Chlorine in PDB 8ird: Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay:
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay, PDB code: 8ird
was solved by
H.Li,
M.Suga,
J.R.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.99 /
2.30
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.77,
231.76,
288.58,
90,
90,
90
|
|
R / Rfree (%)
|
13.9 /
17.9
|
Other elements in 8ird:
The structure of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
(pdb code 8ird). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the
Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay, PDB code: 8ird:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Chlorine binding site 1 out
of 8 in 8ird
Go back to
Chlorine Binding Sites List in 8ird
Chlorine binding site 1 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl402
b:43.1
occ:0.49
|
CL
|
A:CL402
|
0.0
|
43.1
|
0.5
|
|
CL
|
A:CL402
|
0.1
|
43.0
|
0.5
|
|
NZ
|
D:LYS317
|
3.0
|
42.8
|
0.5
|
|
O
|
D:HOH551
|
3.0
|
42.2
|
0.5
|
|
O
|
D:HOH551
|
3.1
|
42.3
|
0.5
|
|
NZ
|
D:LYS317
|
3.1
|
42.8
|
0.5
|
|
O
|
A:HOH536
|
3.2
|
45.1
|
0.5
|
|
N
|
A:GLU333
|
3.3
|
38.9
|
0.5
|
|
O
|
A:HOH536
|
3.4
|
45.5
|
0.5
|
|
ND2
|
A:ASN181
|
3.4
|
39.0
|
0.5
|
|
N
|
A:GLU333
|
3.4
|
38.9
|
0.5
|
|
ND2
|
A:ASN181
|
3.4
|
38.8
|
0.5
|
|
CE
|
D:LYS317
|
3.7
|
44.5
|
0.5
|
|
CE
|
D:LYS317
|
3.8
|
44.5
|
0.5
|
|
CA
|
A:HIS332
|
3.8
|
40.5
|
0.5
|
|
CB
|
A:HIS332
|
3.8
|
40.8
|
0.5
|
|
CA
|
A:HIS332
|
3.9
|
40.6
|
0.5
|
|
CG
|
A:GLU333
|
3.9
|
44.7
|
0.5
|
|
CG
|
A:GLU333
|
3.9
|
44.7
|
0.5
|
|
CB
|
A:HIS332
|
4.0
|
40.6
|
0.5
|
|
C
|
A:HIS332
|
4.0
|
42.6
|
0.5
|
|
OD1
|
A:ASN181
|
4.1
|
41.8
|
0.5
|
|
OD1
|
A:ASN181
|
4.1
|
41.8
|
0.5
|
|
O
|
D:HOH510
|
4.1
|
42.1
|
0.5
|
|
C
|
A:HIS332
|
4.1
|
42.7
|
0.5
|
|
CG
|
A:ASN181
|
4.2
|
45.4
|
0.5
|
|
CG
|
A:ASN181
|
4.2
|
45.5
|
0.5
|
|
O
|
D:HOH510
|
4.2
|
41.9
|
0.5
|
|
CA
|
A:GLU333
|
4.3
|
43.0
|
0.5
|
|
CA
|
A:GLU333
|
4.3
|
42.8
|
0.5
|
|
CG2
|
A:VAL185
|
4.3
|
37.8
|
0.5
|
|
O
|
A:HOH573
|
4.3
|
48.5
|
0.5
|
|
CD1
|
D:LEU321
|
4.4
|
44.1
|
0.5
|
|
CD1
|
D:LEU321
|
4.4
|
44.0
|
0.5
|
|
O
|
A:HOH573
|
4.4
|
48.3
|
0.5
|
|
CG2
|
A:VAL185
|
4.4
|
37.9
|
0.5
|
|
CB
|
D:LYS317
|
4.4
|
41.9
|
0.5
|
|
CB
|
D:LYS317
|
4.5
|
41.9
|
0.5
|
|
CD2
|
D:LEU321
|
4.5
|
39.9
|
0.5
|
|
CD2
|
D:LEU321
|
4.6
|
39.5
|
0.5
|
|
CG
|
D:LYS317
|
4.7
|
41.0
|
0.5
|
|
CB
|
A:GLU333
|
4.7
|
41.2
|
0.5
|
|
CB
|
A:GLU333
|
4.7
|
41.0
|
0.5
|
|
CG
|
D:LEU321
|
4.8
|
42.6
|
0.5
|
|
CD
|
D:LYS317
|
4.8
|
43.8
|
0.5
|
|
CG
|
D:LEU321
|
4.8
|
42.3
|
0.5
|
|
CG
|
A:HIS332
|
