Iron in PDB 5v2c: Re-Refinement of Crystal Structure of Photosystem II Complex
Enzymatic activity of Re-Refinement of Crystal Structure of Photosystem II Complex
All present enzymatic activity of Re-Refinement of Crystal Structure of Photosystem II Complex:
1.10.3.9;
Protein crystallography data
The structure of Re-Refinement of Crystal Structure of Photosystem II Complex, PDB code: 5v2c
was solved by
J.Wang,
J.M.Wiwczar,
G.W.Brudvig,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
178.62 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
122.190,
228.510,
286.400,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
9.2 /
16.3
|
Other elements in 5v2c:
The structure of Re-Refinement of Crystal Structure of Photosystem II Complex also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Re-Refinement of Crystal Structure of Photosystem II Complex
(pdb code 5v2c). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Re-Refinement of Crystal Structure of Photosystem II Complex, PDB code: 5v2c:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 5v2c
Go back to
Iron Binding Sites List in 5v2c
Iron binding site 1 out
of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe602
b:25.6
occ:1.00
|
NE2
|
D:HIS214
|
2.0
|
25.4
|
1.0
|
NE2
|
A:HIS215
|
2.1
|
25.6
|
1.0
|
NE2
|
A:HIS272
|
2.1
|
28.3
|
1.0
|
NE2
|
D:HIS268
|
2.1
|
26.1
|
1.0
|
O1
|
A:BCT605
|
2.2
|
27.1
|
1.0
|
O2
|
A:BCT605
|
2.2
|
31.6
|
1.0
|
C
|
A:BCT605
|
2.5
|
35.3
|
1.0
|
CE1
|
A:HIS215
|
2.9
|
27.2
|
1.0
|
CE1
|
A:HIS272
|
3.0
|
29.6
|
1.0
|
CE1
|
D:HIS214
|
3.0
|
25.0
|
1.0
|
CE1
|
D:HIS268
|
3.0
|
28.6
|
1.0
|
CD2
|
D:HIS214
|
3.1
|
25.8
|
1.0
|
CD2
|
A:HIS215
|
3.2
|
24.4
|
1.0
|
CD2
|
A:HIS272
|
3.2
|
26.4
|
1.0
|
CD2
|
D:HIS268
|
3.2
|
25.0
|
1.0
|
O3
|
A:BCT605
|
3.9
|
52.0
|
1.0
|
ND1
|
A:HIS215
|
4.1
|
25.0
|
1.0
|
ND1
|
D:HIS214
|
4.1
|
22.8
|
1.0
|
ND1
|
A:HIS272
|
4.2
|
25.2
|
1.0
|
CG
|
D:HIS214
|
4.2
|
23.5
|
1.0
|
ND1
|
D:HIS268
|
4.2
|
27.1
|
1.0
|
CG
|
A:HIS215
|
4.2
|
24.3
|
1.0
|
CG
|
A:HIS272
|
4.3
|
25.4
|
1.0
|
CG
|
D:HIS268
|
4.3
|
22.7
|
1.0
|
CG2
|
A:VAL219
|
4.6
|
29.8
|
1.0
|
CG2
|
D:VAL218
|
4.8
|
22.9
|
1.0
|
O
|
A:HOH702
|
4.8
|
57.7
|
1.0
|
OH
|
D:TYR244
|
4.9
|
36.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 5v2c
Go back to
Iron Binding Sites List in 5v2c
Iron binding site 2 out
of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe113
b:39.9
occ:1.00
|
FE
|
E:HEM113
|
0.0
|
39.9
|
1.0
|
ND
|
E:HEM113
|
1.9
