Iron in PDB 1izl: Crystal Structure of Photosystem II
Protein crystallography data
The structure of Crystal Structure of Photosystem II, PDB code: 1izl
was solved by
N.Kamiya,
J.-R.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
3.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
129.377,
225.192,
308.672,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
53 /
n/a
|
Other elements in 1izl:
The structure of Crystal Structure of Photosystem II also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Photosystem II
(pdb code 1izl). 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 Photosystem II, PDB code: 1izl:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1izl
Go back to
Iron Binding Sites List in 1izl
Iron binding site 1 out
of 6 in the Crystal Structure 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 Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe353
b:46.9
occ:1.00
|
CE1
|
D:HIS214
|
3.5
|
46.9
|
1.0
|
ND1
|
D:HIS214
|
4.3
|
46.9
|
1.0
|
NE2
|
D:HIS214
|
4.4
|
46.9
|
1.0
|
|
Iron binding site 2 out
of 6 in 1izl
Go back to
Iron Binding Sites List in 1izl
Iron binding site 2 out
of 6 in the Crystal Structure 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 Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe84
b:46.9
occ:1.00
|
FE
|
E:HEM84
|
0.0
|
46.9
|
1.0
|
ND
|
E:HEM84
|
2.0
|
46.9
|
1.0
|
NA
|
E:HEM84
|
2.0
|
46.9
|
1.0
|
NC
|
E:HEM84
|
2.1
|
46.9
|
1.0
|
NB
|
E:HEM84
|
2.1
|
46.9
|
1.0
|
C4D
|
E:HEM84
|
3.0
|
46.9
|
1.0
|
C4A
|
E:HEM84
|
3.0
|
46.9
|
1.0
|
C1D
|
E:HEM84
|
3.0
|
46.9
|
1.0
|
C1A
|
E:HEM84
|
3.1
|
46.9
|
1.0
|
C1B
|
E:HEM84
|
3.1
|
46.9
|
1.0
|
C1C
|
E:HEM84
|
3.1
|
46.9
|
1.0
|
C4C
|
E:HEM84
|
3.1
|
46.9
|
1.0
|
C4B
|
E:HEM84
|
3.2
|
46.9
|
1.0
|
CHA
|
E:HEM84
|
3.4
|
46.9
|
1.0
|
CHB
|
E:HEM84
|
3.4
|
46.9
|
1.0
|
CHD
|
E:HEM84
|
3.4
|
46.9
|
1.0
|
CHC
|
E:HEM84
|
3.5
|
46.9
|
1.0
|
C2D
|
E:HEM84
|
4.2
|
46.9
|
1.0
|
C3D
|
E:HEM84
|
4.3
|
46.9
|
1.0
|
C3A
|
E:HEM84
|
4.3
|
46.9
|
1.0
|
C2B
|
E:HEM84
|
4.3
|
46.9
|
1.0
|
C2A
|
E:HEM84
|
4.4
|
46.9
|
1.0
|
C3B
|
E:HEM84
|
4.4
|
46.9
|
1.0
|
C2C
|
E:HEM84
|
4.5
|
46.9
|
1.0
|
C3C
|
E:HEM84
|
4.5
|
46.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 1izl
Go back to
Iron Binding Sites List in 1izl
Iron binding site 3 out
