Magnesium in PDB 4rvy: Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Enzymatic activity of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
All present enzymatic activity of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3):
1.10.3.9;
Protein crystallography data
The structure of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3), PDB code: 4rvy
was solved by
C.Kupitz,
S.Basu,
I.Grotjohann,
R.Fromme,
N.Zatsepin,
K.N.Rendek,
M.Hunter,
R.L.Shoeman,
T.A.White,
D.Wang,
D.James,
J.-H.Yang,
D.E.Cobb,
B.Reeder,
R.G.Sierra,
H.Liu,
A.Barty,
A.Aquila,
D.Deponte,
R.Kirian,
S.Bari,
J.J.Bergkamp,
K.Beyerlein,
M.J.Bogan,
C.Caleman,
T.-C.Chao,
C.E.Conrad,
K.M.Davis,
H.Fleckenstein,
L.Galli,
S.P.Hau-Riege,
S.Kassemeyer,
H.Laksmono,
M.Liang,
L.Lomb,
S.Marchesini,
A.V.Martin,
M.Messerschmidt,
D.Milathianaki,
K.Nass,
A.Ros,
S.Roy-Chowdhury,
K.Schmidt,
M.Seibert,
J.Steinbrener,
F.Stellato,
L.Yan,
C.Yoon,
T.A.Moore,
A.L.Moore,
Y.Pushkar,
G.J.Williams,
S.Boutet,
R.B.Doak,
U.Weierstall,
M.Frank,
H.N.Chapman,
J.C.H.Spence,
P.Fromme,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
102.30 /
5.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
136.610,
228.090,
308.680,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
28.1 /
29.1
|
Other elements in 4rvy:
The structure of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 1 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:20.8
occ:1.00
|
MG
|
A:CLA603
|
0.0
|
20.8
|
1.0
|
ND
|
A:CLA603
|
2.0
|
18.6
|
1.0
|
NB
|
A:CLA603
|
2.1
|
18.3
|
1.0
|
NC
|
A:CLA603
|
2.1
|
18.8
|
1.0
|
NA
|
A:CLA603
|
2.2
|
18.8
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
19.9
|
1.0
|
C4D
|
A:CLA603
|
3.0
|
19.1
|
1.0
|
C4B
|
A:CLA603
|
3.1
|
18.6
|
1.0
|
C1C
|
A:CLA603
|
3.1
|
17.8
|
1.0
|
C1B
|
A:CLA603
|
3.1
|
18.6
|
1.0
|
C1D
|
A:CLA603
|
3.1
|
18.3
|
1.0
|
C4A
|
A:CLA603
|
3.2
|
18.8
|
1.0
|
C1A
|
A:CLA603
|
3.2
|
19.8
|
1.0
|
CE1
|
A:HIS198
|
3.2
|
18.3
|
1.0
|
C4C
|
A:CLA603
|
3.2
|
17.1
|
1.0
|
CD2
|
A:HIS198
|
3.2
|
19.0
|
1.0
|
CHC
|
A:CLA603
|
3.4
|
17.5
|
1.0
|
CHB
|
A:CLA603
|
3.5
|
18.1
|
1.0
|
CHA
|
A:CLA603
|
3.5
|
18.6
|
1.0
|
CHD
|
A:CLA603
|
3.6
|
19.1
|
1.0
|
CE
|
A:MET183
|
4.1
|
17.2
|
1.0
|
C3D
|
A:CLA603
|
4.2
|
18.1
|
1.0
|
ND1
|
A:HIS198
|
4.3
|
18.9
|
1.0
|
CG
|
A:HIS198
|
4.4
|
19.4
|
1.0
|
C2D
|
A:CLA603
|
4.4
|
19.1
|
1.0
|
C3B
|
A:CLA603
|
4.4
|
17.2
|
1.0
|
CAB
|
D:CLA401
|
4.4
|
