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Iron in PDB 8f4k: Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution, PDB code: 8f4k was solved by A.Bhowmick, R.Hussein, I.Bogacz, P.S.Simon, M.Ibrahim, R.Chatterjee, M.D.Doyle, M.H.Cheah, T.Fransson, P.Chernev, I.-S.Kim, H.Makita, M.Dasgupta, C.J.Kaminsky, M.Zhang, J.Gatcke, S.Haupt, I.I.Nangca, S.M.Keable, O.Aydin, K.Tono, S.Owada, L.B.Gee, F.D.Fuller, A.Batyuk, R.Alonso-Mori, J.M.Holton, D.W.Paley, N.W.Moriarty, F.Mamedov, P.D.Adams, A.S.Brewster, H.Dobbek, N.K.Sauter, U.Bergmann, A.Zouni, J.Messinger, J.Kern, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.52 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.991, 221.755, 307.964, 90, 90, 90
R / Rfree (%) 18.5 / 24.1

Other elements in 8f4k:

The structure of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Manganese (Mn) 16 atoms
Magnesium (Mg) 70 atoms
Calcium (Ca) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution (pdb code 8f4k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution, PDB code: 8f4k:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8f4k

Go back to Iron Binding Sites List in 8f4k
Iron binding site 1 out of 6 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:35.1
occ:1.00
 NE2 A:HIS215 2.1 34.6 1.0
NE2 D:HIS214 2.2 38.2 1.0
O2 D:BCT401 2.2 42.9 1.0
NE2 D:HIS268 2.2 37.7 1.0
O1 D:BCT401 2.2 33.2 1.0
NE2 A:HIS272 2.2 39.9 1.0
C D:BCT401 2.4 41.2 1.0
CE1 A:HIS215 2.9 32.3 1.0
CE1 D:HIS214 3.0 31.6 1.0
CE1 D:HIS268 3.1 36.0 1.0
CE1 A:HIS272 3.2 36.7 1.0
CD2 A:HIS215 3.2 33.6 1.0
CD2 D:HIS268 3.2 34.1 1.0
CD2 A:HIS272 3.3 34.6 1.0
CD2 D:HIS214 3.3 29.0 1.0
O3 D:BCT401 3.9 38.9 1.0
ND1 A:HIS215 4.1 30.6 1.0
ND1 D:HIS214 4.2 33.5 1.0
ND1 D:HIS268 4.3 31.7 1.0
CG A:HIS215 4.3 37.7 1.0
ND1 A:HIS272 4.3 34.5 1.0
CG D:HIS268 4.4 39.2 1.0
CG D:HIS214 4.4 31.6 1.0
CG A:HIS272 4.4 36.3 1.0
CG2 A:VAL219 4.7 34.1 1.0
OH D:TYR244 4.8 39.1 1.0
CG2 D:VAL218 4.9 35.0 1.0

Iron binding site 2 out of 6 in 8f4k

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Iron binding site 2 out of 6 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:53.9
occ:1.00
 FE F:HEM101 0.0 53.9 1.0
NB F:HEM101 2.0 47.6 1.0
ND F:HEM101 2.0 50.3 1.0
NC F:HEM101 2.1 51.8 1.0
NA F:HEM101 2.1 53.3 1.0
NE2 E:HIS23 2.1 56.3 1.0
NE2 F:HIS24 2.1 51.3 1.0
CD2 F:HIS24 2.7 50.6 1.0
CD2 E:HIS23 3.0 53.7 1.0
C4D F:HEM101 3.0 55.3 1.0
C1A F:HEM101 3.0 52.7 1.0
C4B F:HEM101 3.0 48.6 1.0
C1D F:HEM101 3.0 52.1 1.0
C1C F:HEM101 3.0 51.8 1.0
C4A F:HEM101 3.1 49.1 1.0
C1B F:HEM101 3.1 51.3 1.0
C4C F:HEM101 3.1 48.9 1.0
CE1 E:HIS23 3.2 56.6 1.0
CE1 F:HIS24 3.3 53.9 1.0
CHA F:HEM101 3.4 52.1 1.0
CHC F:HEM101 3.4 50.9 1.0
CHD F:HEM101 3.5 46.5 1.0
CHB F:HEM101 3.5 51.1 1.0
CG F:HIS24 4.0 49.5 1.0
CG E:HIS23 4.2 58.1 1.0
C3D F:HEM101 4.2 49.8 1.0
C2D F:HEM101 4.2 52.9 1.0
C2A F:HEM101 4.2 59.4 1.0
ND1 E:HIS23 4.2 57.0 1.0
C3A F:HEM101 4.2 57.0 1.0
ND1 F:HIS24 4.2 54.4 1.0
C3B F:HEM101 4.2 46.7 1.0
C2C F:HEM101 4.3 52.2 1.0
C2B F:HEM101 4.3 48.1 1.0
C3C F:HEM101 4.3 47.0 1.0
CD1 E:ILE22 4.5 55.7 0.1
CZ2 F:TRP20 4.9 52.0 1.0
NE1 F:TRP20 4.9 53.3 1.0

