Iron in PDB 5h2f: Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
Enzymatic activity of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
All present enzymatic activity of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II:
1.10.3.9;
Protein crystallography data
The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f
was solved by
S.Uto,
K.Kawakami,
Y.Umena,
M.Iwai,
M.Ikeuchi,
J.R.Shen,
N.Kamiya,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.954,
226.993,
285.886,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.4 /
22.6
|
Other elements in 5h2f:
The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
(pdb code 5h2f). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 5h2f
Go back to
Iron Binding Sites List in 5h2f
Iron binding site 1 out
of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:40.0
occ:1.00
|
NE2
|
A:HIS215
|
2.0
|
36.8
|
1.0
|
NE2
|
D:HIS214
|
2.2
|
33.3
|
1.0
|
O3
|
A:BCT421
|
2.3
|
27.7
|
0.5
|
NE2
|
A:HIS272
|
2.3
|
43.8
|
1.0
|
O3
|
A:BCT421
|
2.3
|
34.4
|
0.5
|
NE2
|
D:HIS268
|
2.4
|
31.1
|
1.0
|
O2
|
A:BCT421
|
2.5
|
35.0
|
0.5
|
O2
|
A:BCT421
|
2.5
|
36.4
|
0.5
|
C
|
A:BCT421
|
2.7
|
30.1
|
0.5
|
C
|
A:BCT421
|
2.8
|
39.4
|
0.5
|
CE1
|
A:HIS215
|
2.8
|
34.7
|
1.0
|
CD2
|
D:HIS214
|
3.0
|
29.3
|
1.0
|
CE1
|
A:HIS272
|
3.1
|
33.1
|
1.0
|
CD2
|
A:HIS215
|
3.2
|
33.4
|
1.0
|
CE1
|
D:HIS214
|
3.3
|
29.1
|
1.0
|
CD2
|
D:HIS268
|
3.3
|
27.7
|
1.0
|
CE1
|
D:HIS268
|
3.4
|
28.3
|
1.0
|
CD2
|
A:HIS272
|
3.4
|
36.2
|
1.0
|
O1
|
A:BCT421
|
3.9
|
29.9
|
0.5
|
ND1
|
A:HIS215
|
4.1
|
33.0
|
1.0
|
O1
|
A:BCT421
|
4.1
|
39.5
|
0.5
|
CG
|
A:HIS215
|
4.2
|
35.2
|
1.0
|
CG
|
D:HIS214
|
4.2
|
29.1
|
1.0
|
ND1
|
D:HIS214
|
4.4
|
27.9
|
1.0
|
ND1
|
A:HIS272
|
4.4
|
35.8
|
1.0
|
ND1
|
D:HIS268
|
4.5
|
32.1
|
1.0
|
CG2
|
A:VAL219
|
4.5
|
31.8
|
1.0
|
CG
|
A:HIS272
|
4.5
|
33.7
|
1.0
|
CG
|
D:HIS268
|
4.5
|
30.7
|
1.0
|
O
|
A:HOH501
|
4.6
|
40.1
|
1.0
|
CG2
|
D:VAL218
|
4.8
|
26.5
|
1.0
|
|
Iron binding site 2 out
of 6 in 5h2f
Go back to
Iron Binding Sites List in 5h2f
Iron binding site 2 out
of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe102
b:52.2
occ:1.00
|
FE
|
E:HEM102
|
0.0
|
52.2
|
1.0
|
NB
|
E:HEM102
|
2.0
|
53.1
|
1.0
|
NE2
|
E:HIS23
|
2.0
|
63.1
|
1.0
|
NC
|
E:HEM102
|
2.1
|
54.6
|
1.0
|
ND
|
E:HEM102
|
2.1
|
52.6
|
1.0
|
NE2
|
F:HIS24
|
2.1
