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Iron 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
Manganese (Mn) 8 atoms
Calcium (Ca) 2 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 6 in 1s5l

Go back to Iron Binding Sites List in 1s5l
Iron binding site 1 out of 6 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe345

b:58.9
occ:1.00
 NE2 D:HIS268 2.2 60.8 1.0
NE2 A:HIS215 2.2 57.7 1.0
NE2 D:HIS214 2.2 60.3 1.0
O2 D:BCT353 2.2 66.5 1.0
NE2 A:HIS272 2.2 57.6 1.0
O3 D:BCT353 2.2 66.2 1.0
C D:BCT353 2.5 69.7 1.0
CE1 A:HIS215 3.1 57.0 1.0
CD2 A:HIS215 3.1 57.7 1.0
CE1 D:HIS268 3.1 62.2 1.0
CE1 A:HIS272 3.1 53.8 1.0
CD2 D:HIS268 3.2 61.7 1.0
CE1 D:HIS214 3.2 61.5 1.0
CD2 D:HIS214 3.2 60.0 1.0
CD2 A:HIS272 3.2 55.8 1.0
O1 D:BCT353 3.9 69.7 1.0
ND1 A:HIS215 4.1 56.7 1.0
CG A:HIS215 4.2 56.6 1.0
ND1 D:HIS268 4.2 62.8 1.0
ND1 A:HIS272 4.3 54.5 1.0
CG D:HIS268 4.3 62.6 1.0
ND1 D:HIS214 4.3 61.4 1.0
CG A:HIS272 4.3 56.4 1.0
CG D:HIS214 4.3 60.2 1.0
CG2 A:VAL219 4.3 61.3 1.0
NZ D:LYS264 4.9 48.8 1.0

Iron binding site 2 out of 6 in 1s5l

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Iron binding site 2 out of 6 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe2345

b:67.3
occ:1.00
 NE2 d:HIS2214 2.2 66.1 1.0
NE2 a:HIS2215 2.2 64.6 1.0
O3 d:BCT2353 2.2 66.8 1.0
NE2 a:HIS2272 2.2 68.1 1.0
O2 d:BCT2353 2.2 68.7 1.0
NE2 d:HIS2268 2.2 69.1 1.0
C d:BCT2353 2.5 69.4 1.0
CE1 d:HIS2214 3.1 64.5 1.0
CD2 a:HIS2215 3.1 63.8 1.0
CE1 a:HIS2215 3.1 62.5 1.0
CE1 a:HIS2272 3.1 69.0 1.0
CD2 d:HIS2214 3.1 64.3 1.0
CE1 d:HIS2268 3.2 70.1 1.0
CD2 a:HIS2272 3.2 68.7 1.0
CD2 d:HIS2268 3.2 70.1 1.0
O1 d:BCT2353 3.9 69.5 1.0
ND1 a:HIS2215 4.2 63.1 1.0
ND1 d:HIS2214 4.2 65.3 1.0
CG a:HIS2215 4.2 63.8 1.0
ND1 a:HIS2272 4.2 68.6 1.0
CG d:HIS2214 4.2 63.2 1.0
CG a:HIS2272 4.3 67.6 1.0
ND1 d:HIS2268 4.3 69.6 1.0
CG d:HIS2268 4.4 68.6 1.0
CG2 a:VAL2219 4.5 61.4 1.0
OH d:TYR2244 4.8 75.3 1.0

Iron binding site 3 out of 6 in 1s5l

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Iron binding site 3 out of 6 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe84

