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Manganese in PDB 1s5l: Architecture of the Photosynthetic Oxygen Evolving Center

Protein crystallography data

The structure of Architecture of the Photosynthetic Oxygen Evolving Center, PDB code: 1s5l was solved by K.N.Ferreira, T.M.Iverson, K.Maghlaoui, J.Barber, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.992, 228.849, 309.940, 90.00, 90.00, 90.00
R / Rfree (%) 29.6 / 34.2

Other elements in 1s5l:

The structure of Architecture of the Photosynthetic Oxygen Evolving Center also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Iron (Fe) 6 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Architecture of the Photosynthetic Oxygen Evolving Center (pdb code 1s5l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Architecture of the Photosynthetic Oxygen Evolving Center, PDB code: 1s5l:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1s5l

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Manganese binding site 1 out of 8 in the Architecture of the Photosynthetic Oxygen Evolving Center


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn347

b:74.4
occ:1.00
 MN1 A:OEC347 0.0 74.4 1.0
O2 A:OEC347 1.8 71.1 1.0
O3 A:OEC347 1.9 68.3 1.0
O1 A:OEC347 1.9 69.5 1.0
OD2 A:ASP342 2.0 83.0 1.0
MN2 A:OEC347 2.6 66.9 1.0
MN3 A:OEC347 2.7 68.5 1.0
CG A:ASP342 2.8 82.0 1.0
OE1 C:GLU354 3.1 45.6 1.0
O4 A:OEC347 3.3 71.9 1.0
CB A:ASP342 3.3 79.5 1.0
CA1 A:OEC347 3.3 69.6 1.0
NE2 A:HIS332 3.4 46.6 1.0
OE2 A:GLU189 3.4 63.5 1.0
OXT A:ALA344 3.6 76.6 1.0
OE1 A:GLU189 3.6 68.1 1.0
OD1 A:ASP342 3.9 81.4 1.0
CE1 A:HIS332 3.9 44.9 1.0
CD A:GLU189 4.0 65.2 1.0
NE2 A:HIS337 4.1 47.6 1.0
C A:ALA344 4.1 79.7 1.0
CD C:GLU354 4.2 55.0 1.0
O A:ALA344 4.3 78.5 1.0
CA A:ASP342 4.5 77.3 1.0
OE2 C:GLU354 4.5 58.4 1.0
CD2 A:HIS332 4.6 45.3 1.0
N A:ALA344 4.7 79.5 1.0
CE1 A:HIS337 4.7 45.8 1.0
CD2 A:HIS337 4.9 47.4 1.0

Manganese binding site 2 out of 8 in 1s5l

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Manganese binding site 2 out of 8 in the Architecture of the Photosynthetic Oxygen Evolving Center


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn347

b:66.9
occ:1.00
 MN2 A:OEC347 0.0 66.9 1.0
O1 A:OEC347 1.8 69.5 1.0
O2 A:OEC347 1.8 71.1 1.0
O4 A:OEC347 1.9 71.9 1.0
OE2 A:GLU189 2.0 63.5 1.0
NE2 A:HIS332 2.0 46.6 1.0
CD2 A:HIS332 2.6 45.3 1.0
MN1 A:OEC347 2.6 74.4 1.0
MN3 A:OEC347 2.7 68.5 1.0
OE2 A:GLU333 2.9 52.6 1.0
CD A:GLU189 3.2 65.2 1.0
CE1 A:HIS332 3.2 44.9 1.0
MN4 A:OEC347 3.2 74.0 1.0
O3 A:OEC347 3.3 68.3 1.0
CA1 A:OEC347 3.4 69.6 1.0
CD A:GLU333 3.6 45.9 1.0
OE1 A:GLU189 3.7 68.1 1.0
CG A:HIS332 3.8 47.5 1.0
OE1 A:GLU333 4.0 41.4 1.0
ND1 A:HIS332 4.1 46.6 1.0
O2 A:BCT346 4.1 70.9 1.0
OE1 C:GLU354 4.2 45.6 1.0
C A:BCT346 4.3 71.1 1.0
O1 A:BCT346 4.3 74.2 1.0
CG A:GLU189 4.4 65.1 1.0
OD2 A:ASP342 4.4 83.0 1.0
OE2 C:GLU354 4.4 58.4 1.0
NE2 A:HIS337 4.6 47.6 1.0
CG A:GLU333 4.6 51.3 1.0
CD C:GLU354 4.8 55.0 1.0
OXT A:ALA344 4.8 76.6 1.0
CG1 A:VAL185 4.8 41.5 1.0
CB A:GLU333 4.9 54.0 1.0
O3 A:BCT346 4.9 70.8 1.0