|
47.9
|
1.0
|
NA
|
E:HEM102
|
2.1
|
56.9
|
1.0
|
CD2
|
F:HIS24
|
3.0
|
45.8
|
1.0
|
CE1
|
E:HIS23
|
3.0
|
56.8
|
1.0
|
C1B
|
E:HEM102
|
3.0
|
57.8
|
1.0
|
CD2
|
E:HIS23
|
3.0
|
62.2
|
1.0
|
C4B
|
E:HEM102
|
3.0
|
57.8
|
1.0
|
C4D
|
E:HEM102
|
3.1
|
57.8
|
1.0
|
C1C
|
E:HEM102
|
3.1
|
52.3
|
1.0
|
C1A
|
E:HEM102
|
3.1
|
58.0
|
1.0
|
C4C
|
E:HEM102
|
3.1
|
49.5
|
1.0
|
C1D
|
E:HEM102
|
3.1
|
55.3
|
1.0
|
C4A
|
E:HEM102
|
3.1
|
56.6
|
1.0
|
CE1
|
F:HIS24
|
3.2
|
45.3
|
1.0
|
CHC
|
E:HEM102
|
3.4
|
50.8
|
1.0
|
CHA
|
E:HEM102
|
3.4
|
58.2
|
1.0
|
CHB
|
E:HEM102
|
3.4
|
59.5
|
1.0
|
CHD
|
E:HEM102
|
3.5
|
51.3
|
1.0
|
ND1
|
E:HIS23
|
4.1
|
56.1
|
1.0
|
CG
|
E:HIS23
|
4.2
|
59.8
|
1.0
|
CG
|
F:HIS24
|
4.2
|
50.1
|
1.0
|
C2B
|
E:HEM102
|
4.2
|
57.0
|
1.0
|
ND1
|
F:HIS24
|
4.3
|
46.7
|
1.0
|
C3B
|
E:HEM102
|
4.3
|
56.5
|
1.0
|
C2C
|
E:HEM102
|
4.3
|
51.1
|
1.0
|
C3D
|
E:HEM102
|
4.3
|
57.7
|
1.0
|
C2A
|
E:HEM102
|
4.3
|
59.7
|
1.0
|
C3C
|
E:HEM102
|
4.3
|
50.6
|
1.0
|
C3A
|
E:HEM102
|
4.3
|
61.9
|
1.0
|
C2D
|
E:HEM102
|
4.3
|
56.3
|
1.0
|
NE1
|
F:TRP20
|
4.7
|
50.0
|
1.0
|
CE2
|
E:TYR19
|
4.8
|
56.5
|
1.0
|
|
Iron binding site 3 out
of 6 in 5h2f
Go back to
Iron Binding Sites List in 5h2f
Iron binding site 3 out
of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe202
b:30.1
occ:1.00
|
FE
|
V:HEC202
|
0.0
|
30.1
|
1.0
|
NA
|
V:HEC202
|
1.9
|
29.9
|
1.0
|
NE2
|
V:HIS41
|
2.0
|
32.2
|
1.0
|
NE2
|
V:HIS92
|
2.0
|
31.6
|
1.0
|
NC
|
V:HEC202
|
2.0
|
28.3
|
1.0
|
NB
|
V:HEC202
|
2.1
|
29.8
|
1.0
|
ND
|
V:HEC202
|
2.1
|
29.2
|
1.0
|
CD2
|
V:HIS92
|
3.0
|
32.9
|
1.0
|
C1A
|
V:HEC202
|
3.0
|
29.8
|
1.0
|
CE1
|
V:HIS41
|
3.0
|
29.7
|
1.0
|
C4A
|
V:HEC202
|
3.0
|
31.8
|
1.0
|
CD2
|
V:HIS41
|
3.0
|
29.9
|
1.0
|
CE1
|
V:HIS92
|
3.0
|
30.8
|
1.0
|
C4C
|
V:HEC202
|
3.1
|
28.8
|
1.0
|
C4D
|
V:HEC202
|
3.1
|
30.7
|
1.0
|
C1C
|
V:HEC202
|
3.1
|
29.7
|
1.0
|
C1B
|
V:HEC202
|
3.1
|
30.1
|
1.0
|
C1D
|
V:HEC202
|
3.1
|
29.4
|
1.0
|
C4B
|
V:HEC202
|
3.1
|
30.3
|
1.0
|
CHA
|
V:HEC202
|
3.4
|
29.3
|
1.0
|
CHB
|
V:HEC202
|
3.4
|
31.6
|
1.0
|
CHD
|
V:HEC202
|
3.5
|
27.4
|
1.0
|
CHC
|
V:HEC202
|
3.5
|
27.6
|
1.0
|
ND1
|
V:HIS41
|
4.1
|
28.2
|
1.0
|
ND1
|
V:HIS92
|
4.2
|
28.1
|
1.0
|
CG
|
V:HIS92
|
4.2
|
30.5
|
1.0
|
CG
|
V:HIS41
|
4.2
|
29.7
|
1.0
|
C3A
|
V:HEC202
|
4.2
|
31.1
|
1.0
|
C2A
|
V:HEC202
|
4.2
|
30.0
|
1.0
