Iron in PDB 5mx2: Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
Enzymatic activity of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
All present enzymatic activity of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution:
1.10.3.9;
Protein crystallography data
The structure of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution, PDB code: 5mx2
was solved by
M.Zhang,
M.Bommer,
R.Chatterjee,
R.Hussain,
J.Kern,
J.Yano,
H.Dau,
H.Dobbek,
A.Zouni,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.65 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
116.326,
219.617,
304.043,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.1 /
26
|
Other elements in 5mx2:
The structure of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
(pdb code 5mx2). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution, PDB code: 5mx2:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 5mx2
Go back to
Iron Binding Sites List in 5mx2
Iron binding site 1 out
of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe414
b:26.9
occ:1.00
|
O2
|
A:BCT415
|
2.0
|
25.8
|
1.0
|
O1
|
A:BCT415
|
2.1
|
29.4
|
1.0
|
NE2
|
A:HIS215
|
2.2
|
25.9
|
1.0
|
NE2
|
D:HIS214
|
2.2
|
21.9
|
1.0
|
C
|
A:BCT415
|
2.4
|
31.3
|
1.0
|
NE2
|
D:HIS268
|
2.4
|
26.9
|
1.0
|
NE2
|
A:HIS272
|
2.5
|
27.1
|
1.0
|
CE1
|
D:HIS214
|
3.0
|
19.3
|
1.0
|
CE1
|
A:HIS215
|
3.0
|
24.6
|
1.0
|
CD2
|
A:HIS215
|
3.2
|
26.4
|
1.0
|
CD2
|
D:HIS214
|
3.2
|
17.2
|
1.0
|
CE1
|
D:HIS268
|
3.3
|
24.7
|
1.0
|
CD2
|
D:HIS268
|
3.4
|
23.6
|
1.0
|
CE1
|
A:HIS272
|
3.4
|
26.2
|
1.0
|
CD2
|
A:HIS272
|
3.5
|
26.0
|
1.0
|
O3
|
A:BCT415
|
3.7
|
32.6
|
1.0
|
ND1
|
D:HIS214
|
4.2
|
18.5
|
1.0
|
ND1
|
A:HIS215
|
4.2
|
25.9
|
1.0
|
CG
|
D:HIS214
|
4.3
|
18.8
|
1.0
|
CG
|
A:HIS215
|
4.3
|
27.0
|
1.0
|
ND1
|
D:HIS268
|
4.5
|
24.8
|
1.0
|
CG
|
D:HIS268
|
4.5
|
23.9
|
1.0
|
ND1
|
A:HIS272
|
4.6
|
27.9
|
1.0
|
CG
|
A:HIS272
|
4.6
|
28.2
|
1.0
|
OH
|
D:TYR244
|
4.7
|
32.7
|
1.0
|
CG2
|
D:VAL218
|
4.8
|
23.4
|
1.0
|
CG2
|
A:VAL219
|
4.9
|
25.0
|
1.0
|
OH
|
A:TYR246
|
5.0
|
38.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 5mx2
Go back to
Iron Binding Sites List in 5mx2
Iron binding site 2 out
of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe102
b:42.0
occ:1.00
|
FE
|
E:HEM102
|
0.0
|
42.0
|
1.0
|
NC
|
E:HEM102
|
2.0
|
38.1
|
1.0
|
NE2
|
E:HIS23
|
2.0
|
44.6
|
1.0
|
NB
|
E:HEM102
|
2.0
|
42.6
|
1.0
|
NA
|