Iron binding site 3 out of 6 in 8f4k

Go back to Iron Binding Sites List in 8f4k
Iron binding site 3 out of 6 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:38.6
occ:1.00
 FE V:HEC201 0.0 38.6 1.0
NC V:HEC201 2.0 38.8 1.0
NB V:HEC201 2.0 39.7 1.0
NA V:HEC201 2.0 36.0 1.0
NE2 V:HIS92 2.1 42.8 1.0
ND V:HEC201 2.1 38.1 1.0
NE2 V:HIS41 2.1 36.8 1.0
CD2 V:HIS41 2.9 38.4 1.0
CE1 V:HIS92 2.9 34.9 1.0
C1B V:HEC201 3.0 38.9 1.0
C4C V:HEC201 3.0 39.6 1.0
C1C V:HEC201 3.0 43.3 1.0
C4A V:HEC201 3.0 39.7 1.0
C4B V:HEC201 3.1 35.4 1.0
C1D V:HEC201 3.1 36.7 1.0
C1A V:HEC201 3.1 40.2 1.0
C4D V:HEC201 3.1 40.4 1.0
CD2 V:HIS92 3.2 44.0 1.0
CE1 V:HIS41 3.3 37.8 1.0
CHB V:HEC201 3.4 38.1 1.0
CHD V:HEC201 3.4 37.9 1.0
CHC V:HEC201 3.4 42.8 1.0
CHA V:HEC201 3.5 39.8 1.0
ND1 V:HIS92 4.1 37.1 1.0
CG V:HIS41 4.1 36.0 1.0
CG V:HIS92 4.2 42.4 1.0
C2B V:HEC201 4.2 41.5 1.0
C2C V:HEC201 4.3 40.6 1.0
C3C V:HEC201 4.3 37.0 1.0
C3B V:HEC201 4.3 35.1 1.0
C3A V:HEC201 4.3 39.9 1.0
ND1 V:HIS41 4.3 39.2 1.0
C2A V:HEC201 4.3 41.6 1.0
C3D V:HEC201 4.3 36.9 1.0
C2D V:HEC201 4.3 36.6 1.0
CE1 V:TYR75 4.9 43.2 1.0
OH V:TYR75 5.0 43.0 1.0

Iron binding site 4 out of 6 in 8f4k

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Iron binding site 4 out of 6 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe603

b:39.7
occ:1.00
 NE2 a:HIS215 2.1 39.5 1.0
O1 a:BCT606 2.2 40.5 1.0
NE2 d:HIS214 2.2 38.9 1.0
NE2 d:HIS268 2.2 42.2 1.0
O2 a:BCT606 2.2 38.0 1.0
NE2 a:HIS272 2.3 47.6 1.0
C a:BCT606 2.4 49.8 1.0
CE1 a:HIS272 3.0 44.9 1.0
CE1 a:HIS215 3.0 40.2 1.0
CE1 d:HIS214 3.1 37.0 1.0
CE1 d:HIS268 3.1 37.5 1.0
CD2 a:HIS215 3.2 41.8 1.0
CD2 d:HIS214 3.3 34.3 1.0
CD2 d:HIS268 3.3 45.3 1.0
CD2 a:HIS272 3.4 35.5 1.0
O3 a:BCT606 3.9 51.9 1.0
ND1 a:HIS215 4.1 41.8 1.0
ND1 a:HIS272 4.2 39.1 1.0
ND1 d:HIS214 4.2 39.8 1.0
CG a:HIS215 4.3 36.5 1.0
ND1 d:HIS268 4.3 34.7 1.0
CG d:HIS214 4.4 35.8 1.0
CG d:HIS268 4.4 41.3 1.0
CG a:HIS272 4.4 44.3 1.0
CG2 a:VAL219 4.7 43.0 1.0
OH d:TYR244 4.9 45.6 1.0
CG2 d:VAL218 5.0 37.9 1.0