of 6 in the Crystal Structure 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 Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe138
b:46.9
occ:1.00
|
FE
|
V:HEM138
|
0.0
|
46.9
|
1.0
|
ND
|
V:HEM138
|
2.0
|
46.9
|
1.0
|
NA
|
V:HEM138
|
2.0
|
46.9
|
1.0
|
NC
|
V:HEM138
|
2.1
|
46.9
|
1.0
|
NB
|
V:HEM138
|
2.1
|
46.9
|
1.0
|
NE2
|
V:HIS92
|
2.6
|
46.9
|
1.0
|
NE2
|
V:HIS41
|
2.8
|
46.9
|
1.0
|
C4D
|
V:HEM138
|
3.0
|
46.9
|
1.0
|
C4A
|
V:HEM138
|
3.0
|
46.9
|
1.0
|
C1D
|
V:HEM138
|
3.0
|
46.9
|
1.0
|
C1A
|
V:HEM138
|
3.1
|
46.9
|
1.0
|
CE1
|
V:HIS92
|
3.1
|
46.9
|
1.0
|
C1B
|
V:HEM138
|
3.1
|
46.9
|
1.0
|
C1C
|
V:HEM138
|
3.1
|
46.9
|
1.0
|
C4C
|
V:HEM138
|
3.1
|
46.9
|
1.0
|
C4B
|
V:HEM138
|
3.2
|
46.9
|
1.0
|
CHA
|
V:HEM138
|
3.4
|
46.9
|
1.0
|
CHB
|
V:HEM138
|
3.4
|
46.9
|
1.0
|
CD2
|
V:HIS92
|
3.4
|
46.9
|
1.0
|
CHD
|
V:HEM138
|
3.4
|
46.9
|
1.0
|
CHC
|
V:HEM138
|
3.5
|
46.9
|
1.0
|
CE1
|
V:HIS41
|
3.5
|
46.9
|
1.0
|
CD2
|
V:HIS41
|
3.9
|
46.9
|
1.0
|
ND1
|
V:HIS92
|
4.0
|
46.9
|
1.0
|
C2D
|
V:HEM138
|
4.2
|
46.9
|
1.0
|
CG
|
V:HIS92
|
4.2
|
46.9
|
1.0
|
C3D
|
V:HEM138
|
4.3
|
46.9
|
1.0
|
C3A
|
V:HEM138
|
4.3
|
46.9
|
1.0
|
C2B
|
V:HEM138
|
4.3
|
46.9
|
1.0
|
C2A
|
V:HEM138
|
4.4
|
46.9
|
1.0
|
C3B
|
V:HEM138
|
4.4
|
46.9
|
1.0
|
C2C
|
V:HEM138
|
4.5
|
46.9
|
1.0
|
C3C
|
V:HEM138
|
4.5
|
46.9
|
1.0
|
ND1
|
V:HIS41
|
4.7
|
46.9
|
1.0
|
CG
|
V:HIS41
|
4.9
|
46.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 1izl
Go back to
Iron Binding Sites List in 1izl
Iron binding site 4 out
of 6 in the Crystal Structure 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 Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe353
b:46.9
occ:1.00
|
CE1
|
N:HIS214
|
3.5
|
46.9
|
1.0
|
ND1
|
N:HIS214
|
4.3
|
46.9
|
1.0
|
NE2
|
N:HIS214
|
4.4
|
46.9
|
1.0
|
|
Iron binding site 5 out
of 6 in 1izl
Go back to
Iron Binding Sites List in 1izl
Iron binding site 5 out
of 6 in the Crystal Structure 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 Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Fe92
b:46.9
occ:1.00
|
FE
|
P:HEM92
|
0.0
|
46.9
|
1.0
|
ND
|
P:HEM92
|
2.0
|
46.9
|
1.0
|
NA
|
P:HEM92
|
2.0
|
46.9
|
1.0
|
NC
|
P:HEM92
|
2.1
|
46.9
|
1.0
|
NB
|
P:HEM92
|
2.1
|
46.9
|
1.0
|
C4D
|
P:HEM92
|
3.0
|
46.9
|
1.0
|
C4A
|
P:HEM92
|
3.0
|
46.9
|
1.0
|
C1D
|
P:HEM92
|
3.0
|
46.9
|
1.0
|
C1A
|
P:HEM92
|
3.1
|
46.9
|
1.0
|
C1B
|
P:HEM92
|
3.1
|
46.9