17.5
|
1.0
|
C2C
|
A:CLA603
|
4.4
|
15.6
|
1.0
|
C2B
|
A:CLA603
|
4.4
|
18.8
|
1.0
|
C3C
|
A:CLA603
|
4.5
|
17.1
|
1.0
|
C3A
|
A:CLA603
|
4.5
|
19.9
|
1.0
|
C2A
|
A:CLA603
|
4.5
|
18.4
|
1.0
|
CBD
|
A:CLA603
|
5.0
|
19.4
|
1.0
|
|
Magnesium binding site 2 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 2 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:21.3
occ:1.00
|
MG
|
A:CLA604
|
0.0
|
21.3
|
1.0
|
NB
|
A:CLA604
|
2.0
|
21.8
|
1.0
|
ND
|
A:CLA604
|
2.0
|
20.7
|
1.0
|
NC
|
A:CLA604
|
2.1
|
20.1
|
1.0
|
NA
|
A:CLA604
|
2.3
|
21.1
|
1.0
|
C4B
|
A:CLA604
|
3.0
|
20.9
|
1.0
|
C4D
|
A:CLA604
|
3.0
|
21.0
|
1.0
|
C1C
|
A:CLA604
|
3.0
|
20.7
|
1.0
|
C1B
|
A:CLA604
|
3.1
|
21.5
|
1.0
|
C1D
|
A:CLA604
|
3.1
|
19.7
|
1.0
|
C4C
|
A:CLA604
|
3.2
|
19.4
|
1.0
|
C4A
|
A:CLA604
|
3.2
|
20.8
|
1.0
|
C1A
|
A:CLA604
|
3.3
|
20.1
|
1.0
|
CHC
|
A:CLA604
|
3.3
|
19.5
|
1.0
|
CHB
|
A:CLA604
|
3.5
|
20.7
|
1.0
|
CHA
|
A:CLA604
|
3.5
|
20.7
|
1.0
|
CHD
|
A:CLA604
|
3.6
|
20.6
|
1.0
|
CBB
|
A:PHO606
|
3.9
|
23.2
|
1.0
|
C3D
|
A:CLA604
|
4.2
|
19.3
|
1.0
|
C3B
|
A:CLA604
|
4.3
|
21.8
|
1.0
|
C2B
|
A:CLA604
|
4.4
|
21.4
|
1.0
|
C2C
|
A:CLA604
|
4.4
|
20.4
|
1.0
|
C2D
|
A:CLA604
|
4.4
|
20.4
|
1.0
|
C3C
|
A:CLA604
|
4.4
|
21.0
|
1.0
|
CG2
|
D:ILE178
|
4.5
|
19.5
|
1.0
|
C3A
|
A:CLA604
|
4.6
|
21.1
|
1.0
|
C2A
|
A:CLA604
|
4.6
|
20.6
|
1.0
|
C20
|
A:PHO606
|
4.8
|
19.1
|
1.0
|
CG1
|
D:ILE178
|
4.8
|
19.5
|
1.0
|
CE1
|
A:PHE206
|
4.9
|
21.3
|
1.0
|
CBD
|
A:CLA604
|
5.0
|
21.1
|
1.0
|
CBA
|
A:CLA604
|
5.0
|
22.0
|
1.0
|
|
Magnesium binding site 3 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 3 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:24.3
occ:1.00
|
MG
|
A:CLA607
|
0.0
|
24.3
|
1.0
|
NB
|
A:CLA607
|
2.0
|
23.4
|
1.0
|
ND
|
A:CLA607
|
2.0
|
23.8
|
1.0
|
NA
|
A:CLA607
|
2.2
|
23.1
|
1.0
|
NC
|
A:CLA607
|
2.2
|
24.4
|
1.0
|
NE2
|
A:HIS118
|
2.3
|
23.2
|
1.0
|
C4D
|
A:CLA607
|
3.0
|
22.8
|
1.0
|
C1B
|
A:CLA607
|
3.0
|
23.1
|
1.0
|
C4B
|
A:CLA607
|
3.0
|
23.5
|
1.0
|
C4A
|
A:CLA607
|
3.1
|
22.8
|
1.0
|
C1A
|
A:CLA607
|
3.2
|
23.3
|
1.0
|
C1D
|
A:CLA607
|
3.2
|
21.8
|
1.0
|
C1C
|
A:CLA607
|
3.2
|
22.9
|
1.0
|
CE1
|
A:HIS118
|
3.2
|
24.8
|
1.0
|
C4C
|
A:CLA607
|
3.2
|
23.1
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
23.8
|
1.0
|
CHB
|
A:CLA607
|
3.4
|
21.8
|
1.0
|
CHC
|
A:CLA607
|
3.4
|
24.1
|
1.0
|
CHA
|
A:CLA607
|
3.5
|
21.8
|
1.0
|
CHD
|
A:CLA607
