Manganese 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:
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Photosystem II
(pdb code 1izl). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Crystal Structure of Photosystem II, PDB code: 1izl:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 1izl
Go back to
Manganese Binding Sites List in 1izl
Manganese binding site 1 out
of 8 in the Crystal Structure of Photosystem II
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn361
b:46.9
occ:1.00
|
C
|
A:ALA344
|
1.8
|
46.9
|
1.0
|
O
|
A:ALA344
|
2.3
|
46.9
|
1.0
|
MN
|
A:MN362
|
2.7
|
46.9
|
1.0
|
CA
|
A:ALA344
|
3.2
|
46.9
|
1.0
|
MN
|
A:MN364
|
3.3
|
46.9
|
1.0
|
CB
|
A:ALA344
|
3.6
|
46.9
|
1.0
|
N
|
A:ALA344
|
4.0
|
46.9
|
1.0
|
C
|
A:LEU343
|
4.6
|
46.9
|
1.0
|
OE1
|
A:GLU189
|
4.7
|
46.9
|
1.0
|
O
|
A:LEU343
|
4.8
|
46.9
|
1.0
|
|
Manganese binding site 2 out
of 8 in 1izl
Go back to
Manganese Binding Sites List in 1izl
Manganese binding site 2 out
of 8 in the Crystal Structure of Photosystem II
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn362
b:46.9
occ:1.00
|
MN
|
A:MN361
|
2.7
|
46.9
|
1.0
|
MN
|
A:MN363
|
2.7
|
46.9
|
1.0
|
MN
|
A:MN364
|
2.7
|
46.9
|
1.0
|
OE1
|
A:GLU333
|
3.5
|
46.9
|
1.0
|
OE2
|
A:GLU333
|
3.9
|
46.9
|
1.0
|
CD
|
A:GLU333
|
4.1
|
46.9
|
1.0
|
C
|
A:ALA344
|
4.2
|
46.9
|
1.0
|
O
|
A:ALA344
|
4.8
|
46.9
|
1.0
|
OD1
|
A:ASP170
|
4.8
|
46.9
|
1.0
|
CB
|
A:ALA344
|
4.9
|
46.9
|
1.0
|
|
Manganese binding site 3 out
of 8 in 1izl
Go back to
Manganese Binding Sites List in 1izl
Manganese binding site 3 out
of 8 in the Crystal Structure of Photosystem II
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn363
b:46.9
occ:1.00
|
OD1
|
A:ASP170
|
2.2
|
46.9
|
1.0
|
MN
|
A:MN362
|
2.7
|
46.9
|
1.0
|
CG
|
A:ASP170
|
3.2
|
46.9
|
1.0
|
OD2
|
A:ASP170
|
3.8
|
46.9
|
1.0
|
OE1
|
A:GLU333
|
4.0
|
46.9
|
1.0
|
CB
|
A:ASP170
|
4.3
|
46.9
|
1.0
|
OE2
|
A:GLU333
|
4.6
|
46.9
|
1.0
|
CD
|
A:GLU333
|
4.6
|
46.9
|
1.0
|
MN
|
A:MN364
|
5.0
|
46.9
|
1.0
|
|
Manganese binding site 4 out
of 8 in 1izl
Go back to
Manganese Binding Sites List in 1izl
Manganese binding site 4 out
of 8 in the Crystal Structure of Photosystem II
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn364
b:46.9
occ:1.00
|
MN
|
A:MN362
|
2.7
|
46.9
|
1.0
|
CB
|
A:ALA344
|
3.1
|
46.9
|
1.0
|
MN
|
A:MN361
|
3.3
|
46.9
|
1.0
|
OE1
|
A:GLU333
|
3.6
|
46.9
|
1.0
|
C
|
A:ALA344
|
3.9
|
46.9
|
1.0
|
CD
|
A:GLU189
|
3.9
|
46.9
|
1.0
|
OE1
|
A:GLU189
|
4.1
|
46.9
|
1.0
|
CA
|
A:ALA344
|
4.1
|
46.9
|
1.0
|
OE2
|
A:GLU189
|
4.1
|
46.9
|
1.0
|
CG
|
A:GLU189
|
4.3
|
46.9
|
1.0
|
CD
|
A:GLU333
|
4.3
|
46.9
|
1.0
|
OE2
|
A:GLU333
|
4.6
|
46.9
|
1.0
|
N
|
A:ALA344