E:HEM102
|
2.0
|
46.8
|
1.0
|
ND
|
E:HEM102
|
2.0
|
37.8
|
1.0
|
NE2
|
F:HIS24
|
2.1
|
43.0
|
1.0
|
CE1
|
F:HIS24
|
2.9
|
39.8
|
1.0
|
CE1
|
E:HIS23
|
3.0
|
43.0
|
1.0
|
C1C
|
E:HEM102
|
3.0
|
37.4
|
1.0
|
C1D
|
E:HEM102
|
3.0
|
37.4
|
1.0
|
C4B
|
E:HEM102
|
3.0
|
43.0
|
1.0
|
C4A
|
E:HEM102
|
3.0
|
46.0
|
1.0
|
C4C
|
E:HEM102
|
3.1
|
36.7
|
1.0
|
C4D
|
E:HEM102
|
3.1
|
41.1
|
1.0
|
C1B
|
E:HEM102
|
3.1
|
44.5
|
1.0
|
C1A
|
E:HEM102
|
3.1
|
45.0
|
1.0
|
CD2
|
E:HIS23
|
3.1
|
43.8
|
1.0
|
CD2
|
F:HIS24
|
3.1
|
40.1
|
1.0
|
CHC
|
E:HEM102
|
3.4
|
37.7
|
1.0
|
CHB
|
E:HEM102
|
3.4
|
45.3
|
1.0
|
CHD
|
E:HEM102
|
3.4
|
34.5
|
1.0
|
CHA
|
E:HEM102
|
3.4
|
42.6
|
1.0
|
ND1
|
F:HIS24
|
4.0
|
39.5
|
1.0
|
ND1
|
E:HIS23
|
4.1
|
45.3
|
1.0
|
CG
|
F:HIS24
|
4.2
|
44.7
|
1.0
|
CG
|
E:HIS23
|
4.2
|
44.8
|
1.0
|
C2C
|
E:HEM102
|
4.2
|
40.5
|
1.0
|
C2D
|
E:HEM102
|
4.2
|
40.0
|
1.0
|
C2B
|
E:HEM102
|
4.2
|
49.1
|
1.0
|
C3C
|
E:HEM102
|
4.3
|
43.1
|
1.0
|
C3D
|
E:HEM102
|
4.3
|
42.0
|
1.0
|
C3A
|
E:HEM102
|
4.3
|
49.3
|
1.0
|
C2A
|
E:HEM102
|
4.3
|
50.8
|
1.0
|
C3B
|
E:HEM102
|
4.3
|
48.2
|
1.0
|
CE1
|
E:TYR19
|
4.9
|
46.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 5mx2
Go back to
Iron Binding Sites List in 5mx2
Iron binding site 3 out
of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe201
b:34.7
occ:1.00
|
FE
|
V:HEM201
|
0.0
|
34.7
|
1.0
|
NE2
|
V:HIS41
|
1.9
|
35.7
|
1.0
|
NC
|
V:HEM201
|
2.0
|
35.0
|
1.0
|
NB
|
V:HEM201
|
2.0
|
35.8
|
1.0
|
NA
|
V:HEM201
|
2.0
|
33.9
|
1.0
|
ND
|
V:HEM201
|
2.1
|
35.0
|
1.0
|
NE2
|
V:HIS92
|
2.1
|
34.7
|
1.0
|
CD2
|
V:HIS41
|
2.9
|
35.0
|
1.0
|
CE1
|
V:HIS41
|
2.9
|
31.7
|
1.0
|
C1C
|
V:HEM201
|
3.0
|
37.9
|
1.0
|
CE1
|
V:HIS92
|
3.0
|
34.9
|
1.0
|
C4A
|
V:HEM201
|
3.0
|
36.3
|
1.0
|
C4B
|
V:HEM201
|
3.0
|
37.9
|
1.0
|
C1B
|
V:HEM201
|
3.0
|
37.0
|
1.0
|
C4C
|
V:HEM201
|
3.1
|
32.5
|
1.0
|
C4D
|
V:HEM201
|
3.1
|
35.8
|
1.0
|
C1D
|
V:HEM201
|
3.1
|
32.9
|
1.0
|
C1A
|
V:HEM201
|
3.1
|
34.5
|
1.0
|
CD2
|
V:HIS92
|
3.1
|
33.2
|
1.0
|
CHC
|
V:HEM201
|
3.4
|
34.8
|
1.0
|
CHB
|
V:HEM201
|
3.4
|
36.7
|
1.0
|
CHA
|
V:HEM201
|
3.4
|
34.7
|
1.0
|
CHD
|
V:HEM201
|
3.4
|
32.1
|
1.0
|
ND1
|
V:HIS41
|
4.0
|
30.9
|
1.0
|
CG
|
V:HIS41
|
4.0
|
34.1
|
1.0
|
ND1
|
V:HIS92
|
4.1
|
34.5
|
1.0
|
CG
|
V:HIS92
|
4.2
|
33.6
|
1.0
|
C2C
|
V:HEM201
|
4.2
|
37.8
|
1.0
|
C2B
|
V:HEM201
|
4.2
|
38.4
|
1.0
|
C3A
|
V:HEM201
|
4.3
|
40.7
|
1.0
|
C3B
|
