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Iron in PDB 8f4c: Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution, PDB code: 8f4c 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) 19.80 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.328, 222.786, 309.116, 90, 90, 90
R / Rfree (%) 18 / 22.4

Other elements in 8f4c:

The structure of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution (pdb code 8f4c). 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 Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution, PDB code: 8f4c:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8f4c

Go back to Iron Binding Sites List in 8f4c
Iron binding site 1 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:27.5
occ:1.00
 NE2 A:HIS215 2.1 29.4 1.0
O2 D:BCT401 2.1 32.8 1.0
O1 D:BCT401 2.2 29.4 1.0
NE2 D:HIS214 2.2 30.4 1.0
NE2 D:HIS268 2.3 30.2 1.0
NE2 A:HIS272 2.3 30.1 1.0
C D:BCT401 2.4 34.9 1.0
CE1 D:HIS214 3.0 29.2 1.0
CE1 A:HIS215 3.1 28.4 1.0
CD2 A:HIS215 3.2 29.6 1.0
CE1 A:HIS272 3.2 27.6 1.0
CE1 D:HIS268 3.2 27.4 1.0
CD2 D:HIS268 3.3 29.2 1.0
CD2 A:HIS272 3.3 29.7 1.0
CD2 D:HIS214 3.3 23.9 1.0
O3 D:BCT401 3.8 35.4 1.0
ND1 A:HIS215 4.2 25.5 1.0
ND1 D:HIS214 4.2 28.3 1.0
CG A:HIS215 4.3 26.3 1.0
ND1 D:HIS268 4.3 26.3 1.0
ND1 A:HIS272 4.3 28.0 1.0
CG D:HIS214 4.4 28.1 1.0
CG D:HIS268 4.4 28.8 1.0
CG A:HIS272 4.4 31.5 1.0
CG2 A:VAL219 4.8 29.7 1.0
OH D:TYR244 4.9 32.5 1.0
CG2 D:VAL218 4.9 25.4 1.0

Iron binding site 2 out of 6 in 8f4c

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Iron binding site 2 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:47.2
occ:1.00
 FE F:HEM101 0.0 47.2 1.0
ND F:HEM101 2.0 42.5 1.0
NC F:HEM101 2.0 44.2 1.0
NB F:HEM101 2.1 39.5 1.0
NE2 E:HIS23 2.1 46.1 1.0
NA F:HEM101 2.1 45.6 1.0
NE2 F:HIS24 2.1 43.3 1.0
CD2 F:HIS24 2.9 40.8 1.0
C4D F:HEM101 3.0 45.9 1.0
C1D F:HEM101 3.0 44.2 1.0
CE1 E:HIS23 3.0 49.8 1.0
C1A F:HEM101 3.0 47.8 1.0
C1C F:HEM101 3.0 40.5 1.0
C4B F:HEM101 3.0 41.3 1.0
C4C F:HEM101 3.0 42.7 1.0
CD2 E:HIS23 3.1 46.9 1.0
C1B F:HEM101 3.1 46.1 1.0
C4A F:HEM101 3.1 42.7 1.0
CE1 F:HIS24 3.3 44.2 1.0
CHA F:HEM101 3.4 44.7 1.0
CHD F:HEM101 3.4 41.4 1.0
CHC F:HEM101 3.4 41.2 1.0
CHB F:HEM101 3.5 44.3 1.0
CG F:HIS24 4.1 42.6 1.0
ND1 E:HIS23 4.1 49.8 1.0
C3D F:HEM101 4.2 45.2 1.0
C2D F:HEM101 4.2 43.8 1.0
CG E:HIS23 4.2 50.4 1.0
C2A F:HEM101 4.2 49.1 1.0
ND1 F:HIS24 4.2 45.3 1.0
C2C F:HEM101 4.2 44.9 1.0
C3C F:HEM101 4.3 39.8 1.0
C3B F:HEM101 4.3 43.7 1.0
C3A F:HEM101 4.3 48.3 1.0
C2B F:HEM101 4.3 43.7 1.0
CD1 E:ILE22 4.5 49.3 0.1
NE1 F:TRP20 4.8 44.9 1.0