Manganese binding site 3 out of 8 in 1s5l

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Manganese binding site 3 out of 8 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn347

b:68.5
occ:1.00
 MN3 A:OEC347 0.0 68.5 1.0
O2 A:OEC347 1.8 71.1 1.0
O3 A:OEC347 1.8 68.3 1.0
O4 A:OEC347 1.9 71.9 1.0
OE1 C:GLU354 1.9 45.6 1.0
OE2 C:GLU354 2.0 58.4 1.0
CD C:GLU354 2.2 55.0 1.0
MN1 A:OEC347 2.7 74.4 1.0
MN2 A:OEC347 2.7 66.9 1.0
OE1 A:GLU333 3.0 41.4 1.0
O1 A:OEC347 3.2 69.5 1.0
MN4 A:OEC347 3.3 74.0 1.0
CA1 A:OEC347 3.4 69.6 1.0
OE2 A:GLU333 3.5 52.6 1.0
CD A:GLU333 3.5 45.9 1.0
OXT A:ALA344 3.7 76.6 1.0
CG C:GLU354 3.8 57.1 1.0
O1 A:BCT346 4.0 74.2 1.0
O3 A:BCT346 4.1 70.8 1.0
C A:BCT346 4.1 71.1 1.0
NE2 A:HIS332 4.2 46.6 1.0
OD2 A:ASP342 4.3 83.0 1.0
NH1 C:ARG357 4.3 26.6 1.0
NE2 A:HIS337 4.3 47.6 1.0
OE2 A:GLU189 4.5 63.5 1.0
CB C:GLU354 4.5 55.6 1.0
O2 A:BCT346 4.7 70.9 1.0
CD2 A:HIS332 4.8 45.3 1.0
C A:ALA344 4.8 79.7 1.0
CG A:GLU333 4.9 51.3 1.0
CD2 A:HIS337 4.9 47.4 1.0

Manganese binding site 4 out of 8 in 1s5l

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Manganese binding site 4 out of 8 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn347

b:74.0
occ:1.00
 MN4 A:OEC347 0.0 74.0 1.0
O4 A:OEC347 1.9 71.9 1.0
O1 A:BCT346 1.9 74.2 1.0
OD2 A:ASP170 2.0 70.1 1.0
OE2 A:GLU333 2.0 52.6 1.0
C A:BCT346 2.8 71.1 1.0
CD A:GLU333 2.9 45.9 1.0
CG A:ASP170 3.0 61.5 1.0
OE1 A:GLU333 3.2 41.4 1.0
MN2 A:OEC347 3.2 66.9 1.0
MN3 A:OEC347 3.3 68.5 1.0
O2 A:BCT346 3.4 70.9 1.0
O3 A:BCT346 3.7 70.8 1.0
CB A:ASP170 3.7 60.4 1.0
OE2 C:GLU354 3.8 58.4 1.0
OD1 A:ASP170 3.8 61.4 1.0
CA1 A:OEC347 3.9 69.6 1.0
O2 A:OEC347 4.0 71.1 1.0
CG A:GLU333 4.2 51.3 1.0
O1 A:OEC347 4.4 69.5 1.0
O3 A:OEC347 4.4 68.3 1.0
OD1 A:ASP61 4.5 74.3 1.0
OE2 A:GLU189 4.6 63.5 1.0
NH1 C:ARG357 4.8 26.6 1.0
CD2 A:HIS332 4.8 45.3 1.0
CD C:GLU354 4.8 55.0 1.0
NE2 A:HIS332 5.0 46.6 1.0