V:HEM201
|
4.3
|
36.8
|
1.0
|
C3C
|
V:HEM201
|
4.3
|
38.7
|
1.0
|
C2D
|
V:HEM201
|
4.3
|
31.4
|
1.0
|
C2A
|
V:HEM201
|
4.3
|
41.3
|
1.0
|
C3D
|
V:HEM201
|
4.3
|
36.5
|
1.0
|
CE1
|
V:TYR75
|
4.9
|
37.5
|
1.0
|
OH
|
V:TYR75
|
4.9
|
37.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 5mx2
Go back to
Iron Binding Sites List in 5mx2
Iron binding site 4 out
of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe401
b:40.0
occ:1.00
|
O2
|
a:BCT413
|
2.0
|
33.3
|
1.0
|
O1
|
a:BCT413
|
2.0
|
31.3
|
1.0
|
NE2
|
d:HIS214
|
2.1
|
27.1
|
1.0
|
NE2
|
a:HIS215
|
2.2
|
30.1
|
1.0
|
C
|
a:BCT413
|
2.4
|
34.1
|
1.0
|
NE2
|
d:HIS268
|
2.4
|
28.6
|
1.0
|
NE2
|
a:HIS272
|
2.4
|
37.3
|
1.0
|
CE1
|
a:HIS215
|
2.9
|
33.4
|
1.0
|
CE1
|
d:HIS214
|
3.0
|
24.1
|
1.0
|
CD2
|
d:HIS214
|
3.1
|
25.5
|
1.0
|
CE1
|
d:HIS268
|
3.3
|
28.9
|
1.0
|
CD2
|
a:HIS215
|
3.3
|
33.0
|
1.0
|
CD2
|
a:HIS272
|
3.4
|
33.5
|
1.0
|
CD2
|
d:HIS268
|
3.4
|
26.8
|
1.0
|
CE1
|
a:HIS272
|
3.4
|
34.9
|
1.0
|
O3
|
a:BCT413
|
3.7
|
40.6
|
1.0
|
ND1
|
d:HIS214
|
4.1
|
22.1
|
1.0
|
ND1
|
a:HIS215
|
4.1
|
34.2
|
1.0
|
CG
|
d:HIS214
|
4.2
|
23.0
|
1.0
|
CG
|
a:HIS215
|
4.3
|
32.5
|
1.0
|
ND1
|
d:HIS268
|
4.4
|
28.3
|
1.0
|
CG
|
d:HIS268
|
4.5
|
30.9
|
1.0
|
CG
|
a:HIS272
|
4.5
|
30.9
|
1.0
|
ND1
|
a:HIS272
|
4.5
|
31.8
|
1.0
|
OH
|
d:TYR244
|
4.8
|
35.7
|
1.0
|
CG2
|
a:VAL219
|
4.8
|
33.5
|
1.0
|
CG2
|
d:VAL218
|
4.8
|
26.1
|
1.0
|
|
Iron binding site 5 out
of 6 in 5mx2
Go back to
Iron Binding Sites List in 5mx2
Iron binding site 5 out
of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Fe102
b:47.2
occ:1.00
|
FE
|
e:HEM102
|
0.0
|
47.2
|
1.0
|
NE2
|
e:HIS23
|
1.9
|
50.3
|
1.0
|
NC
|
e:HEM102
|
2.0
|
44.9
|
1.0
|
NB
|
e:HEM102
|
2.0
|
48.6
|
1.0
|
NA
|
e:HEM102
|
2.0
|
47.0
|
1.0
|
ND
|
e:HEM102
|
2.1
|
45.7
|
1.0
|
NE2
|
f:HIS24
|
2.2
|
45.6
|
1.0
|
CE1
|
e:HIS23
|
2.8
|
48.4
|
1.0
|
CD2
|
e:HIS23
|
2.9
|
48.4
|
1.0
|
C1C
|
e:HEM102
|
3.0
|
46.9
|
1.0
|
C4B
|
e:HEM102
|
3.0
|
49.7
|
1.0
|
C4A
|
e:HEM102
|
3.0
|
50.1
|
1.0
|
C4C
|
e:HEM102
|
3.1
|
42.1
|
1.0
|
C1B
|
e:HEM102
|
3.1
|
47.7
|
1.0
|
C1D
|
e:HEM102
|
3.1
|
46.2
|
1.0
|
C1A
|
e:HEM102
|
3.1
|
46.3
|
1.0
|
C4D
|
e:HEM102
|
3.1
|
49.6
|
1.0
|
CE1
|
f:HIS24
|
3.1
|
46.8
|
1.0
|
CD2
|
f:HIS24
|
3.2
|
44.2
|
1.0
|
CHC
|
e:HEM102
|
3.3
|
48.8
|
1.0
|
CHB
|
e:HEM102
|
3.4
|
46.9
|
1.0
|
CHD
|
e:HEM102
|
3.4
|
44.7
|
1.0
|
CHA
|
e:HEM102
|
3.5
|
51.0
|
1.0
