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Manganese in PDB 2axt: Crystal Structure of Photosystem II From Thermosynechococcus Elongatus

Protein crystallography data

The structure of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus, PDB code: 2axt was solved by B.Loll, J.Kern, W.Saenger, A.Zouni, J.Biesiadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.692, 225.403, 306.106, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 28.6

Other elements in 2axt:

The structure of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Calcium (Ca) 4 atoms
Iron (Fe) 6 atoms
Neon (Ne) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus (pdb code 2axt). 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 From Thermosynechococcus Elongatus, PDB code: 2axt:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 2axt

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Manganese binding site 1 out of 8 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn565

b:63.8
occ:1.00
 MN1 A:OEC565 0.0 63.8 1.0
OE2 A:GLU189 1.8 65.8 1.0
NE2 A:HIS332 2.2 51.4 1.0
OD2 A:ASP342 2.4 63.8 1.0
MN2 A:OEC565 2.6 63.0 1.0
CD A:GLU189 3.0 66.0 1.0
CD2 A:HIS332 3.1 50.1 1.0
CE1 A:HIS332 3.2 52.9 1.0
MN3 A:OEC565 3.3 65.5 1.0
CG A:ASP342 3.3 63.4 1.0
CA1 A:OEC565 3.4 62.6 1.0
OD1 A:ASP342 3.4 64.2 1.0
OE1 A:GLU189 3.6 67.5 1.0
OE1 A:GLU333 4.0 48.0 1.0
CG A:GLU189 4.1 64.0 1.0
NE2 A:HIS337 4.2 54.1 1.0
ND1 A:HIS332 4.3 49.8 1.0
CG A:HIS332 4.3 48.4 1.0
OXT A:ALA344 4.4 72.9 1.0
OE2 C:GLU354 4.5 64.6 1.0
OE1 C:GLU354 4.6 65.1 1.0
CE1 A:HIS337 4.6 54.8 1.0
CB A:ASP342 4.8 60.4 1.0
CD A:GLU333 4.8 49.0 1.0
O A:ALA344 4.8 73.8 1.0
C A:ALA344 4.9 72.4 1.0
CG1 A:VAL185 4.9 48.4 1.0
CD C:GLU354 5.0 63.9 1.0

Manganese binding site 2 out of 8 in 2axt

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Manganese binding site 2 out of 8 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn565

b:63.0
occ:1.00
 MN2 A:OEC565 0.0 63.0 1.0
OXT A:ALA344 1.8 72.9 1.0
OD1 A:ASP342 2.2 64.2 1.0
OE1 C:GLU354 2.5 65.1 1.0
C A:ALA344 2.6 72.4 1.0
MN1 A:OEC565 2.6 63.8 1.0
MN3 A:OEC565 2.7 65.5 1.0
OE2 C:GLU354 2.9 64.6 1.0
O A:ALA344 3.0 73.8 1.0
CD C:GLU354 3.1 63.9 1.0
CG A:ASP342 3.1 63.4 1.0
OD2 A:ASP342 3.2 63.8 1.0
CA1 A:OEC565 3.2 62.6 1.0
OE2 A:GLU189 3.7 65.8 1.0
CA A:ALA344 3.8 71.8 1.0
N A:ALA344 4.0 71.1 1.0
NE2 A:HIS337 4.0 54.1 1.0
OE1 A:GLU333 4.5 48.0 1.0
CB A:ASP342 4.5 60.4 1.0
CB A:ALA344 4.6 71.8 1.0
CG C:GLU354 4.6 62.5 1.0
NE2 A:HIS332 4.6 51.4 1.0
CD A:GLU189 4.7 66.0 1.0
OE1 A:GLU189 4.8 67.5 1.0
CE1 A:HIS337 4.9 54.8 1.0
CD2 A:HIS337 4.9 52.1 1.0
C A:ASP342 4.9 62.3 1.0
CA A:ASP342 4.9 60.3 1.0

