Iron in PDB 7m78: Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
Enzymatic activity of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
All present enzymatic activity of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I:
1.97.1.12;
Protein crystallography data
The structure of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I, PDB code: 7m78
was solved by
S.M.Keable,
P.S.Simon,
A.Kolsch,
J.Kern,
V.K.Yachandra,
A.Zouni,
J.Yano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
31.63 /
3.00
|
|
Space group
|
P 63
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
284.864,
284.864,
166.177,
90,
90,
120
|
|
R / Rfree (%)
|
33.4 /
35
|
Other elements in 7m78:
The structure of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Iron atom in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
(pdb code 7m78). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the
Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I, PDB code: 7m78:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 1 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe846
b:92.2
occ:1.00
|
FE1
|
A:SF4846
|
0.0
|
92.2
|
1.0
|
|
SG
|
B:CYS574
|
2.3
|
16.8
|
1.0
|
|
S3
|
A:SF4846
|
2.3
|
9.8
|
1.0
|
|
S2
|
A:SF4846
|
2.3
|
40.0
|
1.0
|
|
S4
|
A:SF4846
|
2.3
|
3.7
|
1.0
|
|
FE3
|
A:SF4846
|
2.7
|
20.0
|
1.0
|
|
FE2
|
A:SF4846
|
2.7
|
37.5
|
1.0
|
|
FE4
|
A:SF4846
|
2.7
|
62.6
|
1.0
|
|
HB3
|
B:CYS574
|
3.0
|
41.1
|
1.0
|
|
CB
|
B:CYS574
|
3.3
|
24.1
|
1.0
|
|
HZ3
|
B:TRP673
|
3.5
|
4.6
|
1.0
|
|
HD13
|
A:ILE724
|
3.7
|
56.0
|
1.0
|
|
S1
|
A:SF4846
|
3.9
|
11.2
|
1.0
|
|
HB2
|
B:CYS574
|
3.9
|
41.1
|
1.0
|
|
HG
|
A:CYS578
|
4.0
|
16.1
|
1.0
|
|
HA
|
B:CYS574
|
4.1
|
39.8
|
1.0
|
|
HG21
|
A:ILE724
|
4.2
|
63.6
|
1.0
|
|
CZ3
|
B:TRP673
|
4.2
|
2.0
|
1.0
|
|
HB3
|
B:CYS565
|
4.2
|
8.1
|
1.0
|
|
CA
|
B:CYS574
|
4.3
|
23.0
|
1.0
|
|
HG23
|
A:ILE724
|
4.6
|
63.6
|
1.0
|
|
HB2
|
B:CYS565
|
4.6
|
8.1
|
1.0
|
|
HH21
|
B:ARG712
|
4.6
|
12.5
|
1.0
|
|
HB3
|
A:CYS587
|
4.6
|
21.6
|
1.0
|
|
CD1
|
A:ILE724
|
4.6
|
36.5
|
1.0
|
|
CB
|
B:CYS565
|
4.7
|
2.0
|
1.0
|
|
HH2
|
B:TRP673
|
4.7
|
29.7
|
1.0
|
|
HH22
|
B:ARG712
|
4.8
|
12.5
|
1.0
|
|
SG
|
B:CYS565
|
4.8
|
19.2
|
1.0
|
|
CH2
|
B:TRP673
|
4.8
|
14.6
|
1.0
|
|
HE3
|
B:TRP673
|
4.8
|
13.8
|
1.0
|
|
CG2
|
A:ILE724
|
4.8
|
42.8
|
1.0
|
|
SG
|
A:CYS587
|
4.9