|
3.6
|
21.8
|
1.0
|
C3D
|
A:CLA607
|
4.2
|
21.7
|
1.0
|
CG1
|
I:VAL8
|
4.3
|
30.8
|
1.0
|
C3B
|
A:CLA607
|
4.3
|
24.0
|
1.0
|
ND1
|
A:HIS118
|
4.3
|
23.5
|
1.0
|
C2B
|
A:CLA607
|
4.3
|
23.1
|
1.0
|
C3A
|
A:CLA607
|
4.4
|
24.2
|
1.0
|
C2D
|
A:CLA607
|
4.4
|
22.1
|
1.0
|
CG
|
A:HIS118
|
4.4
|
23.3
|
1.0
|
C2A
|
A:CLA607
|
4.5
|
24.4
|
1.0
|
CG2
|
I:VAL12
|
4.5
|
31.4
|
1.0
|
C2C
|
A:CLA607
|
4.5
|
23.4
|
1.0
|
C3C
|
A:CLA607
|
4.5
|
23.5
|
1.0
|
CMA
|
A:CLA607
|
4.9
|
23.6
|
1.0
|
CBD
|
A:CLA607
|
5.0
|
23.6
|
1.0
|
|
Magnesium binding site 4 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 4 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg603
b:20.8
occ:1.00
|
MG
|
a:CLA603
|
0.0
|
20.8
|
1.0
|
ND
|
a:CLA603
|
2.0
|
18.6
|
1.0
|
NB
|
a:CLA603
|
2.1
|
18.3
|
1.0
|
NC
|
a:CLA603
|
2.1
|
18.8
|
1.0
|
NA
|
a:CLA603
|
2.2
|
18.8
|
1.0
|
NE2
|
a:HIS198
|
2.2
|
19.9
|
1.0
|
C4D
|
a:CLA603
|
3.0
|
19.1
|
1.0
|
C4B
|
a:CLA603
|
3.1
|
18.6
|
1.0
|
C1C
|
a:CLA603
|
3.1
|
17.8
|
1.0
|
C1B
|
a:CLA603
|
3.1
|
18.6
|
1.0
|
C1D
|
a:CLA603
|
3.1
|
18.3
|
1.0
|
C4A
|
a:CLA603
|
3.2
|
18.8
|
1.0
|
C1A
|
a:CLA603
|
3.2
|
19.8
|
1.0
|
CE1
|
a:HIS198
|
3.2
|
18.3
|
1.0
|
C4C
|
a:CLA603
|
3.2
|
17.1
|
1.0
|
CD2
|
a:HIS198
|
3.2
|
19.0
|
1.0
|
CHC
|
a:CLA603
|
3.4
|
17.5
|
1.0
|
CHB
|
a:CLA603
|
3.5
|
18.1
|
1.0
|
CHA
|
a:CLA603
|
3.5
|
18.6
|
1.0
|
CHD
|
a:CLA603
|
3.6
|
19.1
|
1.0
|
CE
|
a:MET183
|
4.1
|
17.2
|
1.0
|
C3D
|
a:CLA603
|
4.2
|
18.1
|
1.0
|
ND1
|
a:HIS198
|
4.3
|
18.9
|
1.0
|
CG
|
a:HIS198
|
4.4
|
19.4
|
1.0
|
C2D
|
a:CLA603
|
4.4
|
19.1
|
1.0
|
C3B
|
a:CLA603
|
4.4
|
17.2
|
1.0
|
CAB
|
d:CLA401
|
4.4
|
17.5
|
1.0
|
C2C
|
a:CLA603
|
4.4
|
15.6
|
1.0
|
C2B
|
a:CLA603
|
4.4
|
18.8
|
1.0
|
C3C
|
a:CLA603
|
4.5
|
17.1
|
1.0
|
C3A
|
a:CLA603
|
4.5
|
19.9
|
1.0
|
C2A
|
a:CLA603
|
4.5
|
18.4
|
1.0
|
CBD
|
a:CLA603
|
5.0
|
19.4
|
1.0
|
|
Magnesium binding site 5 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 5 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg604
b:21.3
occ:1.00
|
MG
|
a:CLA604
|
0.0
|
21.3
|
1.0
|
NB
|
a:CLA604
|
2.0
|
21.8
|
1.0
|
ND
|
a:CLA604
|
2.0
|
20.7
|
1.0
|
NC
|
a:CLA604
|
2.1
|
20.1
|
1.0
|
NA
|
a:CLA604
|
2.3
|
21.1
|
1.0
|
C4B
|
a:CLA604
|
3.0
|
20.9
|
1.0
|
C4D
|
a:CLA604
|
3.0
|
21.0
|
1.0
|
C1C
|
a:CLA604
|
3.0
|
20.7
|
1.0
|
C1B
|
a:CLA604
|
3.1
|
21.5
|
1.0
|
C1D
|
a:CLA604
|
3.1
|
19.7
|
1.0
|
C4C
|
a:CLA604
|
3.2