4.8
|
47.7
|
0.5
|
|
CG
|
D:LYS317
|
4.8
|
40.8
|
0.5
|
|
O
|
D:LYS317
|
4.9
|
40.8
|
0.5
|
|
CD
|
D:LYS317
|
4.9
|
43.8
|
0.5
|
|
CD
|
A:GLU333
|
4.9
|
43.8
|
0.5
|
|
O
|
D:LYS317
|
4.9
|
40.8
|
0.5
|
|
OE2
|
A:GLU333
|
5.0
|
45.7
|
0.5
|
|
CG
|
A:HIS332
|
5.0
|
47.8
|
0.5
|
|
CD
|
A:GLU333
|
5.0
|
43.9
|
0.5
|
|
CD2
|
A:HIS332
|
5.0
|
40.3
|
0.5
|
|
Chlorine binding site 2 out
of 8 in 8ird
Go back to
Chlorine Binding Sites List in 8ird
Chlorine binding site 2 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl402
b:43.0
occ:0.51
|
CL
|
A:CL402
|
0.0
|
43.0
|
0.5
|
|
CL
|
A:CL402
|
0.1
|
43.1
|
0.5
|
|
NZ
|
D:LYS317
|
3.1
|
42.8
|
0.5
|
|
O
|
D:HOH551
|
3.1
|
42.2
|
0.5
|
|
O
|
D:HOH551
|
3.1
|
42.3
|
0.5
|
|
O
|
A:HOH536
|
3.2
|
45.1
|
0.5
|
|
NZ
|
D:LYS317
|
3.2
|
42.8
|
0.5
|
|
O
|
A:HOH536
|
3.3
|
45.5
|
0.5
|
|
N
|
A:GLU333
|
3.3
|
38.9
|
0.5
|
|
ND2
|
A:ASN181
|
3.4
|
39.0
|
0.5
|
|
ND2
|
A:ASN181
|
3.4
|
38.8
|
0.5
|
|
N
|
A:GLU333
|
3.4
|
38.9
|
0.5
|
|
CB
|
A:HIS332
|
3.7
|
40.8
|
0.5
|
|
CA
|
A:HIS332
|
3.7
|
40.5
|
0.5
|
|
CE
|
D:LYS317
|
3.8
|
44.5
|
0.5
|
|
CA
|
A:HIS332
|
3.8
|
40.6
|
0.5
|
|
CE
|
D:LYS317
|
3.9
|
44.5
|
0.5
|
|
CB
|
A:HIS332
|
3.9
|
40.6
|
0.5
|
|
CG
|
A:GLU333
|
3.9
|
44.7
|
0.5
|
|
CG
|
A:GLU333
|
3.9
|
44.7
|
0.5
|
|
C
|
A:HIS332
|
4.0
|
42.6
|
0.5
|
|
OD1
|
A:ASN181
|
4.0
|
41.8
|
0.5
|
|
OD1
|
A:ASN181
|
4.1
|
41.8
|
0.5
|
|
C
|
A:HIS332
|
4.1
|
42.7
|
0.5
|
|
CG
|
A:ASN181
|
4.2
|
45.4
|
0.5
|
|
CG
|
A:ASN181
|
4.2
|
45.5
|
0.5
|
|
O
|
D:HOH510
|
4.2
|
42.1
|
0.5
|
|
CG2
|
A:VAL185
|
4.2
|
37.8
|
0.5
|
|
O
|
D:HOH510
|
4.3
|
41.9
|
0.5
|
|
CA
|
A:GLU333
|
4.3
|
43.0
|
0.5
|
|
CA
|
A:GLU333
|
4.3
|
42.8
|
0.5
|
|
CG2
|
A:VAL185
|
4.3
|
37.9
|
0.5
|
|
CD1
|
D:LEU321
|
4.4
|
44.1
|
0.5
|
|
CD1
|
D:LEU321
|
4.4
|
44.0
|
0.5
|
|
O
|
A:HOH573
|
4.4
|
48.5
|
0.5
|
|
CD2
|
D:LEU321
|
4.4
|
39.9
|
0.5
|
|
O
|
A:HOH573
|
4.5
|
48.3
|
0.5
|
|
CB
|
D:LYS317
|
4.5
|
41.9
|
0.5
|
|
CD2
|
D:LEU321
|
4.5
|
39.5
|
0.5
|
|
CB
|
D:LYS317
|
4.5
|
41.9
|
0.5
|
|
CB
|
A:GLU333
|
4.7
|
41.2
|
0.5
|
|
CG
|
A:HIS332
|
4.7
|
47.7
|
0.5
|
|
CG
|
D:LEU321
|
4.7
|
42.6
|
0.5
|
|
CB
|
A:GLU333
|
4.7
|
41.0
|
0.5
|
|
CG
|
D:LEU321
|
4.7
|
42.3
|
0.5
|
|
CG
|
D:LYS317
|
4.8
|
41.0
|
0.5
|
|
CD
|
D:LYS317
|
4.9
|
43.8
|
0.5
|
|
CG
|
A:HIS332
|
4.9
|
47.8
|
0.5
|
|
CG
|
D:LYS317
|
4.9
|
40.8
|
0.5
|
|
CD
|
A:GLU333
|
4.9
|
43.8
|
0.5
|
|
CD2
|
A:HIS332
|
4.9
|
40.3
|
0.5
|
|
OE2
|
A:GLU333
|
4.9
|
45.7
|
0.5
|
|
O
|
D:LYS317
|
4.9
|
40.8
|
0.5
|
|
CD
|
A:GLU333
|
5.0
|
43.9
|
0.5
|
|
O
|
D:LYS317
|
5.0
|