|
2.0
|
1.0
|
|
N
|
B:CYS574
|
4.9
|
29.0
|
1.0
|
|
CE3
|
B:TRP673
|
4.9
|
2.0
|
1.0
|
|
HD11
|
A:ILE724
|
4.9
|
56.0
|
1.0
|
|
H
|
B:CYS574
|
4.9
|
47.0
|
1.0
|
|
SG
|
A:CYS578
|
5.0
|
3.2
|
1.0
|
|
HH22
|
A:ARG728
|
5.0
|
35.7
|
1.0
|
|
HH21
|
A:ARG728
|
5.0
|
35.7
|
1.0
|
|
Iron binding site 2 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 2 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe846
b:37.5
occ:1.00
|
FE2
|
A:SF4846
|
0.0
|
37.5
|
1.0
|
|
SG
|
A:CYS587
|
2.3
|
2.0
|
1.0
|
|
S1
|
A:SF4846
|
2.3
|
11.2
|
1.0
|
|
S3
|
A:SF4846
|
2.3
|
9.8
|
1.0
|
|
S4
|
A:SF4846
|
2.3
|
3.7
|
1.0
|
|
FE3
|
A:SF4846
|
2.7
|
20.0
|
1.0
|
|
FE4
|
A:SF4846
|
2.7
|
62.6
|
1.0
|
|
FE1
|
A:SF4846
|
2.7
|
92.2
|
1.0
|
|
HB3
|
A:CYS587
|
2.9
|
21.6
|
1.0
|
|
CB
|
A:CYS587
|
3.1
|
7.8
|
1.0
|
|
HD13
|
B:ILE708
|
3.4
|
25.0
|
1.0
|
|
HG
|
A:CYS578
|
3.6
|
16.1
|
1.0
|
|
HA
|
A:CYS587
|
3.6
|
15.8
|
1.0
|
|
CA
|
A:CYS587
|
3.9
|
2.9
|
1.0
|
|
S2
|
A:SF4846
|
3.9
|
40.0
|
1.0
|
|
HB2
|
A:CYS587
|
3.9
|
21.6
|
1.0
|
|
HE3
|
B:TRP673
|
4.0
|
13.8
|
1.0
|
|
HB3
|
A:CYS578
|
4.1
|
35.2
|
1.0
|
|
HZ3
|
B:TRP673
|
4.2
|
4.6
|
1.0
|
|
HD11
|
B:ILE708
|
4.2
|
25.0
|
1.0
|
|
CD1
|
B:ILE708
|
4.2
|
10.6
|
1.0
|
|
HG21
|
B:ILE708
|
4.2
|
26.9
|
1.0
|
|
N
|
A:CYS587
|
4.3
|
12.1
|
1.0
|
|
HB2
|
A:CYS578
|
4.4
|
35.2
|
1.0
|
|
H
|
A:CYS587
|
4.4
|
26.7
|
1.0
|
|
HG23
|
B:ILE708
|
4.4
|
26.9
|
1.0
|
|
CE3
|
B:TRP673
|
4.4
|
2.0
|
1.0
|
|
CB
|
A:CYS578
|
4.5
|
19.1
|
1.0
|
|
SG
|
B:CYS565
|
4.5
|
19.2
|
1.0
|
|
CZ3
|
B:TRP673
|
4.5
|
2.0
|
1.0
|
|
SG
|
A:CYS578
|
4.6
|
3.2
|
1.0
|
|
HD12
|
B:ILE708
|
4.7
|
25.0
|
1.0
|
|
CG2
|
B:ILE708
|
4.8
|
12.2
|
1.0
|
|
H
|
A:THR586
|
4.8
|
31.5
|
1.0
|
|
HH22
|
A:ARG728
|
4.9
|
35.7
|
1.0
|
|
C
|
A:THR586
|
4.9
|
20.7
|
1.0
|
|
HB3
|
B:CYS565
|
5.0
|
8.1
|
1.0
|
|
SG
|
B:CYS574
|
5.0
|
16.8
|
1.0
|
|
Iron binding site 3 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 3 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe846
b:20.0
occ:1.00
|
FE3
|
A:SF4846
|
0.0
|
20.0
|
1.0
|
|
HG
|
A:CYS578
|
1.3
|
16.1
|
1.0
|
|
SG
|
A:CYS578
|
2.3
|
3.2
|
1.0
|
|
S4
|
A:SF4846
|
2.3
|
3.7
|
1.0
|
|
S2
|
A:SF4846
|
2.3
|
40.0
|
1.0
|
|
S1
|
A:SF4846
|
2.3
|
11.2
|
1.0
|
|
FE1
|
A:SF4846
|
2.7
|
92.2
|
1.0
|
|
FE2
|
A:SF4846
|
2.7
|
37.5
|
1.0
|
|
FE4
|
A:SF4846
|
2.7