Manganese binding site 3 out of 8 in 2axt

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Manganese binding site 3 out of 8 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn565

b:65.5
occ:1.00
 MN3 A:OEC565 0.0 65.5 1.0
OE2 C:GLU354 2.1 64.6 1.0
OE1 A:GLU333 2.3 48.0 1.0
MN2 A:OEC565 2.7 63.0 1.0
OXT A:ALA344 3.2 72.9 1.0
CD C:GLU354 3.2 63.9 1.0
MN4 A:OEC565 3.2 66.9 1.0
MN1 A:OEC565 3.3 63.8 1.0
CA1 A:OEC565 3.3 62.6 1.0
CD A:GLU333 3.4 49.0 1.0
OE1 C:GLU354 3.7 65.1 1.0
OE2 A:GLU333 3.9 50.5 1.0
OD1 A:ASP170 3.9 65.4 1.0
O A:ALA344 4.0 73.8 1.0
C A:ALA344 4.0 72.4 1.0
NH2 C:ARG357 4.3 53.0 1.0
OD2 A:ASP170 4.3 62.2 1.0
CG C:GLU354 4.5 62.5 1.0
CG A:ASP170 4.6 63.1 1.0
OE2 A:GLU189 4.6 65.8 1.0
NE2 A:HIS332 4.6 51.4 1.0
CG A:GLU333 4.7 46.8 1.0
OD1 A:ASP342 4.8 64.2 1.0
CD2 A:HIS332 4.9 50.1 1.0
NE2 A:HIS337 4.9 54.1 1.0

Manganese binding site 4 out of 8 in 2axt

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Manganese binding site 4 out of 8 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn565

b:66.9
occ:1.00
 MN4 A:OEC565 0.0 66.9 1.0
OD1 A:ASP170 2.4 65.4 1.0
OE2 A:GLU333 2.5 50.5 1.0
CD A:GLU333 3.2 49.0 1.0
OE1 A:GLU333 3.2 48.0 1.0
MN3 A:OEC565 3.2 65.5 1.0
CG A:ASP170 3.6 63.1 1.0
OD1 A:ASP61 4.2 62.1 1.0
OD2 A:ASP170 4.3 62.2 1.0
CA A:ASP170 4.5 57.2 1.0
CG A:GLU333 4.5 46.8 1.0
O A:SER169 4.6 52.8 1.0
CB A:ASP170 4.6 58.8 1.0
CA1 A:OEC565 4.6 62.6 1.0
OE2 C:GLU354 4.9 64.6 1.0
N A:ASP170 5.0 55.2 1.0

Manganese binding site 5 out of 8 in 2axt

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Manganese binding site 5 out of 8 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn5565

b:63.4
occ:1.00
 MN1 a:OEC5565 0.0 63.4 1.0
OE2 a:GLU5189 1.8 68.2 1.0
NE2 a:HIS5332 2.3 64.9 1.0
OD2 a:ASP5342 2.5 65.7 1.0
MN2 a:OEC5565 2.7 67.5 1.0
CD a:GLU5189 3.0 67.2 1.0
MN3 a:OEC5565 3.1 71.1 1.0
CD2 a:HIS5332 3.2 63.6 1.0
CA1 a:OEC5565 3.3 64.2 1.0
CE1 a:HIS5332 3.3 64.8 1.0
CG a:ASP5342 3.3 67.1 1.0
OD1 a:ASP5342 3.4 67.3 1.0
OE1 a:GLU5189 3.6 69.3 1.0
OE1 a:GLU5333 4.0 53.7 1.0
CG a:GLU5189 4.2 64.5 1.0
OXT a:ALA5344 4.3 77.8 1.0
NE2 a:HIS5337 4.3 63.5 1.0
CG a:HIS5332 4.4 62.5 1.0
ND1 a:HIS5332 4.4 63.1 1.0
OE2 c:GLU5354 4.4 64.8 1.0
OE1 c:GLU5354 4.5 63.6 1.0
CE1 a:HIS5337 4.7 64.2 1.0
O a:ALA5344 4.7 78.7 1.0
CD a:GLU5333 4.8 54.1 1.0
CB a:ASP5342 4.8 67.8 1.0
C a:ALA5344 4.8 78.0 1.0
CD c:GLU5354 4.9 64.0 1.0
CG1 a:VAL5185 5.0 52.2 1.0

