
B:HIS455
|
3.7
|
0.2
|
1.0
|
C14
|
B:CLA611
|
3.7
|
0.3
|
1.0
|
CE1
|
B:HIS455
|
3.9
|
0.9
|
1.0
|
C15
|
B:CLA611
|
4.2
|
0.5
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
0.7
|
1.0
|
C2B
|
B:CLA603
|
4.3
|
0.0
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
0.0
|
1.0
|
C13
|
B:CLA611
|
4.3
|
0.4
|
1.0
|
C2C
|
B:CLA603
|
4.3
|
0.7
|
1.0
|
C2D
|
B:CLA603
|
4.4
|
0.3
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
0.3
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
0.2
|
1.0
|
C2A
|
B:CLA603
|
4.5
|
0.4
|
1.0
|
CG
|
B:HIS455
|
4.8
|
0.5
|
1.0
|
ND1
|
B:HIS455
|
4.9
|
0.7
|
1.0
|
CBD
|
B:CLA603
|
5.0
|
0.9
|
1.0
|
|
Magnesium binding site 8 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 8 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:0.3
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
0.3
|
1.0
|
NB
|
B:CLA604
|
2.0
|
0.3
|
1.0
|
ND
|
B:CLA604
|
2.0
|
0.2
|
1.0
|
NC
|
B:CLA604
|
2.1
|
0.9
|
1.0
|
NA
|
B:CLA604
|
2.1
|
0.6
|
1.0
|
C4D
|
B:CLA604
|
2.9
|
0.3
|
1.0
|
NE2
|
B:HIS100
|
3.0
|
0.8
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
0.4
|
1.0
|
C4A
|
B:CLA604
|
3.0
|
0.3
|
1.0
|
C4B
|
B:CLA604
|
3.1
|
0.8
|
1.0
|
C1C
|
B:CLA604
|
3.1
|
0.5
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
0.7
|
1.0
|
C1A
|
B:CLA604
|
3.2
|
0.9
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
0.2
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
0.2
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
0.9
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
0.4
|
1.0
|
CHD
|
B:CLA604
|
3.5
|
0.5
|
1.0
|
CD2
|
B:HIS100
|
3.8
|
0.8
|
1.0
|
CE1
|
B:HIS100
|
3.9
|
0.7
|
1.0
|
C2
|
B:CLA603
|
3.9
|
0.3
|
1.0
|
C1
|
B:CLA603
|
4.1
|
0.1
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
0.9
|
1.0
|
C2B
|
B:CLA604
|
4.3
|
0.3
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
0.0
|
1.0
|
C2C
|
B:CLA604
|
4.3
|
1.0
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
0.7
|
1.0
|
C2D
|
B:CLA604
|
4.4
|
0.4
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
0.7
|
1.0
|
C2A
|
B:CLA604
|
4.5
|
1.0
|
1.0
|
O2A
|
B:CLA603
|
4.7
|
0.9
|
1.0
|
O1A
|
B:CLA603
|
4.7
|
0.1
|
1.0
|
C3
|
B:CLA603
|
4.7
|
0.2
|
1.0
|
CBD
|
B:CLA604
|
4.9
|
0.3
|
1.0
|
CBA
|
B:CLA604
|
4.9
|
0.6
|
1.0
|
CG
|
B:HIS100
|
4.9
|
0.7
|
1.0
|
ND1
|
B:HIS100
|
5.0
|
0.4
|
1.0
|
|
Magnesium binding site 9 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 9 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:0.7
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
0.7
|
1.0
|
NB
|
B:CLA605
|
2.0
|
0.9
|
1.0
|
ND
|
B:CLA605
|
2.0
|
0.8
|
1.0
|
NA
|
B:CLA605
|
2.1
|
0.9
|
1.0
|
NC
|
B:CLA605
|
2.1
|
0.7
|
1.0
|
C4D
|
B:CLA605
|
2.9
|
0.7
|
1.0
|
ND1
|
B:HIS157
|
3.0
|
0.4
|
1.0
|
C1B
|
B:CLA605
|
3.0
|
0.9
|
1.0
|
C4A
|
B:CLA605
|
3.0
|
0.2
|
1.0
|
C4B
|
B:CLA605
|
3.1
|
0.6
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
0.9
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
0.0
|
1.0
|
C1A
|
B:CLA605
|
3.2
|
0.0
|
1.0
|
C1D
|
B:CLA605
|
3.2
|
0.4
|
1.0
|
CE1
|
B:HIS157
|
3.4
|
0.0
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