|
62.6
|
1.0
|
|
HB3
|
A:CYS578
|
2.8
|
35.2
|
1.0
|
|
CB
|
A:CYS578
|
3.1
|
19.1
|
1.0
|
|
HB2
|
A:CYS578
|
3.4
|
35.2
|
1.0
|
|
S3
|
A:SF4846
|
3.9
|
9.8
|
1.0
|
|
HD3
|
B:PRO568
|
4.0
|
14.8
|
1.0
|
|
HB3
|
B:PRO568
|
4.0
|
35.3
|
1.0
|
|
HD13
|
A:ILE724
|
4.0
|
56.0
|
1.0
|
|
HB2
|
A:PRO577
|
4.2
|
33.5
|
1.0
|
|
SG
|
B:CYS574
|
4.2
|
16.8
|
1.0
|
|
H
|
A:GLY580
|
4.3
|
12.1
|
1.0
|
|
HA
|
A:CYS587
|
4.4
|
15.8
|
1.0
|
|
CA
|
A:CYS578
|
4.4
|
10.3
|
1.0
|
|
HB3
|
A:CYS587
|
4.6
|
21.6
|
1.0
|
|
HD12
|
A:ILE724
|
4.6
|
56.0
|
1.0
|
|
SG
|
A:CYS587
|
4.7
|
2.0
|
1.0
|
|
CD
|
B:PRO568
|
4.7
|
2.1
|
1.0
|
|
HA
|
B:PRO568
|
4.7
|
15.1
|
1.0
|
|
CD1
|
A:ILE724
|
4.7
|
36.5
|
1.0
|
|
HH22
|
A:ARG728
|
4.7
|
35.7
|
1.0
|
|
N
|
A:CYS578
|
4.7
|
16.9
|
1.0
|
|
N
|
B:PRO568
|
4.8
|
2.0
|
1.0
|
|
CB
|
B:PRO568
|
4.8
|
19.2
|
1.0
|
|
HA2
|
A:GLY580
|
4.8
|
3.8
|
1.0
|
|
HG21
|
A:ILE724
|
4.8
|
63.6
|
1.0
|
|
SG
|
B:CYS565
|
4.9
|
19.2
|
1.0
|
|
O
|
A:PRO577
|
4.9
|
14.9
|
1.0
|
|
C
|
A:PRO577
|
4.9
|
21.6
|
1.0
|
|
HG3
|
B:PRO568
|
4.9
|
31.8
|
1.0
|
|
HA2
|
B:GLY567
|
5.0
|
11.9
|
1.0
|
|
HD11
|
A:ILE724
|
5.0
|
56.0
|
1.0
|
|
Iron binding site 4 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 4 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe846
b:62.6
occ:1.00
|
FE4
|
A:SF4846
|
0.0
|
62.6
|
1.0
|
|
SG
|
B:CYS565
|
2.3
|
19.2
|
1.0
|
|
S2
|
A:SF4846
|
2.3
|
40.0
|
1.0
|
|
S3
|
A:SF4846
|
2.3
|
9.8
|
1.0
|
|
S1
|
A:SF4846
|
2.3
|
11.2
|
1.0
|
|
FE3
|
A:SF4846
|
2.7
|
20.0
|
1.0
|
|
FE2
|
A:SF4846
|
2.7
|
37.5
|
1.0
|
|
FE1
|
A:SF4846
|
2.7
|
92.2
|
1.0
|
|
HB3
|
B:CYS565
|
2.9
|
8.1
|
1.0
|
|
CB
|
B:CYS565
|
2.9
|
2.0
|
1.0
|
|
HB2
|
B:CYS565
|
3.0
|
8.1
|
1.0
|
|
HG
|
A:CYS578
|
3.3
|
16.1
|
1.0
|
|
S4
|
A:SF4846
|
3.9
|
3.7
|
1.0
|
|
H
|
B:GLY567
|
4.0
|
8.1
|
1.0
|
|
SG
|
B:CYS574
|
4.1
|
16.8
|
1.0
|
|
HD13
|
B:ILE708
|
4.1
|
25.0
|
1.0
|
|
HD3
|
A:PRO581
|
4.2
|
2.0
|
1.0
|
|
HB3
|
A:PRO581
|
4.4
|
14.2
|
1.0
|
|
CA
|
B:CYS565
|
4.4
|
15.8
|
1.0
|
|
HA2
|
B:GLY567
|
4.4
|
11.9
|
1.0
|
|
SG
|
A:CYS578
|
4.5
|
3.2
|
1.0
|
|
HA
|
B:CYS574
|
4.5
|
39.8
|
1.0
|
|
SG
|
A:CYS587
|
4.7
|
2.0
|
1.0
|
|
HB3
|
B:CYS574
|
4.7
|
41.1
|
1.0
|
|
N
|
B:GLY567
|
4.7
|
2.0
|
1.0
|
|
HD12
|
B:ILE708
|
4.8
|
25.0
|
1.0
|
|
CD1
|
B:ILE708
|
4.8
|
10.6
|
1.0
|
|
HB2
|
B:PRO564
|
4.8
|
9.1
|