Manganese binding site 5 out of 8 in 1s5l

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Manganese binding site 5 out of 8 in the Architecture of the Photosynthetic Oxygen Evolving Center


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn2347

b:69.9
occ:1.00
 MN1 a:OEC2347 0.0 69.9 1.0
O2 a:OEC2347 1.8 71.8 1.0
O3 a:OEC2347 1.9 69.0 1.0
O1 a:OEC2347 1.9 69.7 1.0
OD2 a:ASP2342 2.0 81.3 1.0
MN2 a:OEC2347 2.7 74.0 1.0
MN3 a:OEC2347 2.7 74.4 1.0
CG a:ASP2342 3.0 81.7 1.0
OE2 a:GLU2189 3.2 69.7 1.0
OE1 c:GLU2354 3.3 67.3 1.0
O4 a:OEC2347 3.3 70.9 1.0
CA1 a:OEC2347 3.3 74.0 1.0
NE2 a:HIS2332 3.4 59.8 1.0
CB a:ASP2342 3.4 78.8 1.0
OE1 a:GLU2189 3.7 71.2 1.0
CD a:GLU2189 3.8 68.4 1.0
CE1 a:HIS2332 3.9 56.7 1.0
OD1 a:ASP2342 4.1 81.8 1.0
C a:ALA2344 4.1 82.6 1.0
NE2 a:HIS2337 4.2 68.5 1.0
CD c:GLU2354 4.3 63.7 1.0
O a:ALA2344 4.3 80.3 1.0
OE2 c:GLU2354 4.4 67.4 1.0
CA a:ASP2342 4.5 77.7 1.0
CD2 a:HIS2332 4.6 56.0 1.0
CD2 a:HIS2337 4.7 67.0 1.0
N a:ALA2344 4.8 80.6 1.0

Manganese binding site 6 out of 8 in 1s5l

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Manganese binding site 6 out of 8 in the Architecture of the Photosynthetic Oxygen Evolving Center


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn2347

b:74.0
occ:1.00
 MN2 a:OEC2347 0.0 74.0 1.0
O1 a:OEC2347 1.8 69.7 1.0
O2 a:OEC2347 1.8 71.8 1.0
O4 a:OEC2347 1.9 70.9 1.0
OE2 a:GLU2189 2.0 69.7 1.0
NE2 a:HIS2332 2.0 59.8 1.0
CD2 a:HIS2332 2.6 56.0 1.0
MN1 a:OEC2347 2.7 69.9 1.0
MN3 a:OEC2347 2.7 74.4 1.0
OE2 a:GLU2333 3.0 63.7 1.0
CE1 a:HIS2332 3.2 56.7 1.0
MN4 a:OEC2347 3.2 75.4 1.0
O3 a:OEC2347 3.2 69.0 1.0
CD a:GLU2189 3.3 68.4 1.0
CA1 a:OEC2347 3.4 74.0 1.0
CD a:GLU2333 3.7 57.0 1.0
CG a:HIS2332 3.8 56.2 1.0
OE1 a:GLU2189 4.0 71.2 1.0
O2 a:BCT2346 4.0 71.7 1.0
OE1 a:GLU2333 4.1 51.1 1.0
ND1 a:HIS2332 4.1 55.3 1.0
C a:BCT2346 4.2 73.2 1.0
O1 a:BCT2346 4.3 76.0 1.0
CG a:GLU2189 4.3 67.6 1.0
OD2 a:ASP2342 4.4 81.3 1.0
OE2 c:GLU2354 4.4 67.4 1.0
CG1 a:VAL2185 4.6 47.4 1.0
OE1 c:GLU2354 4.6 67.3 1.0
CG a:GLU2333 4.7 59.7 1.0
NE2 a:HIS2337 4.7 68.5 1.0
O3 a:BCT2346 4.8 72.6 1.0
CB a:GLU2333 4.9 58.7 1.0
CD c:GLU2354 5.0 63.7 1.0