|
ND1
|
e:HIS23
|
3.9
|
52.4
|
1.0
|
CG
|
e:HIS23
|
4.0
|
50.0
|
1.0
|
C2C
|
e:HEM102
|
4.2
|
44.8
|
1.0
|
ND1
|
f:HIS24
|
4.2
|
48.4
|
1.0
|
C3B
|
e:HEM102
|
4.2
|
48.8
|
1.0
|
C2B
|
e:HEM102
|
4.3
|
48.0
|
1.0
|
C3C
|
e:HEM102
|
4.3
|
42.3
|
1.0
|
C3A
|
e:HEM102
|
4.3
|
53.6
|
1.0
|
CG
|
f:HIS24
|
4.3
|
44.9
|
1.0
|
C2D
|
e:HEM102
|
4.3
|
47.9
|
1.0
|
C2A
|
e:HEM102
|
4.3
|
50.0
|
1.0
|
C3D
|
e:HEM102
|
4.3
|
48.5
|
1.0
|
CE2
|
e:TYR19
|
4.9
|
48.1
|
1.0
|
|
Iron binding site 6 out
of 6 in 5mx2
Go back to
Iron Binding Sites List in 5mx2
Iron binding site 6 out
of 6 in the Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Photosystem II Depleted of the MN4CAO5 Cluster at 2.55 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
v:Fe201
b:35.2
occ:1.00
|
FE
|
v:HEM201
|
0.0
|
35.2
|
1.0
|
NE2
|
v:HIS41
|
1.9
|
38.2
|
1.0
|
NB
|
v:HEM201
|
2.0
|
36.1
|
1.0
|
NC
|
v:HEM201
|
2.0
|
38.1
|
1.0
|
ND
|
v:HEM201
|
2.0
|
33.0
|
1.0
|
NA
|
v:HEM201
|
2.1
|
37.1
|
1.0
|
NE2
|
v:HIS92
|
2.1
|
34.0
|
1.0
|
CE1
|
v:HIS41
|
2.8
|
38.1
|
1.0
|
CE1
|
v:HIS92
|
2.9
|
33.9
|
1.0
|
CD2
|
v:HIS41
|
3.0
|
37.2
|
1.0
|
C1C
|
v:HEM201
|
3.0
|
39.8
|
1.0
|
C4B
|
v:HEM201
|
3.0
|
37.6
|
1.0
|
C1D
|
v:HEM201
|
3.0
|
33.5
|
1.0
|
C1B
|
v:HEM201
|
3.1
|
33.8
|
1.0
|
C4A
|
v:HEM201
|
3.1
|
32.6
|
1.0
|
C4C
|
v:HEM201
|
3.1
|
34.6
|
1.0
|
C4D
|
v:HEM201
|
3.1
|
34.6
|
1.0
|
C1A
|
v:HEM201
|
3.1
|
37.0
|
1.0
|
CD2
|
v:HIS92
|
3.1
|
37.0
|
1.0
|
CHC
|
v:HEM201
|
3.3
|
37.9
|
1.0
|
CHB
|
v:HEM201
|
3.4
|
31.3
|
1.0
|
CHD
|
v:HEM201
|
3.4
|
32.7
|
1.0
|
CHA
|
v:HEM201
|
3.5
|
33.9
|
1.0
|
ND1
|
v:HIS41
|
3.9
|
39.1
|
1.0
|
ND1
|
v:HIS92
|
4.0
|
36.6
|
1.0
|
CG
|
v:HIS41
|
4.0
|
41.6
|
1.0
|
CG
|
v:HIS92
|
4.2
|
34.5
|
1.0
|
C2C
|
v:HEM201
|
4.2
|
33.1
|
1.0
|
C3B
|
v:HEM201
|
4.2
|
41.1
|
1.0
|
C2B
|
v:HEM201
|
4.2
|
35.7
|
1.0
|
C2D
|
v:HEM201
|
4.3
|
35.7
|
1.0
|
C3C
|
v:HEM201
|
4.3
|
31.9
|
1.0
|
C3D
|
v:HEM201
|
4.3
|
36.8
|
1.0
|
C3A
|
v:HEM201
|
4.3
|
33.9
|
1.0
|
C2A
|
v:HEM201
|
4.3
|
34.8
|
1.0
|
CE1
|
v:TYR75
|
5.0
|
37.1
|
1.0
|
|
Reference:
M.Zhang,
M.Bommer,
R.Chatterjee,
R.Hussein,
J.Yano,
H.Dau,
J.Kern,
H.Dobbek,
A.Zouni.
Structural Insights Into the Light-Driven Auto-Assembly Process of the Water-Oxidizing MN4CAO5-Cluster in Photosystem II. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28718766
DOI: 10.7554/ELIFE.26933
Page generated: Tue Aug 6 06:01:42 2024
|