1.0
|
|
HD3
|
B:PRO568
|
4.8
|
14.8
|
1.0
|
|
HA2
|
A:GLY580
|
4.9
|
3.8
|
1.0
|
|
CA
|
B:GLY567
|
4.9
|
2.0
|
1.0
|
|
HD11
|
B:ILE708
|
4.9
|
25.0
|
1.0
|
|
N
|
A:PRO581
|
4.9
|
2.0
|
1.0
|
|
CD
|
A:PRO581
|
4.9
|
2.0
|
1.0
|
|
CB
|
B:CYS574
|
4.9
|
24.1
|
1.0
|
|
N
|
B:CYS565
|
4.9
|
10.6
|
1.0
|
|
HA
|
B:CYS565
|
5.0
|
31.2
|
1.0
|
|
HA
|
A:PRO581
|
5.0
|
4.4
|
1.0
|
|
C
|
B:GLY567
|
5.0
|
6.3
|
1.0
|
|
Iron binding site 5 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 5 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:28.7
occ:1.00
|
FE1
|
C:SF4101
|
0.0
|
28.7
|
1.0
|
|
H
|
C:CYS50
|
2.3
|
5.3
|
1.0
|
|
SG
|
C:CYS50
|
2.3
|
59.3
|
1.0
|
|
S4
|
C:SF4101
|
2.3
|
25.4
|
1.0
|
|
S3
|
C:SF4101
|
2.3
|
27.5
|
1.0
|
|
S2
|
C:SF4101
|
2.3
|
2.0
|
1.0
|
|
FE2
|
C:SF4101
|
2.7
|
14.9
|
1.0
|
|
FE3
|
C:SF4101
|
2.7
|
45.7
|
1.0
|
|
FE4
|
C:SF4101
|
2.7
|
21.9
|
1.0
|
|
H
|
C:LYS51
|
2.8
|
19.3
|
1.0
|
|
N
|
C:CYS50
|
2.8
|
2.0
|
1.0
|
|
H
|
C:GLY49
|
3.1
|
6.8
|
1.0
|
|
CB
|
C:CYS50
|
3.2
|
10.7
|
1.0
|
|
HB3
|
C:CYS50
|
3.3
|
25.1
|
1.0
|
|
CA
|
C:CYS50
|
3.4
|
4.0
|
1.0
|
|
N
|
C:LYS51
|
3.5
|
5.9
|
1.0
|
|
C
|
C:GLY49
|
3.7
|
2.0
|
1.0
|
|
HA2
|
C:GLY49
|
3.8
|
2.0
|
1.0
|
|
N
|
C:GLY49
|
3.8
|
2.0
|
1.0
|
|
HG22
|
C:VAL48
|
3.8
|
2.0
|
1.0
|
|
S1
|
C:SF4101
|
3.9
|
32.4
|
1.0
|
|
C
|
C:CYS50
|
3.9
|
2.0
|
1.0
|
|
CA
|
C:GLY49
|
4.0
|
2.0
|
1.0
|
|
HB2
|
C:CYS50
|
4.1
|
25.1
|
1.0
|
|
H
|
C:ARG52
|
4.1
|
11.3
|
1.0
|
|
H
|
C:VAL48
|
4.2
|
32.0
|
1.0
|
|
SG
|
C:CYS47
|
4.2
|
2.0
|
1.0
|
|
HG23
|
C:VAL48
|
4.2
|
2.0
|
1.0
|
|
HA
|
C:CYS50
|
4.3
|
17.0
|
1.0
|
|
H
|
C:CYS53
|
4.3
|
31.6
|
1.0
|
|
HB2
|
C:CYS20
|
4.3
|
38.4
|
1.0
|
|
HA
|
C:CYS20
|
4.4
|
44.0
|
1.0
|
|
HA
|
C:LYS51
|
4.5
|
9.9
|
1.0
|
|
CG2
|
C:VAL48
|
4.5
|
2.0
|
1.0
|
|
HD2
|
C:PRO21
|
4.5
|
46.6
|
1.0
|
|
CA
|
C:LYS51
|
4.6
|
2.0
|
1.0
|
|
SG
|
C:CYS53
|
4.7
|
54.3
|
1.0
|
|
O
|
C:GLY49
|
4.7
|
2.2
|
1.0
|
|
SG
|
C:CYS20
|
4.7
|
3.3
|
1.0
|
|
N
|
C:ARG52
|
4.7
|
2.0
|
1.0
|
|
HB3
|
C:CYS53
|
4.8
|
18.0
|
1.0
|
|
N
|
C:VAL48
|
4.9
|
16.5
|
1.0
|
|
CB
|
C:CYS20
|
4.9
|
21.8
|
1.0
|
|
HA3
|
C:GLY49
|
4.9
|
2.0
|
1.0
|
|
HG21
|
C:VAL48
|
5.0
|
2.0
|
1.0
|
|
C
|
C:VAL48
|
5.0
|
2.0
|
1.0
|
|
Iron binding site 6 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 6 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:14.9