Manganese binding site 7 out of 8 in 1s5l

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Manganese binding site 7 out of 8 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn2347

b:74.4
occ:1.00
 MN3 a:OEC2347 0.0 74.4 1.0
O3 a:OEC2347 1.8 69.0 1.0
O2 a:OEC2347 1.8 71.8 1.0
O4 a:OEC2347 1.9 70.9 1.0
OE2 c:GLU2354 2.0 67.4 1.0
OE1 c:GLU2354 2.2 67.3 1.0
CD c:GLU2354 2.4 63.7 1.0
MN1 a:OEC2347 2.7 69.9 1.0
MN2 a:OEC2347 2.7 74.0 1.0
OE1 a:GLU2333 3.2 51.1 1.0
MN4 a:OEC2347 3.2 75.4 1.0
O1 a:OEC2347 3.2 69.7 1.0
CA1 a:OEC2347 3.4 74.0 1.0
OE2 a:GLU2333 3.6 63.7 1.0
CD a:GLU2333 3.7 57.0 1.0
CG c:GLU2354 3.9 59.0 1.0
O3 a:BCT2346 4.0 72.6 1.0
O1 a:BCT2346 4.0 76.0 1.0
C a:BCT2346 4.0 73.2 1.0
NE2 a:HIS2332 4.3 59.8 1.0
OD2 a:ASP2342 4.3 81.3 1.0
OE2 a:GLU2189 4.4 69.7 1.0
NE2 a:HIS2337 4.5 68.5 1.0
O2 a:BCT2346 4.6 71.7 1.0
NH1 c:ARG2357 4.7 32.5 1.0
CB c:GLU2354 4.7 52.2 1.0
C a:ALA2344 4.8 82.6 1.0
CD2 a:HIS2332 4.8 56.0 1.0
NH2 c:ARG2357 5.0 29.0 1.0
CD2 a:HIS2337 5.0 67.0 1.0

Manganese binding site 8 out of 8 in 1s5l

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Manganese binding site 8 out of 8 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mn2347

b:75.4
occ:1.00
 MN4 a:OEC2347 0.0 75.4 1.0
O1 a:BCT2346 1.9 76.0 1.0
O4 a:OEC2347 1.9 70.9 1.0
OD2 a:ASP2170 2.0 71.3 1.0
OE2 a:GLU2333 2.0 63.7 1.0
C a:BCT2346 2.8 73.2 1.0
CD a:GLU2333 2.9 57.0 1.0
OE1 a:GLU2333 3.1 51.1 1.0
CG a:ASP2170 3.1 61.8 1.0
MN3 a:OEC2347 3.2 74.4 1.0
MN2 a:OEC2347 3.2 74.0 1.0
O2 a:BCT2346 3.4 71.7 1.0
O3 a:BCT2346 3.7 72.6 1.0
CB a:ASP2170 3.7 60.8 1.0
OE2 c:GLU2354 3.9 67.4 1.0
CA1 a:OEC2347 4.0 74.0 1.0
O2 a:OEC2347 4.0 71.8 1.0
OD1 a:ASP2170 4.1 59.1 1.0
CG a:GLU2333 4.2 59.7 1.0
O1 a:OEC2347 4.4 69.7 1.0
O3 a:OEC2347 4.4 69.0 1.0
OD1 a:ASP2061 4.5 92.4 1.0
CD2 a:HIS2332 4.8 56.0 1.0
OE2 a:GLU2189 4.8 69.7 1.0
NH1 c:ARG2357 5.0 32.5 1.0
NE2 a:HIS2332 5.0 59.8 1.0

Reference:

K.N.Ferreira, T.M.Iverson, K.Maghlaoui, J.Barber, S.Iwata. Architecture of the Photosynthetic Oxygen-Evolving Center Science V. 303 1831 2004.
ISSN: ISSN 0036-8075
PubMed: 14764885
DOI: 10.1126/SCIENCE.1093087
Page generated: Sat Oct 5 12:23:05 2024

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