|
1.0
|
C1C
|
P:HEM92
|
3.1
|
46.9
|
1.0
|
C4C
|
P:HEM92
|
3.1
|
46.9
|
1.0
|
C4B
|
P:HEM92
|
3.2
|
46.9
|
1.0
|
CHA
|
P:HEM92
|
3.4
|
46.9
|
1.0
|
CHB
|
P:HEM92
|
3.4
|
46.9
|
1.0
|
CHD
|
P:HEM92
|
3.4
|
46.9
|
1.0
|
CHC
|
P:HEM92
|
3.5
|
46.9
|
1.0
|
C2D
|
P:HEM92
|
4.2
|
46.9
|
1.0
|
C3D
|
P:HEM92
|
4.3
|
46.9
|
1.0
|
C3A
|
P:HEM92
|
4.3
|
46.9
|
1.0
|
C2B
|
P:HEM92
|
4.3
|
46.9
|
1.0
|
C2A
|
P:HEM92
|
4.4
|
46.9
|
1.0
|
C3B
|
P:HEM92
|
4.4
|
46.9
|
1.0
|
C2C
|
P:HEM92
|
4.5
|
46.9
|
1.0
|
C3C
|
P:HEM92
|
4.5
|
46.9
|
1.0
|
|
Iron binding site 6 out
of 6 in 1izl
Go back to
Iron Binding Sites List in 1izl
Iron binding site 6 out
of 6 in the Crystal Structure 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 Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
0:Fe138
b:46.9
occ:1.00
|
FE
|
0:HEM138
|
0.0
|
46.9
|
1.0
|
ND
|
0:HEM138
|
2.0
|
46.9
|
1.0
|
NA
|
0:HEM138
|
2.0
|
46.9
|
1.0
|
NC
|
0:HEM138
|
2.1
|
46.9
|
1.0
|
NB
|
0:HEM138
|
2.1
|
46.9
|
1.0
|
NE2
|
0:HIS92
|
2.6
|
46.9
|
1.0
|
NE2
|
0:HIS41
|
2.8
|
46.9
|
1.0
|
C4D
|
0:HEM138
|
3.0
|
46.9
|
1.0
|
C4A
|
0:HEM138
|
3.0
|
46.9
|
1.0
|
C1D
|
0:HEM138
|
3.0
|
46.9
|
1.0
|
C1A
|
0:HEM138
|
3.1
|
46.9
|
1.0
|
CE1
|
0:HIS92
|
3.1
|
46.9
|
1.0
|
C1B
|
0:HEM138
|
3.1
|
46.9
|
1.0
|
C1C
|
0:HEM138
|
3.1
|
46.9
|
1.0
|
C4C
|
0:HEM138
|
3.1
|
46.9
|
1.0
|
C4B
|
0:HEM138
|
3.2
|
46.9
|
1.0
|
CHB
|
0:HEM138
|
3.4
|
46.9
|
1.0
|
CHA
|
0:HEM138
|
3.4
|
46.9
|
1.0
|
CE1
|
0:HIS41
|
3.4
|
46.9
|
1.0
|
CD2
|
0:HIS92
|
3.4
|
46.9
|
1.0
|
CHD
|
0:HEM138
|
3.4
|
46.9
|
1.0
|
CHC
|
0:HEM138
|
3.5
|
46.9
|
1.0
|
CD2
|
0:HIS41
|
3.9
|
46.9
|
1.0
|
ND1
|
0:HIS92
|
4.0
|
46.9
|
1.0
|
C2D
|
0:HEM138
|
4.2
|
46.9
|
1.0
|
CG
|
0:HIS92
|
4.2
|
46.9
|
1.0
|
C3D
|
0:HEM138
|
4.3
|
46.9
|
1.0
|
C3A
|
0:HEM138
|
4.3
|
46.9
|
1.0
|
C2B
|
0:HEM138
|
4.3
|
46.9
|
1.0
|
C2A
|
0:HEM138
|
4.4
|
46.9
|
1.0
|
C3B
|
0:HEM138
|
4.4
|
46.9
|
1.0
|
C2C
|
0:HEM138
|
4.5
|
46.9
|
1.0
|
C3C
|
0:HEM138
|
4.5
|
46.9
|
1.0
|
ND1
|
0:HIS41
|
4.6
|
46.9
|
1.0
|
CG
|
0:HIS41
|
4.9
|
46.9
|
1.0
|
|
Reference:
N.Kamiya,
J.-R.Shen.
Crystal Structure of Oxygen-Evolving Photosystem II From Thermosynechococcus Vulcanus at 3.7-A Resolution Proc.Natl.Acad.Sci.Usa V. 100 98 2003.
ISSN: ISSN 0027-8424
PubMed: 12518057
DOI: 10.1073/PNAS.0135651100
Page generated: Sat Aug 3 08:18:22 2024
|