occ:1.00
|
FE2
|
C:SF4101
|
0.0
|
14.9
|
1.0
|
|
HB2
|
C:CYS20
|
1.9
|
38.4
|
1.0
|
|
SG
|
C:CYS20
|
2.3
|
3.3
|
1.0
|
|
S4
|
C:SF4101
|
2.3
|
25.4
|
1.0
|
|
S3
|
C:SF4101
|
2.3
|
27.5
|
1.0
|
|
S1
|
C:SF4101
|
2.3
|
32.4
|
1.0
|
|
CB
|
C:CYS20
|
2.4
|
21.8
|
1.0
|
|
FE1
|
C:SF4101
|
2.7
|
28.7
|
1.0
|
|
FE3
|
C:SF4101
|
2.7
|
45.7
|
1.0
|
|
FE4
|
C:SF4101
|
2.7
|
21.9
|
1.0
|
|
HA
|
C:CYS20
|
2.8
|
44.0
|
1.0
|
|
CA
|
C:CYS20
|
3.2
|
26.5
|
1.0
|
|
HB3
|
C:CYS20
|
3.2
|
38.4
|
1.0
|
|
SG
|
C:CYS50
|
3.6
|
59.3
|
1.0
|
|
HB
|
C:VAL24
|
3.8
|
41.6
|
1.0
|
|
HB3
|
C:CYS53
|
3.9
|
18.0
|
1.0
|
|
S2
|
C:SF4101
|
3.9
|
2.0
|
1.0
|
|
HD2
|
C:PRO21
|
3.9
|
46.6
|
1.0
|
|
HG21
|
C:VAL24
|
4.1
|
42.3
|
1.0
|
|
N
|
C:CYS20
|
4.2
|
34.9
|
1.0
|
|
C
|
C:CYS20
|
4.2
|
26.1
|
1.0
|
|
H
|
C:CYS20
|
4.3
|
54.1
|
1.0
|
|
HG1
|
C:THR22
|
4.3
|
24.8
|
1.0
|
|
OG1
|
C:THR22
|
4.3
|
10.4
|
1.0
|
|
H
|
C:CYS53
|
4.5
|
31.6
|
1.0
|
|
H
|
C:THR22
|
4.6
|
33.6
|
1.0
|
|
CD
|
C:PRO21
|
4.6
|
28.6
|
1.0
|
|
CB
|
C:VAL24
|
4.6
|
24.5
|
1.0
|
|
HD11
|
C:LEU25
|
4.7
|
21.2
|
1.0
|
|
N
|
C:PRO21
|
4.7
|
25.9
|
1.0
|
|
CB
|
C:CYS53
|
4.7
|
4.8
|
1.0
|
|
HD12
|
C:LEU25
|
4.7
|
21.2
|
1.0
|
|
H
|
C:VAL24
|
4.8
|
30.2
|
1.0
|
|
HD3
|
C:PRO21
|
4.8
|
46.6
|
1.0
|
|
CG2
|
C:VAL24
|
4.8
|
25.0
|
1.0
|
|
SG
|
C:CYS53
|
4.8
|
54.3
|
1.0
|
|
HG
|
C:LEU25
|
4.8
|
33.6
|
1.0
|
|
H
|
C:CYS50
|
4.9
|
5.3
|
1.0
|
|
SG
|
C:CYS47
|
4.9
|
2.0
|
1.0
|
|
Iron binding site 7 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 7 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:45.7
occ:1.00
|
FE3
|
C:SF4101
|
0.0
|
45.7
|
1.0
|
|
SG
|
C:CYS53
|
2.3
|
54.3
|
1.0
|
|
S1
|
C:SF4101
|
2.3
|
32.4
|
1.0
|
|
S2
|
C:SF4101
|
2.3
|
2.0
|
1.0
|
|
S4
|
C:SF4101
|
2.3
|
25.4
|
1.0
|
|
HB3
|
C:CYS53
|
2.6
|
18.0
|
1.0
|
|
FE2
|
C:SF4101
|
2.7
|
14.9
|
1.0
|
|
FE1
|
C:SF4101
|
2.7
|
28.7
|
1.0
|
|
FE4
|
C:SF4101
|
2.7
|
21.9
|
1.0
|
|
CB
|
C:CYS53
|
3.0
|
4.8
|
1.0
|
|
H
|
C:CYS53
|
3.2
|
31.6
|
1.0
|
|
HB2
|
C:CYS53
|
3.6
|
18.0
|
1.0
|
|
H
|
C:LYS51
|
3.7
|
19.3
|
1.0
|
|
HG21
|
C:VAL66
|
3.7
|
11.9
|
1.0
|
|
HB2
|
C:CYS20
|
3.8
|
38.4
|
1.0
|
|
S3
|
C:SF4101
|
3.9
|
27.5
|
1.0
|
|
N
|
C:CYS53
|
3.9
|
16.1
|
1.0
|
|
SG
|
C:CYS50
|
3.9
|
59.3
|
1.0
|
|
HG22
|
C:VAL66
|
4.0
|
11.9
|
1.0
|
|
CA
|
C:CYS53
|
4.1
|
8.8
|
1.0
|