|
19.4
|
1.0
|
C4A
|
a:CLA604
|
3.2
|
20.8
|
1.0
|
C1A
|
a:CLA604
|
3.3
|
20.1
|
1.0
|
CHC
|
a:CLA604
|
3.3
|
19.5
|
1.0
|
CHB
|
a:CLA604
|
3.5
|
20.7
|
1.0
|
CHA
|
a:CLA604
|
3.5
|
20.7
|
1.0
|
CHD
|
a:CLA604
|
3.6
|
20.6
|
1.0
|
CBB
|
a:PHO606
|
3.9
|
23.2
|
1.0
|
C3D
|
a:CLA604
|
4.2
|
19.3
|
1.0
|
C3B
|
a:CLA604
|
4.3
|
21.8
|
1.0
|
C2B
|
a:CLA604
|
4.4
|
21.4
|
1.0
|
C2C
|
a:CLA604
|
4.4
|
20.4
|
1.0
|
C2D
|
a:CLA604
|
4.4
|
20.4
|
1.0
|
C3C
|
a:CLA604
|
4.4
|
21.0
|
1.0
|
CG2
|
d:ILE178
|
4.5
|
19.5
|
1.0
|
C3A
|
a:CLA604
|
4.6
|
21.1
|
1.0
|
C2A
|
a:CLA604
|
4.6
|
20.6
|
1.0
|
C20
|
a:PHO606
|
4.8
|
19.1
|
1.0
|
CG1
|
d:ILE178
|
4.8
|
19.5
|
1.0
|
CE1
|
a:PHE206
|
4.9
|
21.3
|
1.0
|
CBD
|
a:CLA604
|
5.0
|
21.1
|
1.0
|
CBA
|
a:CLA604
|
5.0
|
22.0
|
1.0
|
|
Magnesium binding site 6 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 6 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Mg607
b:24.3
occ:1.00
|
MG
|
a:CLA607
|
0.0
|
24.3
|
1.0
|
NB
|
a:CLA607
|
2.0
|
23.4
|
1.0
|
ND
|
a:CLA607
|
2.0
|
23.8
|
1.0
|
NA
|
a:CLA607
|
2.2
|
23.1
|
1.0
|
NC
|
a:CLA607
|
2.2
|
24.4
|
1.0
|
NE2
|
a:HIS118
|
2.3
|
23.2
|
1.0
|
C4D
|
a:CLA607
|
3.0
|
22.8
|
1.0
|
C1B
|
a:CLA607
|
3.0
|
23.1
|
1.0
|
C4B
|
a:CLA607
|
3.0
|
23.5
|
1.0
|
C4A
|
a:CLA607
|
3.1
|
22.8
|
1.0
|
C1A
|
a:CLA607
|
3.2
|
23.3
|
1.0
|
C1D
|
a:CLA607
|
3.2
|
21.8
|
1.0
|
C1C
|
a:CLA607
|
3.2
|
22.9
|
1.0
|
CE1
|
a:HIS118
|
3.2
|
24.8
|
1.0
|
C4C
|
a:CLA607
|
3.2
|
23.1
|
1.0
|
CD2
|
a:HIS118
|
3.3
|
23.8
|
1.0
|
CHB
|
a:CLA607
|
3.4
|
21.8
|
1.0
|
CHC
|
a:CLA607
|
3.4
|
24.1
|
1.0
|
CHA
|
a:CLA607
|
3.5
|
21.8
|
1.0
|
CHD
|
a:CLA607
|
3.6
|
21.8
|
1.0
|
C3D
|
a:CLA607
|
4.2
|
21.7
|
1.0
|
CG1
|
i:VAL8
|
4.3
|
30.8
|
1.0
|
C3B
|
a:CLA607
|
4.3
|
24.0
|
1.0
|
ND1
|
a:HIS118
|
4.3
|
23.5
|
1.0
|
C2B
|
a:CLA607
|
4.3
|
23.1
|
1.0
|
C3A
|
a:CLA607
|
4.4
|
24.2
|
1.0
|
C2D
|
a:CLA607
|
4.4
|
22.1
|
1.0
|
CG
|
a:HIS118
|
4.4
|
23.3
|
1.0
|
C2A
|
a:CLA607
|
4.5
|
24.4
|
1.0
|
CG2
|
i:VAL12
|
4.5
|
31.4
|
1.0
|
C2C
|
a:CLA607
|
4.5
|
23.4
|
1.0
|
C3C
|
a:CLA607
|
4.5
|
23.5
|
1.0
|
CMA
|
a:CLA607
|
4.9
|
23.6
|
1.0
|
CBD
|
a:CLA607
|
5.0
|
23.6
|
1.0
|
|
Magnesium binding site 7 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 7 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:36.5
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
36.5
|
1.0
|
ND
|
B:CLA602
|
2.0
|
38.0
|
1.0
|
NB
|
