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Manganese in PDB 1w5c: Photosystem II From Thermosynechococcus Elongatus

Protein crystallography data

The structure of Photosystem II From Thermosynechococcus Elongatus, PDB code: 1w5c was solved by J.Biesiadka, B.Loll, J.Kern, K.-D.Irrgang, A.Zouni, W.Saenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.0 / 3.2
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.517, 224.612, 305.632, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1w5c:

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

Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Photosystem II From Thermosynechococcus Elongatus (pdb code 1w5c). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Photosystem II From Thermosynechococcus Elongatus, PDB code: 1w5c:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1w5c

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Manganese binding site 1 out of 8 in the 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 Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1347

b:45.2
occ:1.00
 OE1 A:GLU333 2.0 45.2 1.0
OE2 A:GLU333 2.2 45.2 1.0
CD A:GLU333 2.4 45.2 1.0
OD1 A:ASP170 2.4 45.2 1.0
MN A:MN1349 2.9 45.2 1.0
CG A:ASP170 3.0 45.2 1.0
OD2 A:ASP170 3.3 45.2 1.0
CG A:GLU333 3.9 45.2 1.0
CB A:ASP170 4.3 45.2 1.0
OD1 A:ASP61 4.5 45.2 1.0
MN A:MN1354 4.6 45.2 1.0
CB A:GLU333 4.7 45.2 1.0
MN A:MN1348 4.9 45.2 1.0

Manganese binding site 2 out of 8 in 1w5c

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Manganese binding site 2 out of 8 in the 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 Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1348

b:45.2
occ:1.00
 MN A:MN1349 2.3 45.2 1.0
NE2 A:HIS332 2.9 45.2 1.0
OE2 A:GLU189 3.1 45.2 1.0
MN A:MN1354 3.1 45.2 1.0
CE1 A:HIS332 3.6 45.2 1.0
CD2 A:HIS332 4.1 45.2 1.0
CD A:GLU189 4.3 45.2 1.0
CA A:LEU341 4.3 45.2 1.0
OE1 A:GLU333 4.7 45.2 1.0
ND1 A:HIS332 4.8 45.2 1.0
MN A:MN1347 4.9 45.2 1.0
CG A:GLU189 4.9 45.2 1.0

Manganese binding site 3 out of 8 in 1w5c

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Manganese binding site 3 out of 8 in the 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 Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1349

b:45.2
occ:1.00
 MN A:MN1348 2.3 45.2 1.0
MN A:MN1354 2.7 45.2 1.0
MN A:MN1347 2.9 45.2 1.0
OE2 A:GLU189 3.0 45.2 1.0
OE1 A:GLU333 3.6 45.2 1.0
NE2 A:HIS332 4.0 45.2 1.0
OD2 A:ASP170 4.1 45.2 1.0
CD A:GLU189 4.2 45.2 1.0
CD A:GLU333 4.3 45.2 1.0
OE2 A:GLU333 4.4 45.2 1.0
CG A:ASP170 4.5 45.2 1.0
OD1 A:ASP170 4.6 45.2 1.0
CD2 A:HIS332 4.7 45.2 1.0
OE1 A:GLU189 4.8 45.2 1.0

Manganese binding site 4 out of 8 in 1w5c

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Manganese binding site 4 out of 8 in the 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 Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1354

b:45.2
occ:1.00
 MN A:MN1349 2.7 45.2 1.0
MN A:MN1348 3.1 45.2 1.0
OD2 A:ASP170 4.5 45.2 1.0
MN A:MN1347 4.6 45.2 1.0
OE2 A:GLU189 4.9 45.2 1.0
CA A:LEU341 4.9 45.2 1.0

Manganese binding site 5 out of 8 in 1w5c

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Manganese binding site 5 out of 8 in the 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 Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1347

b:45.2
occ:1.00
 OE1 G:GLU333 2.0 45.2 1.0
OE2 G:GLU333 2.0 45.2 1.0
CD G:GLU333 2.2 45.2 1.0
OD1 G:ASP170 2.3 45.2 1.0
OD2 G:ASP170 2.6 45.2 1.0
MN G:MN1349 2.8 45.2 1.0
CG G:ASP170 2.8 45.2 1.0
CG G:GLU333 3.8 45.2 1.0
MN G:MN5054 4.3 45.2 1.0
CB G:ASP170 4.3 45.2 1.0
OD1 G:ASP61 4.4 45.2 1.0
CB G:GLU333 4.6 45.2 1.0
MN G:MN1348 4.7 45.2 1.0

Manganese binding site 6 out of 8 in 1w5c

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Manganese binding site 6 out of 8 in the 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 Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1348

b:45.2
occ:1.00
 NE2 G:HIS332 2.4 45.2 1.0
MN G:MN1349 2.5 45.2 1.0
OE2 G:GLU189 2.9 45.2 1.0
MN G:MN5054 3.1 45.2 1.0
CE1 G:HIS332 3.2 45.2 1.0
CD2 G:HIS332 3.5 45.2 1.0
CD G:GLU189 4.2 45.2 1.0
OE1 G:GLU333 4.4 45.2 1.0
ND1 G:HIS332 4.4 45.2 1.0
CG G:HIS332 4.6 45.2 1.0
MN G:MN1347 4.7 45.2 1.0
CA G:LEU341 4.8 45.2 1.0
CG G:GLU189 5.0 45.2 1.0

Manganese binding site 7 out of 8 in 1w5c

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Manganese binding site 7 out of 8 in the 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 Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1349

b:45.2
occ:1.00
 MN G:MN1348 2.5 45.2 1.0
MN G:MN5054 2.6 45.2 1.0
MN G:MN1347 2.8 45.2 1.0
OD2 G:ASP170 2.9 45.2 1.0
OE2 G:GLU189 3.1 45.2 1.0
OE1 G:GLU333 3.5 45.2 1.0
CG G:ASP170 3.9 45.2 1.0
NE2 G:HIS332 4.0 45.2 1.0
CD G:GLU333 4.0 45.2 1.0
OE2 G:GLU333 4.0 45.2 1.0
CD G:GLU189 4.1 45.2 1.0
OD1 G:ASP170 4.3 45.2 1.0
CD2 G:HIS332 4.5 45.2 1.0
OE1 G:GLU189 4.5 45.2 1.0

Manganese binding site 8 out of 8 in 1w5c

Go back to Manganese Binding Sites List in 1w5c
Manganese binding site 8 out of 8 in the 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 Photosystem II From Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn5054

b:45.2
occ:1.00
 MN G:MN1349 2.6 45.2 1.0
MN G:MN1348 3.1 45.2 1.0
OD2 G:ASP170 4.0 45.2 1.0
MN G:MN1347 4.3 45.2 1.0
OE2 G:GLU189 4.5 45.2 1.0
OE1 G:GLU333 4.6 45.2 1.0

Reference:

J.Biesiadka, B.Loll, J.Kern, K.-D.Irrgang, A.Zouni. Crystal Structure of Cyanobacterial Photosystem II at 3.2 A Resolution: A Closer Look at the Mn- Cluster Phys.Chem.Chem.Phys. V. 6 4733 2004.
ISSN: ISSN 1463-9076
Page generated: Sat Oct 5 12:53:16 2024

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