Manganese binding site 6 out of 8 in 2axt

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Manganese binding site 6 out of 8 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn5565

b:67.5
occ:1.00
 MN2 a:OEC5565 0.0 67.5 1.0
OXT a:ALA5344 1.7 77.8 1.0
OD1 a:ASP5342 2.1 67.3 1.0
OE1 c:GLU5354 2.3 63.6 1.0
C a:ALA5344 2.5 78.0 1.0
MN1 a:OEC5565 2.7 63.4 1.0
MN3 a:OEC5565 2.8 71.1 1.0
OE2 c:GLU5354 2.8 64.8 1.0
CD c:GLU5354 2.9 64.0 1.0
O a:ALA5344 3.0 78.7 1.0
CG a:ASP5342 3.0 67.1 1.0
OD2 a:ASP5342 3.3 65.7 1.0
CA1 a:OEC5565 3.3 64.2 1.0
CA a:ALA5344 3.7 77.0 1.0
OE2 a:GLU5189 3.8 68.2 1.0
N a:ALA5344 3.9 76.2 1.0
NE2 a:HIS5337 4.0 63.5 1.0
CG c:GLU5354 4.4 64.2 1.0
CB a:ALA5344 4.5 76.4 1.0
CB a:ASP5342 4.5 67.8 1.0
OE1 a:GLU5333 4.5 53.7 1.0
NE2 a:HIS5332 4.7 64.9 1.0
CD a:GLU5189 4.8 67.2 1.0
CD2 a:HIS5337 4.8 62.8 1.0
CA a:ASP5342 4.8 67.4 1.0
C a:ASP5342 4.9 68.7 1.0
CE1 a:HIS5337 4.9 64.2 1.0
OE1 a:GLU5189 5.0 69.3 1.0

Manganese binding site 7 out of 8 in 2axt

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Manganese binding site 7 out of 8 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn5565

b:71.1
occ:1.00
 MN3 a:OEC5565 0.0 71.1 1.0
OE2 c:GLU5354 2.1 64.8 1.0
OE1 a:GLU5333 2.2 53.7 1.0
MN2 a:OEC5565 2.8 67.5 1.0
MN4 a:OEC5565 3.1 87.9 1.0
MN1 a:OEC5565 3.1 63.4 1.0
CA1 a:OEC5565 3.2 64.2 1.0
CD c:GLU5354 3.2 64.0 1.0
CD a:GLU5333 3.3 54.1 1.0
OXT a:ALA5344 3.3 77.8 1.0
OE1 c:GLU5354 3.7 63.6 1.0
OE2 a:GLU5333 3.8 53.5 1.0
OD1 a:ASP5170 4.0 67.1 1.0
O a:ALA5344 4.1 78.7 1.0
C a:ALA5344 4.1 78.0 1.0
NH2 c:ARG5357 4.4 58.6 1.0
OD2 a:ASP5170 4.4 69.0 1.0
CG c:GLU5354 4.5 64.2 1.0
NE2 a:HIS5332 4.6 64.9 1.0
OE2 a:GLU5189 4.6 68.2 1.0
CG a:GLU5333 4.6 54.2 1.0
CG a:ASP5170 4.7 66.3 1.0
OD1 a:ASP5342 4.8 67.3 1.0
CD2 a:HIS5332 4.8 63.6 1.0
NE2 a:HIS5337 4.9 63.5 1.0
CB a:GLU5333 5.0 55.1 1.0

Manganese binding site 8 out of 8 in 2axt

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Manganese binding site 8 out of 8 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn5565

b:87.9
occ:1.00
 MN4 a:OEC5565 0.0 87.9 1.0
OE2 a:GLU5333 2.2 53.5 1.0
OD1 a:ASP5170 2.7 67.1 1.0
CD a:GLU5333 2.8 54.1 1.0
OE1 a:GLU5333 2.9 53.7 1.0
MN3 a:OEC5565 3.1 71.1 1.0
CG a:ASP5170 3.9 66.3 1.0
OD1 a:ASP5061 4.0 64.4 1.0
CG a:GLU5333 4.2 54.2 1.0
OD2 a:ASP5170 4.5 69.0 1.0
CA1 a:OEC5565 4.6 64.2 1.0
OE2 c:GLU5354 4.8 64.8 1.0
CA a:ASP5170 4.9 63.3 1.0
O a:SER5169 4.9 61.5 1.0
CB a:ASP5170 5.0 63.6 1.0

Reference:

B.Loll, J.Kern, W.Saenger, A.Zouni, J.Biesiadka. Towards Complete Cofactor Arrangement in the 3.0 A Resolution Structure of Photosystem II Nature V. 438 1040 2005.
ISSN: ISSN 0028-0836
PubMed: 16355230
DOI: 10.1038/NATURE04224
Page generated: Sat Oct 5 13:30:06 2024

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