B:CLA602
|
2.1
|
36.1
|
1.0
|
NC
|
B:CLA602
|
2.2
|
35.6
|
1.0
|
NA
|
B:CLA602
|
2.3
|
39.0
|
1.0
|
C4D
|
B:CLA602
|
2.9
|
39.9
|
1.0
|
C4B
|
B:CLA602
|
3.1
|
35.7
|
1.0
|
C1B
|
B:CLA602
|
3.2
|
35.9
|
1.0
|
C1D
|
B:CLA602
|
3.2
|
37.9
|
1.0
|
C1C
|
B:CLA602
|
3.2
|
35.8
|
1.0
|
C1A
|
B:CLA602
|
3.2
|
41.6
|
1.0
|
C4A
|
B:CLA602
|
3.2
|
39.3
|
1.0
|
C4C
|
B:CLA602
|
3.3
|
35.5
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
35.4
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
40.8
|
1.0
|
CHB
|
B:CLA602
|
3.5
|
37.0
|
1.0
|
CHD
|
B:CLA602
|
3.6
|
36.9
|
1.0
|
C10
|
B:CLA602
|
3.9
|
66.0
|
1.0
|
O
|
B:TRP185
|
4.1
|
33.7
|
1.0
|
C3D
|
B:CLA602
|
4.2
|
39.7
|
1.0
|
CE2
|
B:PHE190
|
4.2
|
31.2
|
1.0
|
C12
|
B:CLA602
|
4.3
|
65.5
|
1.0
|
C3B
|
B:CLA602
|
4.4
|
34.8
|
1.0
|
C2D
|
B:CLA602
|
4.4
|
38.6
|
1.0
|
C2B
|
B:CLA602
|
4.5
|
34.8
|
1.0
|
CZ
|
B:PHE190
|
4.5
|
31.7
|
1.0
|
C2C
|
B:CLA602
|
4.5
|
34.6
|
1.0
|
C2A
|
B:CLA602
|
4.5
|
42.9
|
1.0
|
C3A
|
B:CLA602
|
4.5
|
41.0
|
1.0
|
C3C
|
B:CLA602
|
4.6
|
35.2
|
1.0
|
CBB
|
B:CLA603
|
4.6
|
29.6
|
1.0
|
C8
|
B:CLA602
|
4.6
|
66.3
|
1.0
|
C11
|
B:CLA602
|
4.7
|
65.6
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
42.2
|
1.0
|
|
Magnesium binding site 8 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 8 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:28.4
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
28.4
|
1.0
|
ND
|
B:CLA603
|
2.0
|
25.7
|
1.0
|
NB
|
B:CLA603
|
2.1
|
27.9
|
1.0
|
NC
|
B:CLA603
|
2.2
|
27.9
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
26.5
|
1.0
|
NA
|
B:CLA603
|
2.3
|
26.9
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
25.4
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
26.8
|
1.0
|
C4B
|
B:CLA603
|
3.1
|
28.4
|
1.0
|
C1C
|
B:CLA603
|
3.1
|
28.0
|
1.0
|
C1B
|
B:CLA603
|
3.1
|
28.0
|
1.0
|
C1D
|
B:CLA603
|
3.2
|
26.2
|
1.0
|
C4A
|
B:CLA603
|
3.2
|
27.8
|
1.0
|
C4C
|
B:CLA603
|
3.2
|
27.2
|
1.0
|
C1A
|
B:CLA603
|
3.2
|
26.9
|
1.0
|
CG
|
B:HIS201
|
3.3
|
25.7
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
27.9
|
1.0
|
CHB
|
B:CLA603
|
3.5
|
27.2
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
25.1
|
1.0
|
CHD
|
B:CLA603
|
3.6
|
26.2
|
1.0
|
CB
|
B:HIS201
|
3.8
|
26.2
|
1.0
|
CZ
|
H:PHE41
|
3.8
|
29.6
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
27.7
|
1.0
|
C3D
|
B:CLA603
|
4.2
|
25.9
|
1.0
|
CE2
|
H:PHE41
|
4.3
|