|
HA
|
C:LYS51
|
4.1
|
9.9
|
1.0
|
|
HD11
|
C:LEU25
|
4.1
|
21.2
|
1.0
|
|
CG2
|
C:VAL66
|
4.3
|
2.0
|
1.0
|
|
HG11
|
C:VAL4
|
4.3
|
19.9
|
1.0
|
|
N
|
C:LYS51
|
4.4
|
5.9
|
1.0
|
|
HG21
|
C:VAL4
|
4.4
|
21.9
|
1.0
|
|
CB
|
C:CYS20
|
4.6
|
21.8
|
1.0
|
|
CA
|
C:LYS51
|
4.6
|
2.0
|
1.0
|
|
H
|
C:ARG52
|
4.7
|
11.3
|
1.0
|
|
HA
|
C:CYS53
|
4.7
|
22.8
|
1.0
|
|
SG
|
C:CYS47
|
4.7
|
2.0
|
1.0
|
|
H
|
C:CYS50
|
4.8
|
5.3
|
1.0
|
|
HG23
|
C:VAL66
|
4.8
|
11.9
|
1.0
|
|
HG11
|
C:VAL66
|
4.8
|
14.6
|
1.0
|
|
SG
|
C:CYS20
|
4.8
|
3.3
|
1.0
|
|
N
|
C:ARG52
|
4.9
|
2.0
|
1.0
|
|
HD12
|
C:LEU25
|
4.9
|
21.2
|
1.0
|
|
CD1
|
C:LEU25
|
4.9
|
7.5
|
1.0
|
|
Iron binding site 8 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 8 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe101
b:21.9
occ:1.00
|
FE4
|
C:SF4101
|
0.0
|
21.9
|
1.0
|
|
S2
|
C:SF4101
|
2.3
|
2.0
|
1.0
|
|
S1
|
C:SF4101
|
2.3
|
32.4
|
1.0
|
|
SG
|
C:CYS47
|
2.3
|
2.0
|
1.0
|
|
S3
|
C:SF4101
|
2.3
|
27.5
|
1.0
|
|
FE1
|
C:SF4101
|
2.7
|
28.7
|
1.0
|
|
FE3
|
C:SF4101
|
2.7
|
45.7
|
1.0
|
|
FE2
|
C:SF4101
|
2.7
|
14.9
|
1.0
|
|
HB2
|
C:CYS47
|
3.4
|
37.3
|
1.0
|
|
HG21
|
C:VAL24
|
3.4
|
42.3
|
1.0
|
|
CB
|
C:CYS47
|
3.4
|
20.9
|
1.0
|
|
HG21
|
C:VAL4
|
3.5
|
21.9
|
1.0
|
|
HG11
|
C:VAL24
|
3.6
|
22.8
|
1.0
|
|
HA
|
C:CYS47
|
3.7
|
37.7
|
1.0
|
|
H
|
C:GLY49
|
3.7
|
6.8
|
1.0
|
|
HB
|
C:VAL24
|
3.8
|
41.6
|
1.0
|
|
S4
|
C:SF4101
|
3.9
|
25.4
|
1.0
|
|
H
|
C:VAL48
|
4.0
|
32.0
|
1.0
|
|
CA
|
C:CYS47
|
4.1
|
21.2
|
1.0
|
|
SG
|
C:CYS20
|
4.1
|
3.3
|
1.0
|
|
CG2
|
C:VAL24
|
4.2
|
25.0
|
1.0
|
|
HB3
|
C:CYS47
|
4.2
|
37.3
|
1.0
|
|
CB
|
C:VAL24
|
4.3
|
24.5
|
1.0
|
|
CG1
|
C:VAL24
|
4.3
|
8.8
|
1.0
|
|
HG1
|
C:THR22
|
4.3
|
24.8
|
1.0
|
|
HA2
|
C:GLY49
|
4.4
|
2.0
|
1.0
|
|
CG2
|
C:VAL4
|
4.4
|
8.1
|
1.0
|
|
H
|
C:CYS50
|
4.4
|
5.3
|
1.0
|
|
HB2
|
C:CYS20
|
4.5
|
38.4
|
1.0
|
|
N
|
C:GLY49
|
4.5
|
2.0
|
1.0
|
|
HG12
|
C:VAL24
|
4.5
|
22.8
|
1.0
|
|
N
|
C:VAL48
|
4.5
|
16.5
|
1.0
|
|
HG22
|
C:VAL24
|
4.5
|
42.3
|
1.0
|
|
HG23
|
C:VAL4
|
4.6
|
21.9
|
1.0
|
|
HG11
|
C:VAL4
|
4.6
|
19.9
|
1.0
|
|
HG22
|
C:VAL4
|
4.7
|
21.9
|
1.0
|
|
C
|
C:CYS47
|
4.7
|
17.8
|
1.0
|
|
OG1
|
C:THR22
|
4.8
|
10.4
|
1.0
|
|
SG
|
C:CYS53
|
4.8
|
54.3
|
1.0
|
|
HG22
|
C:VAL48
|
4.9
|
2.0
|
1.0
|
|
SG
|
C:CYS50
|
4.9
|
59.3
|
1.0
|
|
H
|
C:LYS51
|
4.9
|
19.3