40.8
|
0.5
|
|
Chlorine binding site 3 out
of 8 in 8ird
Go back to
Chlorine Binding Sites List in 8ird
Chlorine binding site 3 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl403
b:46.6
occ:0.49
|
CL
|
A:CL403
|
0.0
|
46.6
|
0.5
|
|
CL
|
A:CL403
|
0.1
|
46.5
|
0.5
|
|
O
|
C:HOH701
|
2.9
|
45.2
|
0.5
|
|
O
|
C:HOH701
|
3.1
|
45.2
|
0.5
|
|
N
|
A:ASN338
|
3.1
|
45.2
|
0.5
|
|
N
|
A:ASN338
|
3.1
|
45.3
|
0.5
|
|
O
|
A:HOH588
|
3.2
|
48.6
|
0.5
|
|
O
|
A:HOH588
|
3.2
|
47.3
|
0.5
|
|
N
|
C:GLU354
|
3.3
|
44.4
|
0.5
|
|
N
|
C:GLU354
|
3.3
|
44.5
|
0.5
|
|
CA
|
A:HIS337
|
3.6
|
45.3
|
0.5
|
|
N
|
A:PHE339
|
3.6
|
45.7
|
0.5
|
|
CA
|
A:HIS337
|
3.7
|
45.4
|
0.5
|
|
N
|
A:PHE339
|
3.7
|
45.6
|
0.5
|
|
CA
|
C:GLY353
|
3.7
|
43.5
|
0.5
|
|
CD2
|
A:PHE339
|
3.8
|
48.5
|
0.5
|
|
CA
|
C:GLY353
|
3.8
|
43.5
|
0.5
|
|
CD2
|
A:PHE339
|
3.8
|
48.4
|
0.5
|
|
C
|
A:HIS337
|
3.8
|
49.7
|
0.5
|
|
C
|
A:HIS337
|
3.9
|
49.6
|
0.5
|
|
C
|
C:GLY353
|
4.0
|
50.5
|
0.5
|
|
C
|
C:GLY353
|
4.1
|
50.5
|
0.5
|
|
CA
|
A:ASN338
|
4.1
|
44.3
|
0.5
|
|
CA
|
A:ASN338
|
4.1
|
44.4
|
0.5
|
|
CB
|
A:HIS337
|
4.1
|
41.6
|
0.5
|
|
CB
|
C:GLU354
|
4.2
|
40.6
|
0.5
|
|
CB
|
C:GLU354
|
4.2
|
40.7
|
0.5
|
|
O
|
A:ALA336
|
4.2
|
49.8
|
0.5
|
|
CB
|
A:HIS337
|
4.2
|
41.9
|
0.5
|
|
O
|
A:ALA336
|
4.2
|
48.9
|
0.5
|
|
CA
|
C:GLU354
|
4.3
|
46.4
|
0.5
|
|
CB
|
A:PHE339
|
4.3
|
44.7
|
0.5
|
|
CA
|
C:GLU354
|
4.3
|
46.4
|
0.5
|
|
C
|
A:ASN338
|
4.3
|
48.7
|
0.5
|
|
C
|
A:ASN338
|
4.3
|
48.7
|
0.5
|
|
CB
|
A:ASN338
|
4.4
|
45.7
|
0.5
|
|
CB
|
A:ASN338
|
4.4
|
45.7
|
0.5
|
|
CB
|
A:PHE339
|
4.4
|
44.6
|
0.5
|
|
O
|
C:HOH690
|
4.4
|
44.2
|
0.5
|
|
CG
|
A:PHE339
|
4.4
|
51.0
|
0.5
|
|
CG
|
A:PHE339
|
4.4
|
51.0
|
0.5
|
|
CA
|
A:PHE339
|
4.5
|
47.3
|
0.5
|
|
O
|
A:PHE339
|
4.5
|
47.0
|
0.5
|
|
O
|
C:HOH690
|
4.5
|
43.9
|
0.5
|
|
O
|
C:HOH733
|
4.5
|
49.0
|
0.5
|
|
O
|
A:PHE339
|
4.5
|
47.0
|
0.5
|
|
CE2
|
A:PHE339
|
4.6
|
44.0
|
0.5
|
|
CA
|
A:PHE339
|
4.6
|
47.3
|
0.5
|
|
CE2
|
A:PHE339
|
4.7
|
43.8
|
0.5
|
|
O
|
C:HOH733
|
4.7
|
49.3
|
0.5
|
|
N
|
A:HIS337
|
4.7
|
42.5
|
0.5
|
|
N
|
C:THR355
|
4.8
|
40.0
|
0.5
|
|
N
|
A:HIS337
|
4.8
|
42.5
|
0.5
|
|
N
|
C:THR355
|
4.8
|
40.1
|
0.5
|
|
CD2
|
A:HIS337
|
4.8
|
46.2
|
0.5
|
|
CD2
|
A:HIS337
|
4.8
|
46.2
|
0.5
|
|
O
|
C:GLY352
|
4.9
|
47.5
|
0.5
|
|
CG
|
A:HIS337
|
4.9
|
46.4
|
0.5
|
|
CG
|
A:HIS337
|
4.9
|
46.5
|
0.5
|
|
C
|
A:ALA336
|
4.9
|
44.7
|
0.5
|
|
C
|
A:PHE339
|
5.0
|
46.9
|
0.5
|
|
NE2
|
C:GLN313
|
5.0
|
43.4
|
0.5
|
|
N
|
C:GLY353
|
5.0
|
48.3
|
0.5
|
|
CG
|
A:ASN338
|
5.0
|
48.0
|
0.5
|
|
CG
|
A:ASN338
|