27.8
|
1.0
|
CA
|
B:HIS201
|
4.3
|
26.3
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
25.4
|
1.0
|
C3B
|
B:CLA603
|
4.4
|
28.2
|
1.0
|
C2D
|
B:CLA603
|
4.4
|
25.8
|
1.0
|
C2C
|
B:CLA603
|
4.5
|
27.8
|
1.0
|
C2B
|
B:CLA603
|
4.5
|
28.4
|
1.0
|
C3A
|
B:CLA603
|
4.5
|
26.5
|
1.0
|
C3C
|
B:CLA603
|
4.5
|
27.0
|
1.0
|
C2A
|
B:CLA603
|
4.5
|
26.5
|
1.0
|
CE1
|
H:PHE41
|
4.9
|
28.0
|
1.0
|
CBD
|
B:CLA603
|
5.0
|
25.3
|
1.0
|
O
|
B:HIS201
|
5.0
|
26.7
|
1.0
|
|
Magnesium binding site 9 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 9 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:24.1
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
24.1
|
1.0
|
ND
|
B:CLA604
|
2.0
|
23.5
|
1.0
|
NB
|
B:CLA604
|
2.0
|
22.0
|
1.0
|
NC
|
B:CLA604
|
2.1
|
22.6
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
24.7
|
1.0
|
NA
|
B:CLA604
|
2.3
|
22.8
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
21.7
|
1.0
|
C4B
|
B:CLA604
|
3.0
|
21.5
|
1.0
|
C1B
|
B:CLA604
|
3.1
|
21.4
|
1.0
|
CD2
|
B:HIS202
|
3.1
|
26.2
|
1.0
|
C1C
|
B:CLA604
|
3.1
|
21.5
|
1.0
|
C1D
|
B:CLA604
|
3.1
|
22.6
|
1.0
|
C4C
|
B:CLA604
|
3.2
|
21.5
|
1.0
|
C4A
|
B:CLA604
|
3.2
|
22.7
|
1.0
|
C1A
|
B:CLA604
|
3.2
|
22.5
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
26.5
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
21.2
|
1.0
|
CHB
|
B:CLA604
|
3.5
|
22.0
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
21.9
|
1.0
|
CHD
|
B:CLA604
|
3.5
|
22.3
|
1.0
|
C3D
|
B:CLA604
|
4.2
|
22.0
|
1.0
|
CG
|
B:HIS202
|
4.3
|
25.7
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
25.8
|
1.0
|
C3B
|
B:CLA604
|
4.4
|
20.8
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
20.6
|
1.0
|
C2D
|
B:CLA604
|
4.4
|
22.9
|
1.0
|
C2C
|
B:CLA604
|
4.5
|
20.9
|
1.0
|
C3C
|
B:CLA604
|
4.5
|
21.4
|
1.0
|
C3A
|
B:CLA604
|
4.5
|
23.2
|
1.0
|
C2A
|
B:CLA604
|
4.5
|
22.9
|
1.0
|
C6
|
B:CLA606
|
4.6
|
31.5
|
1.0
|
C4
|
B:CLA606
|
4.6
|
31.6
|
1.0
|
NE2
|
B:HIS201
|
4.7
|
27.7
|
1.0
|
CD2
|
B:HIS201
|
4.7
|
25.4
|
1.0
|
C7
|
B:CLA606
|
4.8
|
32.4
|
1.0
|
C5
|
B:CLA606
|
4.9
|
30.8
|
1.0
|
CBA
|
B:CLA604
|
5.0
|
22.2
|
1.0
|
|
Magnesium binding site 10 out
of 72 in 4rvy
Go back to
Magnesium Binding Sites List in 4rvy
Magnesium binding site 10 out
of 72 in the Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Serial Time Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. the S State After Two Flashes (S3) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:22.4