b:64.6
occ:1.00
 FE E:HEM84 0.0 64.6 1.0
NC E:HEM84 1.9 80.3 1.0
NE2 E:HIS22 2.0 72.5 1.0
NB E:HEM84 2.0 79.7 1.0
NE2 F:HIS23 2.0 77.9 1.0
ND E:HEM84 2.0 78.7 1.0
NA E:HEM84 2.1 79.5 1.0
CE1 E:HIS22 2.9 69.5 1.0
CE1 F:HIS23 2.9 79.0 1.0
CD2 F:HIS23 3.0 76.5 1.0
C4C E:HEM84 3.0 81.0 1.0
C1C E:HEM84 3.0 82.0 1.0
CD2 E:HIS22 3.0 67.8 1.0
C1D E:HEM84 3.1 79.2 1.0
C1B E:HEM84 3.1 79.0 1.0
C4D E:HEM84 3.1 80.5 1.0
C4B E:HEM84 3.1 80.2 1.0
C4A E:HEM84 3.1 79.0 1.0
C1A E:HEM84 3.2 78.8 1.0
CHD E:HEM84 3.4 79.8 1.0
CHB E:HEM84 3.5 78.2 1.0
CHC E:HEM84 3.5 81.1 1.0
CHA E:HEM84 3.5 78.4 1.0
CH2 F:TRP19 3.9 53.3 1.0
ND1 F:HIS23 4.0 78.6 1.0
ND1 E:HIS22 4.0 66.7 1.0
CG F:HIS23 4.1 76.3 1.0
CG E:HIS22 4.1 67.5 1.0
C3C E:HEM84 4.2 81.1 1.0
C2C E:HEM84 4.3 82.2 1.0
CZ3 F:TRP19 4.3 51.7 1.0
C2B E:HEM84 4.3 78.4 1.0
C2D E:HEM84 4.3 79.9 1.0
C3D E:HEM84 4.4 82.4 1.0
C3B E:HEM84 4.4 79.0 1.0
C3A E:HEM84 4.4 79.0 1.0
C2A E:HEM84 4.5 78.9 1.0
CZ2 F:TRP19 4.9 54.2 1.0
CE1 E:TYR18 4.9 89.9 1.0

Iron binding site 4 out of 6 in 1s5l

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Iron binding site 4 out of 6 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe138

b:54.6
occ:1.00
 FE V:HEM138 0.0 54.6 1.0
NE2 V:HIS41 2.0 40.1 1.0
NE2 V:HIS92 2.0 48.0 1.0
NC V:HEM138 2.0 47.0 1.0
NB V:HEM138 2.1 46.1 1.0
ND V:HEM138 2.1 45.7 1.0
NA V:HEM138 2.1 46.7 1.0
CD2 V:HIS92 3.0 50.3 1.0
CD2 V:HIS41 3.0 38.5 1.0
CE1 V:HIS41 3.0 37.7 1.0
CE1 V:HIS92 3.0 51.6 1.0
C4C V:HEM138 3.2 49.2 1.0
C1B V:HEM138 3.2 48.6 1.0
C1C V:HEM138 3.2 50.1 1.0
C1D V:HEM138 3.2 48.2 1.0
C4B V:HEM138 3.3 48.5 1.0
C4D V:HEM138 3.3 47.8 1.0
C1A V:HEM138 3.3 47.0 1.0
C4A V:HEM138 3.4 47.8 1.0
CHD V:HEM138 3.5 49.7 1.0
CHA V:HEM138 3.7 47.6 1.0
CHC V:HEM138 3.7 50.8 1.0
CHB V:HEM138 3.8 48.6 1.0
ND1 V:HIS92 4.1 53.4 1.0
CG V:HIS92 4.1 53.9 1.0
ND1 V:HIS41 4.1 39.4 1.0
CG V:HIS41 4.1 41.7 1.0
C3C V:HEM138 4.4 51.3 1.0
C2B V:HEM138 4.4 49.8 1.0
C3D V:HEM138 4.5 51.0 1.0
C2D V:HEM138 4.5 50.6 1.0
C2C V:HEM138 4.5 52.0 1.0
C3B V:HEM138 4.5 49.2 1.0
C2A V:HEM138 4.6 49.5 1.0
C3A V:HEM138 4.6 49.3 1.0

Iron binding site 5 out of 6 in 1s5l

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Iron binding site 5 out of 6 in the Architecture of the Photosynthetic Oxygen Evolving Center


