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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:

Magnesium (Mg) 72 atoms
Iron (Fe) 6 atoms

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

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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

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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

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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

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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

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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

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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

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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

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