|
40.4
|
1.0
|
NE2
|
F:HIS24
|
1.9
|
37.1
|
1.0
|
NE2
|
E:HIS23
|
2.0
|
43.6
|
1.0
|
NA
|
E:HEM113
|
2.0
|
40.6
|
1.0
|
NC
|
E:HEM113
|
2.1
|
38.9
|
1.0
|
NB
|
E:HEM113
|
2.1
|
38.5
|
1.0
|
C4D
|
E:HEM113
|
2.9
|
43.2
|
1.0
|
CD2
|
F:HIS24
|
2.9
|
44.6
|
1.0
|
C1D
|
E:HEM113
|
2.9
|
41.5
|
1.0
|
CE1
|
E:HIS23
|
2.9
|
42.6
|
1.0
|
CE1
|
F:HIS24
|
2.9
|
45.3
|
1.0
|
C1A
|
E:HEM113
|
3.0
|
46.2
|
1.0
|
C4B
|
E:HEM113
|
3.0
|
38.8
|
1.0
|
C1B
|
E:HEM113
|
3.0
|
41.9
|
1.0
|
CD2
|
E:HIS23
|
3.0
|
36.5
|
1.0
|
C4C
|
E:HEM113
|
3.0
|
40.0
|
1.0
|
C4A
|
E:HEM113
|
3.1
|
45.9
|
1.0
|
C1C
|
E:HEM113
|
3.1
|
41.4
|
1.0
|
CHA
|
E:HEM113
|
3.3
|
36.3
|
1.0
|
CHD
|
E:HEM113
|
3.4
|
37.7
|
1.0
|
CHC
|
E:HEM113
|
3.4
|
35.6
|
1.0
|
CHB
|
E:HEM113
|
3.4
|
44.8
|
1.0
|
ND1
|
F:HIS24
|
4.0
|
42.9
|
1.0
|
CG
|
F:HIS24
|
4.1
|
42.8
|
1.0
|
ND1
|
E:HIS23
|
4.1
|
41.8
|
1.0
|
CG
|
E:HIS23
|
4.1
|
40.5
|
1.0
|
C3D
|
E:HEM113
|
4.2
|
46.5
|
1.0
|
C2D
|
E:HEM113
|
4.2
|
39.7
|
1.0
|
C2A
|
E:HEM113
|
4.2
|
47.9
|
1.0
|
C3C
|
E:HEM113
|
4.2
|
39.1
|
1.0
|
C2C
|
E:HEM113
|
4.3
|
36.7
|
1.0
|
C3A
|
E:HEM113
|
4.3
|
47.4
|
1.0
|
C2B
|
E:HEM113
|
4.3
|
41.3
|
1.0
|
C3B
|
E:HEM113
|
4.3
|
40.8
|
1.0
|
CE1
|
E:TYR19
|
4.8
|
39.3
|
1.0
|
NE1
|
F:TRP20
|
4.9
|
41.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 5v2c
Go back to
Iron Binding Sites List in 5v2c
Iron binding site 3 out
of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe203
b:24.8
occ:1.00
|
FE
|
V:HEM203
|
0.0
|
24.8
|
1.0
|
NE2
|
V:HIS41
|
1.9
|
25.1
|
1.0
|
ND
|
V:HEM203
|
1.9
|
27.1
|
1.0
|
NE2
|
V:HIS92
|
2.0
|
23.4
|
1.0
|
NC
|
V:HEM203
|
2.0
|
21.2
|
1.0
|
NA
|
V:HEM203
|
2.0
|
24.7
|
1.0
|
NB
|
V:HEM203
|
2.1
|
20.6
|
1.0
|
CE1
|
V:HIS41
|
2.9
|
26.1
|
1.0
|
C4D
|
V:HEM203
|
2.9
|
25.0
|
1.0
|
CE1
|
V:HIS92
|
2.9
|
26.1
|
1.0
|
CD2
|
V:HIS41
|
3.0
|
24.2
|
1.0
|
C1D
|
V:HEM203
|
3.0
|
21.4
|
1.0
|
CD2
|
V:HIS92
|
3.0
|
27.1
|
1.0
|
C4C
|
V:HEM203
|
3.0
|
22.6
|
1.0
|
C1C
|
V:HEM203
|
3.0
|
24.3
|
1.0
|
C1A
|
V:HEM203
|
3.0
|
22.7
|
1.0
|
C4B
|
V:HEM203
|
3.0
|
22.8
|
1.0
|
C1B
|
V:HEM203
|
3.1
|
24.1
|
1.0
|
C4A
|
V:HEM203
|
3.1
|
25.1
|
1.0
|
CHA
|
V:HEM203
|
3.4
|
23.5
|
1.0
|
CHC
|
V:HEM203
|
3.4
|
23.5
|
1.0
|
CHD
|
V:HEM203
|
3.4
|
22.2
|
1.0
|
CHB
|
V:HEM203
|
3.4
|
25.7
|
1.0
|
ND1
|
V:HIS92
|
4.1
|
27.5
|
1.0
|
ND1
|
V:HIS41
|
4.1
|
22.8
|
1.0
|
CG
|
V:HIS41
|
4.1
|
22.8
|
1.0
|
CG
|
V:HIS92
|
4.1
|
25.5
|
1.0
|
C2D
|
V:HEM203
|
4.2
|
23.2
|
1.0
|
C3D
|
V:HEM203
|