|
1.0
|
|
CA
|
C:GLY49
|
4.9
|
2.0
|
1.0
|
|
HG23
|
C:VAL24
|
4.9
|
42.3
|
1.0
|
|
CB
|
C:CYS20
|
4.9
|
21.8
|
1.0
|
|
HG13
|
C:VAL66
|
4.9
|
14.6
|
1.0
|
|
HG11
|
C:VAL66
|
5.0
|
14.6
|
1.0
|
|
Iron binding site 9 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 9 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe102
b:38.6
occ:1.00
|
FE1
|
C:SF4102
|
0.0
|
38.6
|
1.0
|
|
HB2
|
C:CYS57
|
2.1
|
32.5
|
1.0
|
|
SG
|
C:CYS57
|
2.3
|
24.7
|
1.0
|
|
S4
|
C:SF4102
|
2.3
|
14.3
|
1.0
|
|
S3
|
C:SF4102
|
2.3
|
12.7
|
1.0
|
|
S2
|
C:SF4102
|
2.3
|
14.3
|
1.0
|
|
CB
|
C:CYS57
|
2.4
|
16.9
|
1.0
|
|
HA
|
C:CYS57
|
2.6
|
18.1
|
1.0
|
|
FE3
|
C:SF4102
|
2.7
|
26.8
|
1.0
|
|
FE2
|
C:SF4102
|
2.7
|
19.4
|
1.0
|
|
FE4
|
C:SF4102
|
2.7
|
28.8
|
1.0
|
|
CA
|
C:CYS57
|
3.0
|
4.9
|
1.0
|
|
SG
|
C:CYS13
|
3.2
|
34.4
|
1.0
|
|
HB3
|
C:CYS57
|
3.3
|
32.5
|
1.0
|
|
HB3
|
C:CYS13
|
3.6
|
60.2
|
1.0
|
|
HD2
|
C:PRO58
|
3.8
|
38.1
|
1.0
|
|
S1
|
C:SF4102
|
3.9
|
36.1
|
1.0
|
|
N
|
C:CYS57
|
4.0
|
11.4
|
1.0
|
|
HD3
|
C:PRO58
|
4.0
|
38.1
|
1.0
|
|
CB
|
C:CYS13
|
4.0
|
40.0
|
1.0
|
|
HB2
|
C:SER63
|
4.0
|
51.2
|
1.0
|
|
C
|
C:CYS57
|
4.1
|
28.7
|
1.0
|
|
H
|
C:CYS57
|
4.1
|
25.9
|
1.0
|
|
CD
|
C:PRO58
|
4.3
|
21.6
|
1.0
|
|
HG22
|
C:ILE64
|
4.3
|
15.2
|
1.0
|
|
HG1
|
C:THR59
|
4.3
|
72.4
|
1.0
|
|
HG23
|
C:THR59
|
4.3
|
66.2
|
1.0
|
|
HG21
|
C:ILE64
|
4.4
|
15.2
|
1.0
|
|
SG
|
C:CYS16
|
4.4
|
38.4
|
1.0
|
|
HB2
|
C:CYS13
|
4.4
|
60.2
|
1.0
|
|
N
|
C:PRO58
|
4.5
|
28.0
|
1.0
|
|
H
|
C:THR59
|
4.6
|
38.9
|
1.0
|
|
HB3
|
C:CYS16
|
4.6
|
29.9
|
1.0
|
|
SG
|
C:CYS10
|
4.6
|
7.5
|
1.0
|
|
HA
|
C:CYS10
|
4.7
|
37.5
|
1.0
|
|
H
|
C:SER63
|
4.7
|
48.8
|
1.0
|
|
H
|
C:ILE11
|
4.7
|
32.5
|
1.0
|
|
H
|
C:CYS13
|
4.7
|
63.1
|
1.0
|
|
HB
|
C:ILE64
|
4.8
|
32.5
|
1.0
|
|
CG2
|
C:ILE64
|
4.8
|
2.5
|
1.0
|
|
HG12
|
C:ILE11
|
4.8
|
54.9
|
1.0
|
|
C
|
C:ALA56
|
4.9
|
21.6
|
1.0
|
|
H
|
C:ILE64
|
4.9
|
46.3
|
1.0
|
|
CB
|
C:SER63
|
5.0
|
32.5
|
1.0
|
|
H
|
C:CYS16
|
5.0
|
40.6
|
1.0
|
|
Iron binding site 10 out
of 12 in 7m78
Go back to
Iron Binding Sites List in 7m78
Iron binding site 10 out
of 12 in the Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe102
b:19.4
occ:1.00
|
FE2
|
C:SF4102
|
0.0
|
19.4
|
1.0
|
|
SG
|
C:CYS16
|
2.3
|
38.4
|
1.0
|
|
S4
|
C:SF4102
|
2.3
|
14.3
|
1.0
|
|
S3
|
C:SF4102
|
2.3
|
12.7
|