5.0
|
48.0
|
0.5
|
|
C
|
A:ALA336
|
5.0
|
44.7
|
0.5
|
|
O
|
C:GLY352
|
5.0
|
47.8
|
0.5
|
|
Chlorine binding site 4 out
of 8 in 8ird
Go back to
Chlorine Binding Sites List in 8ird
Chlorine binding site 4 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl403
b:46.5
occ:0.51
|
CL
|
A:CL403
|
0.0
|
46.5
|
0.5
|
|
CL
|
A:CL403
|
0.1
|
46.6
|
0.5
|
|
O
|
C:HOH701
|
3.0
|
45.2
|
0.5
|
|
N
|
A:ASN338
|
3.1
|
45.2
|
0.5
|
|
O
|
C:HOH701
|
3.1
|
45.2
|
0.5
|
|
O
|
A:HOH588
|
3.1
|
48.6
|
0.5
|
|
N
|
A:ASN338
|
3.1
|
45.3
|
0.5
|
|
O
|
A:HOH588
|
3.2
|
47.3
|
0.5
|
|
N
|
C:GLU354
|
3.3
|
44.4
|
0.5
|
|
N
|
C:GLU354
|
3.3
|
44.5
|
0.5
|
|
CA
|
A:HIS337
|
3.6
|
45.3
|
0.5
|
|
N
|
A:PHE339
|
3.6
|
45.7
|
0.5
|
|
CA
|
A:HIS337
|
3.6
|
45.4
|
0.5
|
|
N
|
A:PHE339
|
3.7
|
45.6
|
0.5
|
|
CA
|
C:GLY353
|
3.8
|
43.5
|
0.5
|
|
C
|
A:HIS337
|
3.8
|
49.7
|
0.5
|
|
CD2
|
A:PHE339
|
3.9
|
48.5
|
0.5
|
|
CA
|
C:GLY353
|
3.9
|
43.5
|
0.5
|
|
CD2
|
A:PHE339
|
3.9
|
48.4
|
0.5
|
|
C
|
A:HIS337
|
3.9
|
49.6
|
0.5
|
|
C
|
C:GLY353
|
4.0
|
50.5
|
0.5
|
|
CA
|
A:ASN338
|
4.1
|
44.3
|
0.5
|
|
CB
|
A:HIS337
|
4.1
|
41.6
|
0.5
|
|
C
|
C:GLY353
|
4.1
|
50.5
|
0.5
|
|
CA
|
A:ASN338
|
4.1
|
44.4
|
0.5
|
|
CB
|
C:GLU354
|
4.1
|
40.6
|
0.5
|
|
CB
|
A:HIS337
|
4.2
|
41.9
|
0.5
|
|
CB
|
C:GLU354
|
4.2
|
40.7
|
0.5
|
|
O
|
A:ALA336
|
4.2
|
49.8
|
0.5
|
|
O
|
A:ALA336
|
4.2
|
48.9
|
0.5
|
|
CA
|
C:GLU354
|
4.3
|
46.4
|
0.5
|
|
CB
|
A:PHE339
|
4.3
|
44.7
|
0.5
|
|
CA
|
C:GLU354
|
4.3
|
46.4
|
0.5
|
|
C
|
A:ASN338
|
4.3
|
48.7
|
0.5
|
|
C
|
A:ASN338
|
4.4
|
48.7
|
0.5
|
|
CB
|
A:ASN338
|
4.4
|
45.7
|
0.5
|
|
CB
|
A:PHE339
|
4.4
|
44.6
|
0.5
|
|
CB
|
A:ASN338
|
4.4
|
45.7
|
0.5
|
|
O
|
C:HOH690
|
4.4
|
44.2
|
0.5
|
|
CG
|
A:PHE339
|
4.5
|
51.0
|
0.5
|
|
CG
|
A:PHE339
|
4.5
|
51.0
|
0.5
|
|
O
|
A:PHE339
|
4.5
|
47.0
|
0.5
|
|
CA
|
A:PHE339
|
4.5
|
47.3
|
0.5
|
|
O
|
C:HOH733
|
4.5
|
49.0
|
0.5
|
|
O
|
A:PHE339
|
4.5
|
47.0
|
0.5
|
|
O
|
C:HOH690
|
4.6
|
43.9
|
0.5
|
|
CA
|
A:PHE339
|
4.6
|
47.3
|
0.5
|
|
CE2
|
A:PHE339
|
4.6
|
44.0
|
0.5
|
|
O
|
C:HOH733
|
4.7
|
49.3
|
0.5
|
|
N
|
A:HIS337
|
4.7
|
42.5
|
0.5
|
|
CE2
|
A:PHE339
|
4.7
|
43.8
|
0.5
|
|
CD2
|
A:HIS337
|
4.8
|
46.2
|
0.5
|
|
N
|
A:HIS337
|
4.8
|
42.5
|
0.5
|
|
CD2
|
A:HIS337
|
4.8
|
46.2
|
0.5
|
|
N
|
C:THR355
|
4.8
|
40.0
|
0.5
|
|
CG
|
A:HIS337
|
4.8
|
46.4
|
0.5
|
|
N
|
C:THR355
|
4.8
|
40.1
|
0.5
|
|
CG
|
A:HIS337
|
4.8
|
46.5
|
0.5
|
|
C
|
A:ALA336
|
4.9
|
44.7
|
0.5
|
|
O
|
C:GLY352
|
4.9
|
47.5
|
0.5
|
|
C
|
A:PHE339
|
4.9
|
46.9
|
0.5
|
|
NE2
|
C:GLN313
|
4.9
|
43.4
|
0.5
|
|
C
|
A:ALA336