4.2
|
23.5
|
1.0
|
C3C
|
V:HEM203
|
4.3
|
23.6
|
1.0
|
C2C
|
V:HEM203
|
4.3
|
22.8
|
1.0
|
C2A
|
V:HEM203
|
4.3
|
25.5
|
1.0
|
C2B
|
V:HEM203
|
4.3
|
24.3
|
1.0
|
C3A
|
V:HEM203
|
4.3
|
25.3
|
1.0
|
C3B
|
V:HEM203
|
4.3
|
24.6
|
1.0
|
CE1
|
V:TYR75
|
4.7
|
24.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 5v2c
Go back to
Iron Binding Sites List in 5v2c
Iron binding site 4 out
of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe403
b:25.8
occ:1.00
|
NE2
|
d:HIS214
|
2.0
|
26.1
|
1.0
|
NE2
|
a:HIS215
|
2.0
|
26.4
|
1.0
|
NE2
|
d:HIS268
|
2.1
|
25.6
|
1.0
|
NE2
|
a:HIS272
|
2.1
|
26.8
|
1.0
|
O2
|
a:BCT406
|
2.1
|
28.9
|
1.0
|
O1
|
a:BCT406
|
2.2
|
27.0
|
1.0
|
C
|
a:BCT406
|
2.5
|
31.7
|
1.0
|
CE1
|
a:HIS215
|
2.9
|
27.1
|
1.0
|
CE1
|
d:HIS268
|
3.0
|
26.4
|
1.0
|
CE1
|
d:HIS214
|
3.0
|
27.8
|
1.0
|
CD2
|
d:HIS214
|
3.0
|
25.5
|
1.0
|
CE1
|
a:HIS272
|
3.0
|
27.6
|
1.0
|
CD2
|
a:HIS215
|
3.2
|
26.1
|
1.0
|
CD2
|
a:HIS272
|
3.2
|
24.9
|
1.0
|
CD2
|
d:HIS268
|
3.2
|
23.1
|
1.0
|
O3
|
a:BCT406
|
3.8
|
50.0
|
1.0
|
ND1
|
a:HIS215
|
4.1
|
27.7
|
1.0
|
ND1
|
d:HIS214
|
4.1
|
22.6
|
1.0
|
ND1
|
d:HIS268
|
4.2
|
24.6
|
1.0
|
CG
|
d:HIS214
|
4.2
|
23.8
|
1.0
|
ND1
|
a:HIS272
|
4.2
|
25.0
|
1.0
|
CG
|
a:HIS215
|
4.2
|
25.9
|
1.0
|
CG
|
a:HIS272
|
4.3
|
26.0
|
1.0
|
CG
|
d:HIS268
|
4.3
|
22.3
|
1.0
|
O
|
a:HOH501
|
4.6
|
58.6
|
1.0
|
CG2
|
a:VAL219
|
4.7
|
25.5
|
1.0
|
CG2
|
d:VAL218
|
4.9
|
23.3
|
1.0
|
OH
|
d:TYR244
|
5.0
|
38.3
|
1.0
|
|
Iron binding site 5 out
of 6 in 5v2c
Go back to
Iron Binding Sites List in 5v2c
Iron binding site 5 out
of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Fe107
b:43.9
occ:1.00
|
FE
|
e:HEM107
|
0.0
|
43.9
|
1.0
|
ND
|
e:HEM107
|
1.9
|
41.9
|
1.0
|
NE2
|
f:HIS24
|
1.9
|
46.1
|
1.0
|
NE2
|
e:HIS23
|
1.9
|
48.8
|
1.0
|
NA
|
e:HEM107
|
2.0
|
43.6
|
1.0
|
NC
|
e:HEM107
|
2.1
|
42.3
|
1.0
|
NB
|
e:HEM107
|
2.1
|
50.1
|
1.0
|
CE1
|
e:HIS23
|
2.9
|
43.6
|
1.0
|
C4D
|
e:HEM107
|
2.9
|
45.1
|
1.0
|
C1D
|
e:HEM107
|
2.9
|
42.8
|
1.0
|
CD2
|
f:HIS24
|
2.9
|
41.0
|
1.0
|
CE1
|
f:HIS24
|
2.9
|
45.5
|
1.0
|
C1A
|
e:HEM107
|
3.0
|
50.8
|
1.0
|
CD2
|
e:HIS23
|
3.0
|
47.3
|
1.0
|
C4A
|
e:HEM107
|
3.0
|
49.3
|
1.0
|
C4C
|
e:HEM107
|
3.1
|
41.3
|
1.0
|
C4B
|
e:HEM107
|
3.1
|
47.3
|
1.0
|
C1C
|
e:HEM107
|
3.1
|
45.3
|
1.0
|
C1B
|
e:HEM107
|
3.1
|
44.3
|
1.0
|
CHA
|
e:HEM107
|
3.4
|
42.8
|
1.0
|
CHD
|
e:HEM107
|
3.4
|
40.5
|
1.0
|
CHC
|
e:HEM107
|
3.4
|
46.0
|
1.0
|
CHB
|
e:HEM107
|
3.4
|
46.3
|
1.0
|