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe2084

b:90.3
occ:1.00
 FE e:HEM2084 0.0 90.3 1.0
NC e:HEM2084 2.0 78.4 1.0
ND e:HEM2084 2.0 76.6 1.0
NE2 e:HIS2022 2.0 69.1 1.0
NE2 f:HIS2023 2.0 73.3 1.0
NA e:HEM2084 2.0 75.8 1.0
NB e:HEM2084 2.1 76.0 1.0
CE1 e:HIS2022 2.9 63.4 1.0
CE1 f:HIS2023 3.0 71.7 1.0
CD2 f:HIS2023 3.0 71.0 1.0
CD2 e:HIS2022 3.0 64.8 1.0
C4D e:HEM2084 3.0 79.3 1.0
C4C e:HEM2084 3.0 80.5 1.0
C1D e:HEM2084 3.1 78.1 1.0
C1C e:HEM2084 3.1 80.7 1.0
C1A e:HEM2084 3.1 77.3 1.0
C4B e:HEM2084 3.2 78.6 1.0
C1B e:HEM2084 3.2 77.2 1.0
C4A e:HEM2084 3.2 77.2 1.0
CHD e:HEM2084 3.4 79.9 1.0
CHA e:HEM2084 3.5 79.2 1.0
CHC e:HEM2084 3.5 81.1 1.0
CHB e:HEM2084 3.6 78.6 1.0
CH2 f:TRP2019 4.0 83.9 1.0
ND1 e:HIS2022 4.0 60.7 1.0
ND1 f:HIS2023 4.1 71.8 1.0
CG f:HIS2023 4.1 71.0 1.0
CG e:HIS2022 4.1 65.4 1.0
C3C e:HEM2084 4.3 82.4 1.0
C3D e:HEM2084 4.3 82.9 1.0
C2D e:HEM2084 4.3 79.7 1.0
C2C e:HEM2084 4.3 83.0 1.0
C2B e:HEM2084 4.4 78.1 1.0
C3B e:HEM2084 4.4 78.9 1.0
C2A e:HEM2084 4.4 79.0 1.0
C3A e:HEM2084 4.5 78.6 1.0
CZ3 f:TRP2019 4.5 81.0 1.0

Iron binding site 6 out of 6 in 1s5l

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Architecture of the Photosynthetic Oxygen Evolving Center within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe2138

b:40.4
occ:1.00
 FE v:HEM2138 0.0 40.4 1.0
NC v:HEM2138 1.9 48.7 1.0
NE2 v:HIS2092 2.0 50.1 1.0
NA v:HEM2138 2.0 48.3 1.0
NB v:HEM2138 2.0 49.5 1.0
NE2 v:HIS2041 2.0 45.1 1.0
ND v:HEM2138 2.0 49.1 1.0
CD2 v:HIS2092 2.9 51.3 1.0
CE1 v:HIS2092 3.0 53.1 1.0
C4C v:HEM2138 3.0 51.9 1.0
CE1 v:HIS2041 3.0 42.1 1.0
CD2 v:HIS2041 3.0 44.4 1.0
C1D v:HEM2138 3.0 50.2 1.0
C1C v:HEM2138 3.0 52.6 1.0
C4D v:HEM2138 3.1 49.5 1.0
C1B v:HEM2138 3.1 50.5 1.0
C4B v:HEM2138 3.1 50.7 1.0
C4A v:HEM2138 3.1 48.7 1.0
C1A v:HEM2138 3.1 48.6 1.0
CHD v:HEM2138 3.4 50.6 1.0
CHC v:HEM2138 3.5 51.4 1.0
CHB v:HEM2138 3.5 48.7 1.0
CHA v:HEM2138 3.6 47.5 1.0
ND1 v:HIS2092 4.0 55.6 1.0
CG v:HIS2092 4.0 55.2 1.0
ND1 v:HIS2041 4.1 42.8 1.0
CG v:HIS2041 4.1 46.2 1.0
C3C v:HEM2138 4.2 53.0 1.0
C3D v:HEM2138 4.3 51.1 1.0
C2C v:HEM2138 4.3 53.6 1.0
C2D v:HEM2138 4.3 51.4 1.0
C2B v:HEM2138 4.3 51.0 1.0
C3B v:HEM2138 4.3 50.6 1.0
C2A v:HEM2138 4.4 49.6 1.0
C3A v:HEM2138 4.4 49.5 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 Aug 3 14:34:07 2024

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