1.0
|
|
S1
|
C:SF4102
|
2.3
|
36.1
|
1.0
|
|
FE3
|
C:SF4102
|
2.7
|
26.8
|
1.0
|
|
FE1
|
C:SF4102
|
2.7
|
38.6
|
1.0
|
|
FE4
|
C:SF4102
|
2.7
|
28.8
|
1.0
|
|
SG
|
C:CYS13
|
3.4
|
34.4
|
1.0
|
|
HB3
|
C:CYS16
|
3.6
|
29.9
|
1.0
|
|
SG
|
C:CYS10
|
3.6
|
7.5
|
1.0
|
|
CB
|
C:CYS16
|
3.7
|
14.7
|
1.0
|
|
HB2
|
C:ALA39
|
3.7
|
59.2
|
1.0
|
|
HB
|
C:ILE64
|
3.8
|
32.5
|
1.0
|
|
S2
|
C:SF4102
|
3.9
|
14.3
|
1.0
|
|
HB2
|
C:CYS57
|
3.9
|
32.5
|
1.0
|
|
H
|
C:CYS16
|
3.9
|
40.6
|
1.0
|
|
HB3
|
C:ALA39
|
4.0
|
59.2
|
1.0
|
|
HG21
|
C:ILE64
|
4.0
|
15.2
|
1.0
|
|
HB2
|
C:CYS16
|
4.2
|
29.9
|
1.0
|
|
H
|
C:THR14
|
4.3
|
70.1
|
1.0
|
|
HD12
|
C:ILE64
|
4.3
|
25.3
|
1.0
|
|
CB
|
C:ALA39
|
4.3
|
39.1
|
1.0
|
|
HD13
|
C:ILE64
|
4.4
|
25.3
|
1.0
|
|
HG23
|
C:ILE6
|
4.4
|
30.9
|
1.0
|
|
HE1
|
C:MET27
|
4.5
|
32.6
|
1.0
|
|
H
|
C:CYS13
|
4.5
|
63.1
|
1.0
|
|
CG2
|
C:ILE64
|
4.6
|
2.5
|
1.0
|
|
N
|
C:CYS16
|
4.6
|
23.6
|
1.0
|
|
CB
|
C:ILE64
|
4.6
|
16.9
|
1.0
|
|
HB3
|
C:CYS13
|
4.6
|
60.2
|
1.0
|
|
HG22
|
C:ILE64
|
4.7
|
15.2
|
1.0
|
|
CB
|
C:CYS57
|
4.7
|
16.9
|
1.0
|
|
CB
|
C:CYS13
|
4.7
|
40.0
|
1.0
|
|
HB1
|
C:ALA39
|
4.7
|
59.2
|
1.0
|
|
CD1
|
C:ILE64
|
4.8
|
10.9
|
1.0
|
|
SG
|
C:CYS57
|
4.8
|
24.7
|
1.0
|
|
CA
|
C:CYS16
|
4.8
|
11.1
|
1.0
|
|
HG21
|
C:ILE6
|
4.8
|
30.9
|
1.0
|
|
H
|
C:ALA39
|
4.8
|
48.0
|
1.0
|
|
HA
|
C:CYS57
|
4.9
|
18.1
|
1.0
|
|
HB2
|
C:CYS10
|
4.9
|
37.3
|
1.0
|
|
N
|
C:THR14
|
4.9
|
48.2
|
1.0
|
|
HB2
|
C:SER63
|
4.9
|
51.2
|
1.0
|
|
H
|
C:GLN15
|
5.0
|
73.8
|
1.0
|
|
CB
|
C:CYS10
|
5.0
|
20.9
|
1.0
|
|
Reference:
S.M.Keable,
A.Kolsch,
P.S.Simon,
M.Dasgupta,
R.Chatterjee,
S.K.Subramanian,
R.Hussein,
M.Ibrahim,
I.S.Kim,
I.Bogacz,
H.Makita,
C.C.Pham,
F.D.Fuller,
S.Gul,
D.Paley,
L.Lassalle,
K.D.Sutherlin,
A.Bhowmick,
N.W.Moriarty,
I.D.Young,
J.P.Blaschke,
C.De Lichtenberg,
P.Chernev,
M.H.Cheah,
S.Park,
G.Park,
J.Kim,
S.J.Lee,
J.Park,
K.Tono,
S.Owada,
M.S.Hunter,
A.Batyuk,
R.Oggenfuss,
M.Sander,
S.Zerdane,
D.Ozerov,
K.Nass,
H.Lemke,
R.Mankowsky,
A.S.Brewster,
J.Messinger,
N.K.Sauter,
V.K.Yachandra,
J.Yano,
A.Zouni,
J.Kern.
Room Temperature Xfel Crystallography Reveals Asymmetry in the Vicinity of the Two Phylloquinones in Photosystem I. Sci Rep V. 11 21787 2021.
ISSN: ESSN 2045-2322
PubMed: 34750381
DOI: 10.1038/S41598-021-00236-3
Page generated: Thu Aug 8 08:11:45 2024
|