|
4.9
|
44.7
|
0.5
|
|
C
|
A:PHE339
|
5.0
|
46.9
|
0.5
|
|
CG
|
A:ASN338
|
5.0
|
48.0
|
0.5
|
|
CG
|
A:ASN338
|
5.0
|
48.0
|
0.5
|
|
Chlorine binding site 5 out
of 8 in 8ird
Go back to
Chlorine Binding Sites List in 8ird
Chlorine binding site 5 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Cl402
b:49.5
occ:0.49
|
CL
|
a:CL402
|
0.0
|
49.5
|
0.5
|
|
CL
|
a:CL402
|
0.2
|
48.5
|
0.5
|
|
O
|
d:HOH564
|
3.1
|
53.3
|
0.5
|
|
NZ
|
d:LYS317
|
3.1
|
46.4
|
0.5
|
|
NZ
|
d:LYS317
|
3.2
|
46.2
|
0.5
|
|
O
|
d:HOH564
|
3.2
|
53.4
|
0.5
|
|
N
|
a:GLU333
|
3.3
|
43.1
|
0.5
|
|
O
|
a:HOH561
|
3.3
|
47.8
|
0.5
|
|
O
|
a:HOH561
|
3.3
|
47.9
|
0.5
|
|
N
|
a:GLU333
|
3.3
|
43.3
|
0.5
|
|
ND2
|
a:ASN181
|
3.4
|
44.4
|
0.5
|
|
ND2
|
a:ASN181
|
3.5
|
44.4
|
0.5
|
|
CG
|
a:GLU333
|
3.7
|
46.5
|
0.5
|
|
CA
|
a:HIS332
|
3.8
|
47.0
|
0.5
|
|
CB
|
a:HIS332
|
3.8
|
48.9
|
0.5
|
|
CA
|
a:HIS332
|
3.8
|
47.0
|
0.5
|
|
CB
|
a:HIS332
|
3.8
|
48.9
|
0.5
|
|
CE
|
d:LYS317
|
3.8
|
45.8
|
0.5
|
|
CG
|
a:GLU333
|
3.9
|
46.6
|
0.5
|
|
CE
|
d:LYS317
|
3.9
|
45.9
|
0.5
|
|
C
|
a:HIS332
|
4.0
|
45.0
|
0.5
|
|
C
|
a:HIS332
|
4.0
|
45.0
|
0.5
|
|
OD1
|
a:ASN181
|
4.1
|
48.7
|
0.5
|
|
OD1
|
a:ASN181
|
4.1
|
48.7
|
0.5
|
|
CG2
|
a:VAL185
|
4.2
|
43.1
|
0.5
|
|
CG2
|
a:VAL185
|
4.2
|
43.1
|
0.5
|
|
CA
|
a:GLU333
|
4.2
|
48.5
|
0.5
|
|
CG
|
a:ASN181
|
4.2
|
48.7
|
0.5
|
|
CG
|
a:ASN181
|
4.2
|
48.7
|
0.5
|
|
O
|
d:HOH524
|
4.3
|
48.1
|
0.5
|
|
CA
|
a:GLU333
|
4.3
|
48.6
|
0.5
|
|
O
|
d:HOH524
|
4.3
|
47.8
|
0.5
|
|
CD1
|
d:LEU321
|
4.4
|
42.7
|
0.5
|
|
O
|
a:HOH571
|
4.4
|
52.0
|
0.5
|
|
CD2
|
d:LEU321
|
4.5
|
44.1
|
0.5
|
|
O
|
a:HOH571
|
4.5
|
52.1
|
0.5
|
|
CD2
|
d:LEU321
|
4.5
|
44.2
|
0.5
|
|
CB
|
a:GLU333
|
4.6
|
47.8
|
0.5
|
|
CB
|
d:LYS317
|
4.6
|
44.2
|
0.5
|
|
CD1
|
d:LEU321
|
4.6
|
42.6
|
0.5
|
|
CB
|
d:LYS317
|
4.6
|
44.1
|
0.5
|
|
CG
|
a:HIS332
|
4.7
|
49.1
|
0.5
|
|
CB
|
a:GLU333
|
4.7
|
47.8
|
0.5
|
|
CG
|
a:HIS332
|
4.7
|
49.1
|
0.5
|
|
CG
|
d:LEU321
|
4.7
|
49.6
|
0.5
|
|
CD
|
a:GLU333
|
4.7
|
51.1
|
0.5
|
|
CD2
|
a:HIS332
|
4.8
|
46.7
|
0.5
|
|
CG
|
d:LEU321
|
4.8
|
49.6
|
0.5
|
|
CG
|
d:LYS317
|
4.8
|
42.5
|
0.5
|
|
OE2
|
a:GLU333
|
4.8
|
50.8
|
0.5
|
|
CD2
|
a:HIS332
|
4.9
|
46.7
|
0.5
|
|
CD
|
a:GLU333
|
4.9
|
51.2
|
0.5
|
|
OE2
|
a:GLU333
|
4.9
|
50.6
|
0.5
|
|
CD
|
d:LYS317
|
4.9
|
44.3
|
0.5
|
|
O
|
d:LYS317
|
4.9
|
46.4
|
0.5
|
|
CG
|
d:LYS317
|
5.0
|
42.2
|
0.5
|
|
Chlorine binding site 6 out
of 8 in 8ird
Go back to
Chlorine Binding Sites List in 8ird
Chlorine binding site 6 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Cl402