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
22.4
|
1.0
|
NB
|
B:CLA605
|
2.0
|
22.6
|
1.0
|
ND
|
B:CLA605
|
2.1
|
21.9
|
1.0
|
NC
|
B:CLA605
|
2.1
|
21.8
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
18.4
|
1.0
|
NA
|
B:CLA605
|
2.3
|
22.1
|
1.0
|
C4B
|
B:CLA605
|
3.0
|
21.6
|
1.0
|
CD2
|
B:HIS455
|
3.0
|
18.5
|
1.0
|
C4D
|
B:CLA605
|
3.1
|
21.9
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
21.9
|
1.0
|
C1B
|
B:CLA605
|
3.1
|
21.0
|
1.0
|
C1D
|
B:CLA605
|
3.2
|
21.5
|
1.0
|
C4C
|
B:CLA605
|
3.2
|
21.9
|
1.0
|
C4A
|
B:CLA605
|
3.2
|
21.4
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
18.1
|
1.0
|
C1A
|
B:CLA605
|
3.3
|
21.8
|
1.0
|
CHC
|
B:CLA605
|
3.3
|
21.6
|
1.0
|
CHB
|
B:CLA605
|
3.5
|
21.1
|
1.0
|
CHD
|
B:CLA605
|
3.6
|
20.8
|
1.0
|
CHA
|
B:CLA605
|
3.6
|
21.7
|
1.0
|
CG
|
B:HIS455
|
4.2
|
18.4
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
21.1
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
19.1
|
1.0
|
C14
|
B:CLA613
|
4.3
|
30.4
|
1.0
|
C3B
|
B:CLA605
|
4.3
|
22.6
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
22.2
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
21.5
|
1.0
|
C2D
|
B:CLA605
|
4.5
|
23.1
|
1.0
|
C3C
|
B:CLA605
|
4.5
|
21.1
|
1.0
|
C3A
|
B:CLA605
|
4.6
|
22.6
|
1.0
|
C2A
|
B:CLA605
|
4.6
|
22.3
|
1.0
|
C13
|
B:CLA613
|
4.9
|
31.2
|
1.0
|
C15
|
B:CLA613
|
4.9
|
30.3
|
1.0
|
|
Reference:
C.Kupitz,
S.Basu,
I.Grotjohann,
R.Fromme,
N.A.Zatsepin,
K.N.Rendek,
M.S.Hunter,
R.L.Shoeman,
T.A.White,
D.Wang,
D.James,
J.H.Yang,
D.E.Cobb,
B.Reeder,
R.G.Sierra,
H.Liu,
A.Barty,
A.L.Aquila,
D.Deponte,
R.A.Kirian,
S.Bari,
J.J.Bergkamp,
K.R.Beyerlein,
M.J.Bogan,
C.Caleman,
T.C.Chao,
C.E.Conrad,
K.M.Davis,
H.Fleckenstein,
L.Galli,
S.P.Hau-Riege,
S.Kassemeyer,
H.Laksmono,
M.Liang,
L.Lomb,
S.Marchesini,
A.V.Martin,
M.Messerschmidt,
D.Milathianaki,
K.Nass,
A.Ros,
S.Roy-Chowdhury,
K.Schmidt,
M.Seibert,
J.Steinbrener,
F.Stellato,
L.Yan,
C.Yoon,
T.A.Moore,
A.L.Moore,
Y.Pushkar,
G.J.Williams,
S.Boutet,
R.B.Doak,
U.Weierstall,
M.Frank,
H.N.Chapman,
J.C.Spence,
P.Fromme.
Serial Time-Resolved Crystallography of Photosystem II Using A Femtosecond X-Ray Laser. Nature V. 513 261 2014.
ISSN: ISSN 0028-0836
PubMed: 25043005
DOI: 10.1038/NATURE13453
Page generated: Tue Aug 20 03:31:24 2024
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