0.3
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
1.0
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
0.5
|
1.0
|
CHD
|
B:CLA605
|
3.5
|
0.4
|
1.0
|
C5
|
B:LMT623
|
3.9
|
0.0
|
1.0
|
C6
|
B:LMT623
|
3.9
|
0.7
|
1.0
|
C4
|
B:LMT623
|
3.9
|
1.0
|
1.0
|
CG
|
B:HIS157
|
4.2
|
0.4
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
0.7
|
1.0
|
C2B
|
B:CLA605
|
4.3
|
0.1
|
1.0
|
C3B
|
B:CLA605
|
4.3
|
0.1
|
1.0
|
C2C
|
B:CLA605
|
4.3
|
1.0
|
1.0
|
C3C
|
B:CLA605
|
4.4
|
0.5
|
1.0
|
C2D
|
B:CLA605
|
4.4
|
0.1
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
0.9
|
1.0
|
C2A
|
B:CLA605
|
4.5
|
0.5
|
1.0
|
NE2
|
B:HIS157
|
4.6
|
0.6
|
1.0
|
CB
|
B:HIS157
|
4.8
|
0.4
|
1.0
|
C3
|
B:LMT623
|
4.9
|
0.0
|
1.0
|
CBD
|
B:CLA605
|
4.9
|
0.8
|
1.0
|
C7
|
B:LMT623
|
5.0
|
0.1
|
1.0
|
|
Magnesium binding site 10 out
of 70 in 4tnh
Go back to
Magnesium Binding Sites List in 4tnh
Magnesium binding site 10 out
of 70 in the Rt Xfel Structure of Photosystem II in the Dark State at 4.9 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 4.9 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:0.4
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
0.4
|
1.0
|
NB
|
B:CLA606
|
2.0
|
0.2
|
1.0
|
ND
|
B:CLA606
|
2.0
|
0.8
|
1.0
|
NC
|
B:CLA606
|
2.1
|
1.0
|
1.0
|
NA
|
B:CLA606
|
2.1
|
0.3
|
1.0
|
C4D
|
B:CLA606
|
2.9
|
0.4
|
1.0
|
C1B
|
B:CLA606
|
3.0
|
0.7
|
1.0
|
C4B
|
B:CLA606
|
3.1
|
0.5
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
0.1
|
1.0
|
C1C
|
B:CLA606
|
3.1
|
0.7
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
0.5
|
1.0
|
C1A
|
B:CLA606
|
3.2
|
0.8
|
1.0
|
C1D
|
B:CLA606
|
3.2
|
0.1
|
1.0
|
C30
|
B:LMG621
|
3.4
|
0.8
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
0.1
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
0.0
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
0.7
|
1.0
|
CHD
|
B:CLA606
|
3.5
|
0.6
|
1.0
|
O10
|
B:LMG621
|
3.7
|
0.8
|
1.0
|
CE
|
B:MET37
|
3.7
|
0.4
|
1.0
|
C32
|
B:LMG621
|
4.0
|
0.9
|
1.0
|
C28
|
B:LMG621
|
4.2
|
0.7
|
1.0
|
C31
|
B:LMG621
|
4.3
|
0.9
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
0.4
|
1.0
|
C2B
|
B:CLA606
|
4.3
|
0.1
|
1.0
|
C29
|
B:LMG621
|
4.3
|
0.5
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
0.4
|
1.0
|
C2C
|
B:CLA606
|
4.3
|
0.9
|
1.0
|
C2D
|
B:CLA606
|
4.4
|
0.5
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
0.8
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
0.4
|
1.0
|
C2A
|
B:CLA606
|
4.5
|
0.5
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
0.7
|
1.0
|
|
Reference:
J.Kern,
R.Tran,
R.Alonso-Mori,
S.Koroidov,
N.Echols,
J.Hattne,
M.Ibrahim,
S.Gul,
H.Laksmono,
R.G.Sierra,
R.J.Gildea,
G.Han,
J.Hellmich,
B.Lassalle-Kaiser,
R.Chatterjee,
A.S.Brewster,
C.A.Stan,
C.Glockner,
A.Lampe,
D.Difiore,
D.Milathianaki,
A.R.Fry,
M.M.Seibert,
J.E.Koglin,
E.Gallo,
J.Uhlig,
D.Sokaras,
T.C.Weng,
P.H.Zwart,
D.E.Skinner,
M.J.Bogan,
M.Messerschmidt,
P.Glatzel,
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ISSN: ESSN 2041-1723
PubMed: 25006873
DOI: 10.1038/NCOMMS5371
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