|
4.9
|
46.9
|
1.0
|
MN
|
A:MN363
|
5.0
|
46.9
|
1.0
|
|
Manganese binding site 5 out
of 8 in 1izl
Go back to
Manganese Binding Sites List in 1izl
Manganese binding site 5 out
of 8 in the Crystal Structure of Photosystem II
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mn361
b:46.9
occ:1.00
|
C
|
J:ALA344
|
1.9
|
46.9
|
1.0
|
O
|
J:ALA344
|
2.5
|
46.9
|
1.0
|
MN
|
J:MN362
|
2.7
|
46.9
|
1.0
|
CA
|
J:ALA344
|
3.2
|
46.9
|
1.0
|
MN
|
J:MN364
|
3.3
|
46.9
|
1.0
|
CB
|
J:ALA344
|
3.5
|
46.9
|
1.0
|
N
|
J:ALA344
|
3.9
|
46.9
|
1.0
|
OE1
|
J:GLU189
|
4.5
|
46.9
|
1.0
|
C
|
J:LEU343
|
4.7
|
46.9
|
1.0
|
O
|
J:LEU343
|
4.9
|
46.9
|
1.0
|
|
Manganese binding site 6 out
of 8 in 1izl
Go back to
Manganese Binding Sites List in 1izl
Manganese binding site 6 out
of 8 in the Crystal Structure of Photosystem II
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Crystal Structure of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mn362
b:46.9
occ:1.00
|
MN
|
J:MN361
|
2.7
|
46.9
|
1.0
|
MN
|
J:MN363
|
2.7
|
46.9
|
1.0
|
MN
|
J:MN364
|
2.8
|
46.9
|
1.0
|
OE1
|
J:GLU333
|
3.5
|
46.9
|
1.0
|
OE2
|
J:GLU333
|
4.0
|
46.9
|
1.0
|
CD
|
J:GLU333
|
4.1
|
46.9
|
1.0
|
C
|
J:ALA344
|
4.3
|
46.9
|
1.0
|
OD1
|
J:ASP170
|
4.8
|
46.9
|
1.0
|
CB
|
J:ALA344
|
4.9
|
46.9
|
1.0
|
O
|
J:ALA344
|
4.9
|
46.9
|
1.0
|
|
Manganese binding site 7 out
of 8 in 1izl
Go back to
Manganese Binding Sites List in 1izl
Manganese binding site 7 out
of 8 in the Crystal Structure of Photosystem II
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mn363
b:46.9
occ:1.00
|
OD1
|
J:ASP170
|
2.2
|
46.9
|
1.0
|
MN
|
J:MN362
|
2.7
|
46.9
|
1.0
|
CG
|
J:ASP170
|
3.3
|
46.9
|
1.0
|
OD2
|
J:ASP170
|
3.9
|
46.9
|
1.0
|
OE1
|
J:GLU333
|
4.0
|
46.9
|
1.0
|
CB
|
J:ASP170
|
4.5
|
46.9
|
1.0
|
CD
|
J:GLU333
|
4.8
|
46.9
|
1.0
|
OE2
|
J:GLU333
|
4.8
|
46.9
|
1.0
|
MN
|
J:MN364
|
4.9
|
46.9
|
1.0
|
|
Manganese binding site 8 out
of 8 in 1izl
Go back to
Manganese Binding Sites List in 1izl
Manganese binding site 8 out
of 8 in the Crystal Structure of Photosystem II
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Crystal Structure of Photosystem II within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mn364
b:46.9
occ:1.00
|
MN
|
J:MN362
|
2.8
|
46.9
|
1.0
|
MN
|
J:MN361
|
3.3
|
46.9
|
1.0
|
CB
|
J:ALA344
|
3.4
|
46.9
|
1.0
|
CD
|
J:GLU189
|
3.5
|
46.9
|
1.0
|
OE1
|
J:GLU189
|
3.6
|
46.9
|
1.0
|
CG
|
J:GLU189
|
3.8
|
46.9
|
1.0
|
OE2
|
J:GLU189
|
3.9
|
46.9
|
1.0
|
OE1
|
J:GLU333
|
3.9
|
46.9
|
1.0
|
C
|
J:ALA344
|
4.2
|
46.9
|
1.0
|
CA
|
J:ALA344
|
4.4
|
46.9
|
1.0
|
CD
|
J:GLU333
|
4.8
|
46.9
|
1.0
|
MN
|
J:MN363
|
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 Oct 5 11:05:05 2024
|