|
C3C
|
V:HEC202
|
4.3
|
27.2
|
1.0
|
C2C
|
V:HEC202
|
4.3
|
28.2
|
1.0
|
C3D
|
V:HEC202
|
4.3
|
28.6
|
1.0
|
C2B
|
V:HEC202
|
4.3
|
30.3
|
1.0
|
C2D
|
V:HEC202
|
4.4
|
29.8
|
1.0
|
C3B
|
V:HEC202
|
4.4
|
31.1
|
1.0
|
CE1
|
V:TYR75
|
4.6
|
30.8
|
1.0
|
OH
|
V:TYR75
|
5.0
|
29.4
|
1.0
|
|
Iron binding site 4 out
of 6 in 5h2f
Go back to
Iron Binding Sites List in 5h2f
Iron binding site 4 out
of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe404
b:42.7
occ:1.00
|
NE2
|
a:HIS215
|
2.0
|
36.2
|
1.0
|
NE2
|
d:HIS214
|
2.1
|
36.0
|
1.0
|
NE2
|
a:HIS272
|
2.3
|
37.8
|
1.0
|
NE2
|
d:HIS268
|
2.3
|
28.3
|
1.0
|
O2
|
a:BCT422
|
2.4
|
51.2
|
1.0
|
O3
|
a:BCT422
|
2.6
|
52.3
|
1.0
|
C
|
a:BCT422
|
2.9
|
57.5
|
1.0
|
CE1
|
a:HIS215
|
2.9
|
35.0
|
1.0
|
CD2
|
d:HIS214
|
3.0
|
32.3
|
1.0
|
CD2
|
a:HIS215
|
3.1
|
35.1
|
1.0
|
CE1
|
d:HIS214
|
3.1
|
33.5
|
1.0
|
CE1
|
d:HIS268
|
3.2
|
26.6
|
1.0
|
CE1
|
a:HIS272
|
3.3
|
33.4
|
1.0
|
CD2
|
a:HIS272
|
3.3
|
35.5
|
1.0
|
CD2
|
d:HIS268
|
3.4
|
30.7
|
1.0
|
ND1
|
a:HIS215
|
4.1
|
32.9
|
1.0
|
CG
|
d:HIS214
|
4.2
|
34.7
|
1.0
|
CG
|
a:HIS215
|
4.2
|
32.5
|
1.0
|
O1
|
a:BCT422
|
4.2
|
56.6
|
1.0
|
ND1
|
d:HIS214
|
4.2
|
35.0
|
1.0
|
ND1
|
a:HIS272
|
4.4
|
37.5
|
1.0
|
ND1
|
d:HIS268
|
4.4
|
28.6
|
1.0
|
CG
|
a:HIS272
|
4.4
|
35.8
|
1.0
|
CG
|
d:HIS268
|
4.5
|
30.4
|
1.0
|
CG2
|
a:VAL219
|
4.7
|
33.5
|
1.0
|
CG2
|
d:VAL218
|
4.8
|
28.8
|
1.0
|
|
Iron binding site 5 out
of 6 in 5h2f
Go back to
Iron Binding Sites List in 5h2f
Iron binding site 5 out
of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Fe101
b:51.2
occ:1.00
|
FE
|
e:HEM101
|
0.0
|
51.2
|
1.0
|
NB
|
e:HEM101
|
2.0
|
51.7
|
1.0
|
NE2
|
f:HIS24
|
2.1
|
60.8
|
1.0
|
ND
|
e:HEM101
|
2.1
|
50.6
|
1.0
|
NE2
|
e:HIS23
|
2.1
|
61.1
|
1.0
|
NC
|
e:HEM101
|
2.1
|
50.4
|
1.0
|
NA
|
e:HEM101
|
2.1
|
57.5
|
1.0
|
CD2
|
f:HIS24
|
2.9
|
52.5
|
1.0
|
C4B
|
e:HEM101
|
3.0
|
53.5
|
1.0
|
C1B
|
e:HEM101
|
3.0
|
56.6
|
1.0
|
CE1
|
e:HIS23
|
3.1
|
60.4
|
1.0
|
C4D
|
e:HEM101
|
3.1
|
55.6
|
1.0
|
CD2
|
e:HIS23
|
3.1
|
59.2
|
1.0
|
C1C
|
e:HEM101
|
3.1
|
47.0
|
1.0
|
C1A
|
e:HEM101
|
3.1
|
60.9
|
1.0
|
C4A
|
e:HEM101
|
3.1
|
56.2
|
1.0
|
C1D
|
e:HEM101
|
3.1
|
50.7
|
1.0
|
CE1
|
f:HIS24
|
3.1
|
54.5
|
1.0
|
C4C
|
e:HEM101
|
3.2
|
46.7
|
1.0
|
CHC
|
e:HEM101
|
3.4
|
48.1
|
1.0
|
CHA
|
e:HEM101
|
3.4
|
57.5
|
1.0
|