Iron binding site 5 out of 6 in 8f4k

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Iron binding site 5 out of 6 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe101

b:59.3
occ:1.00
 FE e:HEM101 0.0 59.3 1.0
ND e:HEM101 2.0 54.4 1.0
NC e:HEM101 2.0 57.1 1.0
NA e:HEM101 2.0 60.6 1.0
NB e:HEM101 2.1 56.3 1.0
NE2 e:HIS23 2.1 65.8 1.0
NE2 f:HIS24 2.1 59.2 1.0
C4D e:HEM101 2.9 59.6 1.0
CE1 e:HIS23 2.9 63.9 1.0
C1D e:HEM101 3.0 52.9 1.0
C1A e:HEM101 3.0 58.0 1.0
C4C e:HEM101 3.0 57.9 1.0
C4A e:HEM101 3.1 58.1 1.0
C1B e:HEM101 3.1 60.5 1.0
CD2 f:HIS24 3.1 56.1 1.0
C1C e:HEM101 3.1 57.6 1.0
C4B e:HEM101 3.1 60.2 1.0
CE1 f:HIS24 3.1 56.4 1.0
CD2 e:HIS23 3.1 63.9 1.0
CHA e:HEM101 3.3 60.3 1.0
CHD e:HEM101 3.4 55.3 1.0
CHC e:HEM101 3.5 60.9 1.0
CHB e:HEM101 3.5 56.5 1.0
ND1 e:HIS23 4.1 67.1 1.0
C3D e:HEM101 4.1 61.7 1.0
C2D e:HEM101 4.1 58.6 1.0
ND1 f:HIS24 4.2 58.8 1.0
C2A e:HEM101 4.2 60.4 1.0
CG f:HIS24 4.2 56.9 1.0
CG e:HIS23 4.2 65.0 1.0
C3A e:HEM101 4.2 66.2 1.0
C3C e:HEM101 4.3 59.6 1.0
C2B e:HEM101 4.3 60.2 1.0
C2C e:HEM101 4.3 57.6 1.0
C3B e:HEM101 4.3 58.2 1.0
CZ2 f:TRP20 4.9 58.2 1.0
CE2 e:TYR19 5.0 62.0 1.0

Iron binding site 6 out of 6 in 8f4k

Go back to Iron Binding Sites List in 8f4k
Iron binding site 6 out of 6 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:42.3
occ:1.00
 FE v:HEC201 0.0 42.3 1.0
ND v:HEC201 2.0 40.3 1.0
NC v:HEC201 2.0 44.4 1.0
NE2 v:HIS41 2.1 40.1 1.0
NB v:HEC201 2.1 40.6 1.0
NA v:HEC201 2.1 41.0 1.0
NE2 v:HIS92 2.1 41.9 1.0
CD2 v:HIS92 3.0 41.4 1.0
CD2 v:HIS41 3.0 39.1 1.0
C1D v:HEC201 3.0 37.9 1.0
C4D v:HEC201 3.0 43.3 1.0
C4C v:HEC201 3.0 40.6 1.0
C1C v:HEC201 3.1 41.6 1.0
C1B v:HEC201 3.1 41.9 1.0
C1A v:HEC201 3.1 39.6 1.0
C4B v:HEC201 3.1 40.4 1.0
CE1 v:HIS41 3.1 40.2 1.0
C4A v:HEC201 3.1 43.5 1.0
CE1 v:HIS92 3.2 40.4 1.0
CHD v:HEC201 3.4 39.4 1.0
CHA v:HEC201 3.4 40.6 1.0
CHC v:HEC201 3.5 39.0 1.0
CHB v:HEC201 3.5 39.5 1.0
CG v:HIS41 4.1 40.7 1.0
CG v:HIS92 4.2 46.9 1.0
ND1 v:HIS41 4.2 43.1 1.0
C3D v:HEC201 4.2 42.4 1.0
C2D v:HEC201 4.2 37.4 1.0
ND1 v:HIS92 4.2 48.0 1.0
C3C v:HEC201 4.3 46.5 1.0
C2C v:HEC201 4.3 44.5 1.0
C2B v:HEC201 4.3 38.7 1.0
C3B v:HEC201 4.3 39.0 1.0
C2A v:HEC201 4.3 42.6 1.0
C3A v:HEC201 4.3 44.9 1.0

Reference:

A.Bhowmick, R.Hussein, I.Bogacz, P.S.Simon, M.Ibrahim, R.Chatterjee, M.D.Doyle, M.H.Cheah, T.Fransson, P.Chernev, I.-S.Kim, H.Makita, M.Dasgupta, C.J.Kaminsky, M.Zhang, J.Gatcke, S.Haupt, I.I.Nangca, S.M.Keable, O.Aydin, K.Tono, S.Owada, L.B.Gee, F.D.Fuller, A.Batyuk, R.Alonso-Mori, J.M.Holton, D.W.Paley, N.W.Moriarty, F.Mamedov, P.D.Adams, A.S.Brewster, H.Dobbek, N.K.Sauter, U.Bergmann, A.Zouni, J.Messinger, J.Kern, J.Yano, V.K.Yachandra. Structural Evidence For Intermediates During O2 Formation in Photosystem II To Be Published.
Page generated: Sat Aug 10 02:38:08 2024

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