b:48.5
occ:0.51
|
CL
|
a:CL402
|
0.0
|
48.5
|
0.5
|
|
CL
|
a:CL402
|
0.2
|
49.5
|
0.5
|
|
O
|
d:HOH564
|
3.0
|
53.3
|
0.5
|
|
O
|
d:HOH564
|
3.1
|
53.4
|
0.5
|
|
NZ
|
d:LYS317
|
3.1
|
46.4
|
0.5
|
|
NZ
|
d:LYS317
|
3.1
|
46.2
|
0.5
|
|
ND2
|
a:ASN181
|
3.2
|
44.4
|
0.5
|
|
ND2
|
a:ASN181
|
3.3
|
44.4
|
0.5
|
|
O
|
a:HOH561
|
3.4
|
47.8
|
0.5
|
|
O
|
a:HOH561
|
3.4
|
47.9
|
0.5
|
|
N
|
a:GLU333
|
3.4
|
43.1
|
0.5
|
|
N
|
a:GLU333
|
3.5
|
43.3
|
0.5
|
|
CE
|
d:LYS317
|
3.8
|
45.8
|
0.5
|
|
CE
|
d:LYS317
|
3.8
|
45.9
|
0.5
|
|
CA
|
a:HIS332
|
3.8
|
47.0
|
0.5
|
|
CA
|
a:HIS332
|
3.9
|
47.0
|
0.5
|
|
CB
|
a:HIS332
|
3.9
|
48.9
|
0.5
|
|
CB
|
a:HIS332
|
3.9
|
48.9
|
0.5
|
|
CG
|
a:GLU333
|
3.9
|
46.5
|
0.5
|
|
OD1
|
a:ASN181
|
4.1
|
48.7
|
0.5
|
|
OD1
|
a:ASN181
|
4.1
|
48.7
|
0.5
|
|
CG
|
a:GLU333
|
4.1
|
46.6
|
0.5
|
|
CG
|
a:ASN181
|
4.1
|
48.7
|
0.5
|
|
C
|
a:HIS332
|
4.1
|
45.0
|
0.5
|
|
CG
|
a:ASN181
|
4.1
|
48.7
|
0.5
|
|
C
|
a:HIS332
|
4.2
|
45.0
|
0.5
|
|
CG2
|
a:VAL185
|
4.2
|
43.1
|
0.5
|
|
CG2
|
a:VAL185
|
4.2
|
43.1
|
0.5
|
|
CD1
|
d:LEU321
|
4.3
|
42.7
|
0.5
|
|
O
|
d:HOH524
|
4.3
|
48.1
|
0.5
|
|
CA
|
a:GLU333
|
4.3
|
48.5
|
0.5
|
|
O
|
d:HOH524
|
4.3
|
47.8
|
0.5
|
|
CD2
|
d:LEU321
|
4.4
|
44.1
|
0.5
|
|
CB
|
d:LYS317
|
4.4
|
44.2
|
0.5
|
|
CA
|
a:GLU333
|
4.4
|
48.6
|
0.5
|
|
O
|
a:HOH571
|
4.4
|
52.0
|
0.5
|
|
CD2
|
d:LEU321
|
4.4
|
44.2
|
0.5
|
|
CB
|
d:LYS317
|
4.5
|
44.1
|
0.5
|
|
O
|
a:HOH571
|
4.5
|
52.1
|
0.5
|
|
CD1
|
d:LEU321
|
4.5
|
42.6
|
0.5
|
|
CG
|
d:LEU321
|
4.6
|
49.6
|
0.5
|
|
CG
|
d:LYS317
|
4.7
|
42.5
|
0.5
|
|
CG
|
d:LEU321
|
4.7
|
49.6
|
0.5
|
|
CB
|
a:GLU333
|
4.7
|
47.8
|
0.5
|
|
O
|
d:LYS317
|
4.8
|
46.4
|
0.5
|
|
CG
|
a:HIS332
|
4.8
|
49.1
|
0.5
|
|
CD
|
d:LYS317
|
4.8
|
44.3
|
0.5
|
|
CG
|
a:HIS332
|
4.8
|
49.1
|
0.5
|
|
CB
|
a:GLU333
|
4.9
|
47.8
|
0.5
|
|
CG
|
d:LYS317
|
4.9
|
42.2
|
0.5
|
|
O
|
d:LYS317
|
4.9
|
46.4
|
0.5
|
|
CD
|
a:GLU333
|
4.9
|
51.1
|
0.5
|
|
CD2
|
a:HIS332
|
4.9
|
46.7
|
0.5
|
|
CD
|
d:LYS317
|
5.0
|
44.2
|
0.5
|
|
Chlorine binding site 7 out
of 8 in 8ird
Go back to
Chlorine Binding Sites List in 8ird
Chlorine binding site 7 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Cl403
b:53.0
occ:0.49
|
CL
|
a:CL403
|
0.0
|
53.0
|
0.5
|
|
CL
|
a:CL403
|
0.2
|
51.6
|
0.5
|
|
O
|
c:HOH678
|
2.9
|
51.5
|
0.5
|
|
O
|
a:HOH604
|
2.9
|
54.0
|
0.5
|
|
O
|
c:HOH678
|
3.0
|
51.2
|
0.5
|
|
N
|
a:ASN338
|
3.2
|
53.5
|
0.5
|
|
N
|
a:ASN338
|
3.2
|
53.6
|
0.5
|
|
O
|
a:HOH604
|
3.2
|
53.8
|
0.5
|
|
N
|
c:GLU354
|
3.4
|
49.8
|
0.5
|
|
N
|
c:GLU354
|
3.4
|
49.7
|
0.5