Iron binding site 3 out of 6 in 8f4c

Go back to Iron Binding Sites List in 8f4c
Iron binding site 3 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:31.6
occ:1.00
 FE V:HEC201 0.0 31.6 1.0
NA V:HEC201 2.0 28.1 1.0
NB V:HEC201 2.0 29.1 1.0
NC V:HEC201 2.1 28.7 1.0
ND V:HEC201 2.1 29.7 1.0
NE2 V:HIS92 2.1 34.3 1.0
NE2 V:HIS41 2.1 30.9 1.0
CD2 V:HIS41 3.0 27.1 1.0
C4A V:HEC201 3.0 31.3 1.0
C1B V:HEC201 3.0 28.9 1.0
CD2 V:HIS92 3.0 33.8 1.0
C1A V:HEC201 3.0 32.6 1.0
CE1 V:HIS92 3.0 28.8 1.0
C4C V:HEC201 3.1 27.9 1.0
C1D V:HEC201 3.1 28.7 1.0
C4D V:HEC201 3.1 33.5 1.0
C1C V:HEC201 3.1 31.5 1.0
C4B V:HEC201 3.1 28.9 1.0
CE1 V:HIS41 3.2 30.0 1.0
CHB V:HEC201 3.4 31.6 1.0
CHD V:HEC201 3.4 25.5 1.0
CHA V:HEC201 3.4 29.1 1.0
CHC V:HEC201 3.5 27.4 1.0
ND1 V:HIS92 4.1 30.4 1.0
CG V:HIS92 4.1 35.2 1.0
CG V:HIS41 4.2 30.9 1.0
C3A V:HEC201 4.2 30.6 1.0
C2A V:HEC201 4.2 30.2 1.0
ND1 V:HIS41 4.2 32.6 1.0
C2B V:HEC201 4.3 31.8 1.0
C3C V:HEC201 4.3 29.8 1.0
C3D V:HEC201 4.3 27.3 1.0
C3B V:HEC201 4.3 28.0 1.0
C2C V:HEC201 4.3 30.2 1.0
C2D V:HEC201 4.3 25.9 1.0
CE1 V:TYR75 4.9 30.4 1.0

Iron binding site 4 out of 6 in 8f4c

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Iron binding site 4 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe603

b:33.8
occ:1.00
 NE2 a:HIS215 2.1 31.6 1.0
O1 a:BCT606 2.2 35.4 1.0
NE2 d:HIS214 2.2 31.0 1.0
O2 a:BCT606 2.2 32.3 1.0
NE2 d:HIS268 2.3 36.7 1.0
NE2 a:HIS272 2.3 39.1 1.0
C a:BCT606 2.4 39.5 1.0
CE1 a:HIS215 3.0 35.0 1.0
CE1 a:HIS272 3.1 35.4 1.0
CE1 d:HIS214 3.1 30.5 1.0
CE1 d:HIS268 3.2 33.4 1.0
CD2 a:HIS215 3.2 33.1 1.0
CD2 d:HIS214 3.2 29.3 1.0
CD2 d:HIS268 3.3 29.3 1.0
CD2 a:HIS272 3.4 28.5 1.0
O3 a:BCT606 3.9 44.3 1.0
ND1 a:HIS215 4.2 33.0 1.0
ND1 a:HIS272 4.3 36.3 1.0
CG a:HIS215 4.3 27.5 1.0
ND1 d:HIS214 4.3 32.0 1.0
ND1 d:HIS268 4.3 35.2 1.0
CG d:HIS214 4.3 29.5 1.0
CG d:HIS268 4.4 33.1 1.0
CG a:HIS272 4.4 35.5 1.0
CG2 a:VAL219 4.7 35.6 1.0