ND1
|
e:HIS23
|
4.0
|
44.9
|
1.0
|
ND1
|
f:HIS24
|
4.1
|
43.2
|
1.0
|
CG
|
f:HIS24
|
4.1
|
43.5
|
1.0
|
CG
|
e:HIS23
|
4.1
|
45.1
|
1.0
|
C3D
|
e:HEM107
|
4.2
|
45.0
|
1.0
|
C2D
|
e:HEM107
|
4.2
|
46.6
|
1.0
|
C2A
|
e:HEM107
|
4.2
|
47.1
|
1.0
|
C3A
|
e:HEM107
|
4.2
|
50.4
|
1.0
|
C3C
|
e:HEM107
|
4.3
|
44.0
|
1.0
|
C2C
|
e:HEM107
|
4.3
|
42.6
|
1.0
|
C2B
|
e:HEM107
|
4.3
|
53.3
|
1.0
|
C3B
|
e:HEM107
|
4.4
|
50.6
|
1.0
|
CE1
|
e:TYR19
|
4.7
|
44.3
|
1.0
|
NE1
|
f:TRP20
|
4.8
|
52.4
|
1.0
|
|
Iron binding site 6 out
of 6 in 5v2c
Go back to
Iron Binding Sites List in 5v2c
Iron binding site 6 out
of 6 in the Re-Refinement of Crystal Structure of Photosystem II Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Re-Refinement of Crystal Structure of Photosystem II Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
v:Fe202
b:31.8
occ:1.00
|
FE
|
v:HEM202
|
0.0
|
31.8
|
1.0
|
NE2
|
v:HIS41
|
1.9
|
33.7
|
1.0
|
NE2
|
v:HIS92
|
1.9
|
26.8
|
1.0
|
ND
|
v:HEM202
|
2.0
|
34.2
|
1.0
|
NA
|
v:HEM202
|
2.0
|
29.6
|
1.0
|
NC
|
v:HEM202
|
2.1
|
33.4
|
1.0
|
NB
|
v:HEM202
|
2.1
|
29.7
|
1.0
|
CE1
|
v:HIS41
|
2.9
|
31.5
|
1.0
|
CE1
|
v:HIS92
|
2.9
|
27.7
|
1.0
|
C4D
|
v:HEM202
|
3.0
|
29.6
|
1.0
|
CD2
|
v:HIS92
|
3.0
|
29.0
|
1.0
|
CD2
|
v:HIS41
|
3.0
|
30.6
|
1.0
|
C1A
|
v:HEM202
|
3.0
|
34.2
|
1.0
|
C1D
|
v:HEM202
|
3.0
|
30.4
|
1.0
|
C4B
|
v:HEM202
|
3.0
|
34.3
|
1.0
|
C1B
|
v:HEM202
|
3.0
|
30.5
|
1.0
|
C1C
|
v:HEM202
|
3.1
|
32.0
|
1.0
|
C4C
|
v:HEM202
|
3.1
|
29.0
|
1.0
|
C4A
|
v:HEM202
|
3.1
|
29.7
|
1.0
|
CHA
|
v:HEM202
|
3.4
|
30.6
|
1.0
|
CHC
|
v:HEM202
|
3.4
|
32.9
|
1.0
|
CHB
|
v:HEM202
|
3.4
|
26.2
|
1.0
|
CHD
|
v:HEM202
|
3.5
|
29.9
|
1.0
|
ND1
|
v:HIS41
|
4.0
|
31.1
|
1.0
|
ND1
|
v:HIS92
|
4.0
|
29.2
|
1.0
|
CG
|
v:HIS92
|
4.1
|
29.1
|
1.0
|
CG
|
v:HIS41
|
4.1
|
30.2
|
1.0
|
C3D
|
v:HEM202
|
4.2
|
28.3
|
1.0
|
C2D
|
v:HEM202
|
4.2
|
31.3
|
1.0
|
C2C
|
v:HEM202
|
4.2
|
27.6
|
1.0
|
C2A
|
v:HEM202
|
4.3
|
30.9
|
1.0
|
C2B
|
v:HEM202
|
4.3
|
31.4
|
1.0
|
C3A
|
v:HEM202
|
4.3
|
30.6
|
1.0
|
C3C
|
v:HEM202
|
4.3
|
30.4
|
1.0
|
C3B
|
v:HEM202
|
4.3
|
32.1
|
1.0
|
CE1
|
v:TYR75
|
4.9
|
35.5
|
1.0
|
|
Reference:
J.M.Wiwczar,
A.M.Lafountain,
J.Wang,
H.A.Frank,
G.W.Brudvig.
Chlorophyll A with A Farnesyl Tail in Thermophilic Cyanobacteria. Photosyn. Res. V. 134 175 2017.
ISSN: ISSN 1573-5079
PubMed: 28741056
DOI: 10.1007/S11120-017-0425-4
Page generated: Tue Aug 6 10:06:26 2024
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