|
|
CD2
|
a:PHE339
|
3.6
|
54.0
|
0.5
|
|
N
|
a:PHE339
|
3.6
|
52.1
|
0.5
|
|
N
|
a:PHE339
|
3.6
|
52.1
|
0.5
|
|
CA
|
a:HIS337
|
3.6
|
49.4
|
0.5
|
|
CD2
|
a:PHE339
|
3.7
|
54.1
|
0.5
|
|
CA
|
a:HIS337
|
3.8
|
49.5
|
0.5
|
|
CA
|
c:GLY353
|
3.9
|
47.5
|
0.5
|
|
CA
|
c:GLY353
|
3.9
|
47.5
|
0.5
|
|
C
|
a:HIS337
|
3.9
|
50.8
|
0.5
|
|
C
|
a:HIS337
|
4.0
|
50.7
|
0.5
|
|
C
|
c:GLY353
|
4.1
|
51.7
|
0.5
|
|
CA
|
a:ASN338
|
4.1
|
50.8
|
0.5
|
|
CB
|
a:HIS337
|
4.1
|
46.4
|
0.5
|
|
CA
|
a:ASN338
|
4.1
|
50.8
|
0.5
|
|
C
|
c:GLY353
|
4.1
|
51.6
|
0.5
|
|
O
|
a:ALA336
|
4.2
|
57.5
|
0.5
|
|
CB
|
a:PHE339
|
4.2
|
49.5
|
0.5
|
|
CB
|
c:GLU354
|
4.2
|
50.6
|
0.5
|
|
O
|
c:HOH689
|
4.2
|
47.9
|
0.5
|
|
CG
|
a:PHE339
|
4.2
|
54.7
|
0.5
|
|
O
|
a:ALA336
|
4.3
|
57.4
|
0.5
|
|
CB
|
c:GLU354
|
4.3
|
50.6
|
0.5
|
|
C
|
a:ASN338
|
4.3
|
54.1
|
0.5
|
|
CB
|
a:HIS337
|
4.3
|
46.5
|
0.5
|
|
CB
|
a:PHE339
|
4.3
|
49.4
|
0.5
|
|
CB
|
a:ASN338
|
4.3
|
54.3
|
0.5
|
|
C
|
a:ASN338
|
4.4
|
54.1
|
0.5
|
|
CA
|
c:GLU354
|
4.4
|
48.9
|
0.5
|
|
CE2
|
a:PHE339
|
4.4
|
53.1
|
0.5
|
|
CG
|
a:PHE339
|
4.4
|
54.4
|
0.5
|
|
CB
|
a:ASN338
|
4.4
|
54.3
|
0.5
|
|
O
|
c:HOH689
|
4.4
|
47.8
|
0.5
|
|
CA
|
a:PHE339
|
4.4
|
53.9
|
0.5
|
|
CA
|
c:GLU354
|
4.4
|
48.9
|
0.5
|
|
CA
|
a:PHE339
|
4.5
|
54.1
|
0.5
|
|
CE2
|
a:PHE339
|
4.5
|
53.1
|
0.5
|
|
O
|
a:PHE339
|
4.5
|
54.7
|
0.5
|
|
O
|
c:HOH737
|
4.5
|
54.4
|
0.5
|
|
O
|
a:PHE339
|
4.6
|
55.0
|
0.5
|
|
O
|
c:HOH737
|
4.6
|
55.2
|
0.5
|
|
N
|
a:HIS337
|
4.8
|
51.4
|
0.5
|
|
CG
|
a:HIS337
|
4.9
|
50.2
|
0.5
|
|
CD2
|
a:HIS337
|
4.9
|
51.4
|
0.5
|
|
N
|
c:THR355
|
4.9
|
50.2
|
0.5
|
|
N
|
a:HIS337
|
4.9
|
51.2
|
0.5
|
|
C
|
a:ALA336
|
4.9
|
49.9
|
0.5
|
|
N
|
c:THR355
|
4.9
|
50.1
|
0.5
|
|
O
|
c:GLY352
|
4.9
|
51.3
|
0.5
|
|
C
|
a:PHE339
|
5.0
|
54.3
|
0.5
|
|
C
|
a:PHE339
|
5.0
|
54.3
|
0.5
|
|
CG
|
a:ASN338
|
5.0
|
53.6
|
0.5
|
|
CG
|
c:GLU354
|
5.0
|
50.9
|
0.5
|
|
NE2
|
c:GLN313
|
5.0
|
47.9
|
0.5
|
|
NE2
|
c:GLN313
|
5.0
|
48.0
|
0.5
|
|
Chlorine binding site 8 out
of 8 in 8ird
Go back to
Chlorine Binding Sites List in 8ird
Chlorine binding site 8 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 20-Nanosecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Cl403
b:51.6
occ:0.51
|
CL
|
a:CL403
|
0.0
|
51.6
|
0.5
|
|
CL
|
a:CL403
|
0.2
|
53.0
|
0.5
|
|
O
|
a:HOH604
|
2.9
|
54.0
|
0.5
|
|
N
|
a:ASN338
|
3.1
|
53.5
|
0.5
|
|
N
|
a:ASN338
|
3.1
|
53.6
|
0.5
|
|
O
|
a:HOH604
|
3.1
|
53.8
|
0.5
|
|
O
|
c:HOH678
|
3.1
|
51.5
|
0.5
|
|
O
|
c:HOH678
|
3.2
|
51.2
|
0.5
|
|
N
|
c:GLU354
|
3.4
|
49.8
|
0.5