Iron binding site 5 out of 6 in 8f4c

Go back to Iron Binding Sites List in 8f4c
Iron binding site 5 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:53.2
occ:1.00
 FE f:HEM101 0.0 53.2 1.0
NC f:HEM101 2.0 47.3 1.0
ND f:HEM101 2.0 49.6 1.0
NB f:HEM101 2.1 50.8 1.0
NE2 e:HIS23 2.1 55.4 1.0
NE2 f:HIS24 2.1 52.9 1.0
NA f:HEM101 2.1 52.0 1.0
C4C f:HEM101 2.9 46.6 1.0
C1D f:HEM101 3.0 51.3 1.0
CD2 e:HIS23 3.0 55.3 1.0
C1C f:HEM101 3.0 49.6 1.0
C4D f:HEM101 3.0 51.8 1.0
CE1 f:HIS24 3.1 47.8 1.0
C4B f:HEM101 3.1 53.7 1.0
C1A f:HEM101 3.1 55.3 1.0
C1B f:HEM101 3.1 52.5 1.0
CD2 f:HIS24 3.1 49.2 1.0
C4A f:HEM101 3.1 52.5 1.0
CE1 e:HIS23 3.2 56.9 1.0
CHD f:HEM101 3.3 50.6 1.0
CHC f:HEM101 3.4 52.9 1.0
CHA f:HEM101 3.5 53.6 1.0
CHB f:HEM101 3.5 56.1 1.0
C2D f:HEM101 4.1 50.4 1.0
C3D f:HEM101 4.2 53.3 1.0
CG e:HIS23 4.2 58.7 1.0
ND1 f:HIS24 4.2 51.3 1.0
C3C f:HEM101 4.2 49.3 1.0
ND1 e:HIS23 4.2 58.2 1.0
C2C f:HEM101 4.2 50.8 1.0
CG f:HIS24 4.2 53.0 1.0
C2A f:HEM101 4.3 57.2 1.0
C2B f:HEM101 4.3 55.2 1.0
C3B f:HEM101 4.3 53.0 1.0
C3A f:HEM101 4.3 60.0 1.0
NE1 f:TRP20 4.9 52.7 1.0
CE1 e:TYR19 5.0 59.2 1.0

Iron binding site 6 out of 6 in 8f4c

Go back to Iron Binding Sites List in 8f4c
Iron binding site 6 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:34.7
occ:1.00
 FE v:HEC201 0.0 34.7 1.0
ND v:HEC201 2.0 33.0 1.0
NB v:HEC201 2.0 30.6 1.0
NC v:HEC201 2.0 35.3 1.0
NE2 v:HIS41 2.1 32.9 1.0
NE2 v:HIS92 2.1 37.0 1.0
NA v:HEC201 2.1 34.3 1.0
CD2 v:HIS92 2.9 31.9 1.0
C1D v:HEC201 3.0 31.4 1.0
CE1 v:HIS41 3.0 33.3 1.0
C4C v:HEC201 3.0 33.1 1.0
C1B v:HEC201 3.0 33.9 1.0
C4D v:HEC201 3.0 33.4 1.0
C4B v:HEC201 3.1 32.1 1.0
CD2 v:HIS41 3.1 30.6 1.0
C1C v:HEC201 3.1 32.8 1.0
C4A v:HEC201 3.1 32.2 1.0
C1A v:HEC201 3.1 32.0 1.0
CE1 v:HIS92 3.2 31.7 1.0
CHD v:HEC201 3.3 29.6 1.0
CHB v:HEC201 3.4 34.9 1.0
CHC v:HEC201 3.5 33.9 1.0
CHA v:HEC201 3.5 31.8 1.0
ND1 v:HIS41 4.1 33.2 1.0
CG v:HIS92 4.1 37.4 1.0
CG v:HIS41 4.2 34.5 1.0
C2D v:HEC201 4.2 30.0 1.0
ND1 v:HIS92 4.2 37.5 1.0
C3D v:HEC201 4.2 32.6 1.0
C3C v:HEC201 4.3 33.5 1.0
C2B v:HEC201 4.3 35.1 1.0
C2C v:HEC201 4.3 34.9 1.0
C3B v:HEC201 4.3 31.3 1.0
C3A v:HEC201 4.4 37.0 1.0
C2A v:HEC201 4.4 30.7 1.0
CE1 v:TYR75 4.9 34.5 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 02:29:37 2024

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