CHB
|
e:HEM101
|
3.4
|
59.0
|
1.0
|
CHD
|
e:HEM101
|
3.5
|
48.0
|
1.0
|
CG
|
f:HIS24
|
4.2
|
56.2
|
1.0
|
ND1
|
e:HIS23
|
4.2
|
55.9
|
1.0
|
CG
|
e:HIS23
|
4.2
|
59.8
|
1.0
|
C3B
|
e:HEM101
|
4.2
|
52.2
|
1.0
|
ND1
|
f:HIS24
|
4.2
|
55.7
|
1.0
|
C2B
|
e:HEM101
|
4.2
|
55.0
|
1.0
|
C3D
|
e:HEM101
|
4.3
|
54.0
|
1.0
|
C3A
|
e:HEM101
|
4.3
|
63.1
|
1.0
|
C2C
|
e:HEM101
|
4.3
|
48.6
|
1.0
|
C2A
|
e:HEM101
|
4.3
|
63.2
|
1.0
|
C2D
|
e:HEM101
|
4.4
|
53.6
|
1.0
|
C3C
|
e:HEM101
|
4.4
|
46.8
|
1.0
|
CE2
|
e:TYR19
|
5.0
|
64.1
|
1.0
|
|
Iron binding site 6 out
of 6 in 5h2f
Go back to
Iron Binding Sites List in 5h2f
Iron binding site 6 out
of 6 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
v:Fe202
b:38.5
occ:1.00
|
FE
|
v:HEC202
|
0.0
|
38.5
|
1.0
|
NE2
|
v:HIS92
|
1.9
|
36.4
|
1.0
|
NA
|
v:HEC202
|
2.0
|
37.4
|
1.0
|
NE2
|
v:HIS41
|
2.0
|
40.4
|
1.0
|
NB
|
v:HEC202
|
2.1
|
37.6
|
1.0
|
NC
|
v:HEC202
|
2.1
|
40.3
|
1.0
|
ND
|
v:HEC202
|
2.1
|
41.7
|
1.0
|
CE1
|
v:HIS92
|
2.8
|
38.2
|
1.0
|
CE1
|
v:HIS41
|
2.9
|
35.0
|
1.0
|
C1A
|
v:HEC202
|
2.9
|
38.0
|
1.0
|
CD2
|
v:HIS92
|
3.0
|
35.4
|
1.0
|
C4D
|
v:HEC202
|
3.0
|
38.8
|
1.0
|
C1C
|
v:HEC202
|
3.0
|
37.7
|
1.0
|
CD2
|
v:HIS41
|
3.0
|
38.7
|
1.0
|
C4B
|
v:HEC202
|
3.0
|
37.3
|
1.0
|
C4A
|
v:HEC202
|
3.1
|
38.0
|
1.0
|
C1B
|
v:HEC202
|
3.1
|
35.4
|
1.0
|
C4C
|
v:HEC202
|
3.1
|
39.9
|
1.0
|
C1D
|
v:HEC202
|
3.1
|
38.7
|
1.0
|
CHA
|
v:HEC202
|
3.3
|
35.2
|
1.0
|
CHC
|
v:HEC202
|
3.4
|
37.9
|
1.0
|
CHB
|
v:HEC202
|
3.5
|
36.7
|
1.0
|
CHD
|
v:HEC202
|
3.5
|
38.2
|
1.0
|
ND1
|
v:HIS92
|
4.0
|
34.5
|
1.0
|
ND1
|
v:HIS41
|
4.1
|
38.0
|
1.0
|
CG
|
v:HIS92
|
4.1
|
33.7
|
1.0
|
CG
|
v:HIS41
|
4.2
|
38.6
|
1.0
|
C2A
|
v:HEC202
|
4.2
|
38.4
|
1.0
|
C3D
|
v:HEC202
|
4.3
|
38.4
|
1.0
|
C3A
|
v:HEC202
|
4.3
|
35.5
|
1.0
|
C2C
|
v:HEC202
|
4.3
|
37.1
|
1.0
|
C3B
|
v:HEC202
|
4.3
|
35.3
|
1.0
|
C2B
|
v:HEC202
|
4.3
|
35.3
|
1.0
|
C3C
|
v:HEC202
|
4.3
|
36.8
|
1.0
|
C2D
|
v:HEC202
|
4.3
|
37.9
|
1.0
|
CE1
|
v:TYR75
|
4.8
|
39.2
|
1.0
|
|
Reference:
S.Uto,
K.Kawakami,
Y.Umena,
M.Iwai,
M.Ikeuchi,
J.R.Shen,
N.Kamiya.
Mutual Relationships Between Structural and Functional Changes in A Psbm-Deletion Mutant of Photosystem II. Faraday Discuss. V. 198 107 2017.
ISSN: ISSN 1359-6640
PubMed: 28272640
DOI: 10.1039/C6FD00213G
Page generated: Tue Aug 6 01:42:26 2024
|