|
|
CA
|
a:HIS337
|
3.4
|
49.4
|
0.5
|
|
N
|
c:GLU354
|
3.5
|
49.7
|
0.5
|
|
CA
|
a:HIS337
|
3.5
|
49.5
|
0.5
|
|
N
|
a:PHE339
|
3.6
|
52.1
|
0.5
|
|
N
|
a:PHE339
|
3.6
|
52.1
|
0.5
|
|
C
|
a:HIS337
|
3.8
|
50.8
|
0.5
|
|
CD2
|
a:PHE339
|
3.8
|
54.0
|
0.5
|
|
C
|
a:HIS337
|
3.8
|
50.7
|
0.5
|
|
CD2
|
a:PHE339
|
3.9
|
54.1
|
0.5
|
|
CB
|
a:HIS337
|
3.9
|
46.4
|
0.5
|
|
CA
|
c:GLY353
|
3.9
|
47.5
|
0.5
|
|
CA
|
c:GLY353
|
4.0
|
47.5
|
0.5
|
|
O
|
a:ALA336
|
4.0
|
57.5
|
0.5
|
|
CA
|
a:ASN338
|
4.1
|
50.8
|
0.5
|
|
CA
|
a:ASN338
|
4.1
|
50.8
|
0.5
|
|
CB
|
a:HIS337
|
4.1
|
46.5
|
0.5
|
|
O
|
a:ALA336
|
4.1
|
57.4
|
0.5
|
|
CB
|
c:GLU354
|
4.2
|
50.6
|
0.5
|
|
C
|
c:GLY353
|
4.2
|
51.7
|
0.5
|
|
C
|
c:GLY353
|
4.2
|
51.6
|
0.5
|
|
CB
|
c:GLU354
|
4.2
|
50.6
|
0.5
|
|
CB
|
a:PHE339
|
4.3
|
49.5
|
0.5
|
|
C
|
a:ASN338
|
4.3
|
54.1
|
0.5
|
|
C
|
a:ASN338
|
4.3
|
54.1
|
0.5
|
|
CB
|
a:ASN338
|
4.4
|
54.3
|
0.5
|
|
CA
|
c:GLU354
|
4.4
|
48.9
|
0.5
|
|
CG
|
a:PHE339
|
4.4
|
54.7
|
0.5
|
|
O
|
c:HOH689
|
4.4
|
47.9
|
0.5
|
|
CB
|
a:ASN338
|
4.4
|
54.3
|
0.5
|
|
CB
|
a:PHE339
|
4.4
|
49.4
|
0.5
|
|
CA
|
c:GLU354
|
4.4
|
48.9
|
0.5
|
|
O
|
a:PHE339
|
4.5
|
54.7
|
0.5
|
|
CA
|
a:PHE339
|
4.5
|
53.9
|
0.5
|
|
O
|
a:PHE339
|
4.5
|
55.0
|
0.5
|
|
O
|
c:HOH737
|
4.5
|
54.4
|
0.5
|
|
CA
|
a:PHE339
|
4.5
|
54.1
|
0.5
|
|
CG
|
a:PHE339
|
4.5
|
54.4
|
0.5
|
|
N
|
a:HIS337
|
4.6
|
51.4
|
0.5
|
|
CE2
|
a:PHE339
|
4.6
|
53.1
|
0.5
|
|
O
|
c:HOH689
|
4.6
|
47.8
|
0.5
|
|
O
|
c:HOH737
|
4.6
|
55.2
|
0.5
|
|
CG
|
a:HIS337
|
4.6
|
50.2
|
0.5
|
|
CD2
|
a:HIS337
|
4.7
|
51.4
|
0.5
|
|
CE2
|
a:PHE339
|
4.7
|
53.1
|
0.5
|
|
N
|
a:HIS337
|
4.7
|
51.2
|
0.5
|
|
C
|
a:ALA336
|
4.7
|
49.9
|
0.5
|
|
CD2
|
a:HIS337
|
4.8
|
51.4
|
0.5
|
|
CG
|
a:HIS337
|
4.8
|
50.5
|
0.5
|
|
C
|
a:ALA336
|
4.9
|
49.7
|
0.5
|
|
CG
|
c:GLU354
|
4.9
|
50.9
|
0.5
|
|
CG
|
c:GLU354
|
4.9
|
51.0
|
0.5
|
|
C
|
a:PHE339
|
4.9
|
54.3
|
0.5
|
|
C
|
a:PHE339
|
4.9
|
54.3
|
0.5
|
|
O
|
a:HIS337
|
5.0
|
54.9
|
0.5
|
|
CG
|
a:ASN338
|
5.0
|
53.6
|
0.5
|
|
N
|
c:THR355
|
5.0
|
50.2
|
0.5
|
|
Reference:
H.Li,
Y.Nakajima,
E.Nango,
S.Owada,
D.Yamada,
K.Hashimoto,
F.Luo,
R.Tanaka,
F.Akita,
K.Kato,
J.M.Kang,
Y.Saitoh,
S.Kishi,
H.Yu,
N.Matsubara,
H.Fujii,
M.Sugahara,
M.Suzuki,
T.Masuda,
T.Kimura,
T.N.Thao,
S.Yonekura,
L.J.Yu,
T.Tosha,
K.Tono,
Y.Joti,
T.Hatsui,
M.Yabashi,
M.Kubo,
S.Iwata,
H.Isobe,
K.Yamaguchi,
M.Suga,
J.R.Shen.
Oxygen-Evolving Photosystem II Structures During S1-S2-S3 Transitions. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
Page generated: Sun Jul 13 12:21:35 2025
|
