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Iron in PDB 8ez5: Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 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 2.09 Angstrom Resolution, PDB code: 8ez5 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) 33.65 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.958, 221.646, 307.786, 90, 90, 90
R / Rfree (%) 18.6 / 23.5

Other elements in 8ez5:

The structure of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution also contains other interesting chemical elements:

Manganese (Mn) 16 atoms
Magnesium (Mg) 70 atoms
Chlorine (Cl) 4 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 2.09 Angstrom Resolution (pdb code 8ez5). 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 2.09 Angstrom Resolution, PDB code: 8ez5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8ez5

Go back to Iron Binding Sites List in 8ez5
Iron binding site 1 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 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 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:32.1
occ:1.00
 NE2 A:HIS215 2.1 31.4 1.0
NE2 D:HIS214 2.1 36.7 1.0
NE2 D:HIS268 2.2 37.5 1.0
O2 D:BCT401 2.2 39.1 1.0
O3 D:BCT401 2.2 34.6 1.0
NE2 A:HIS272 2.2 37.0 1.0
C D:BCT401 2.4 40.7 1.0
CE1 A:HIS215 2.9 34.0 1.0
CE1 D:HIS214 3.0 27.4 1.0
CE1 D:HIS268 3.1 31.8 1.0
CE1 A:HIS272 3.2 35.8 1.0
CD2 D:HIS268 3.2 31.0 1.0
CD2 D:HIS214 3.3 30.3 1.0
CD2 A:HIS272 3.3 31.5 1.0
CD2 A:HIS215 3.3 35.8 1.0
O1 D:BCT401 3.9 39.9 1.0
ND1 A:HIS215 4.1 29.9 1.0
ND1 D:HIS214 4.1 29.0 1.0
ND1 D:HIS268 4.2 32.1 1.0
ND1 A:HIS272 4.3 36.9 1.0
CG A:HIS215 4.3 34.9 1.0
CG D:HIS214 4.3 27.8 1.0
CG D:HIS268 4.3 36.0 1.0
CG A:HIS272 4.4 35.2 1.0
CG2 A:VAL219 4.6 33.6 1.0
OH D:TYR244 4.9 35.4 1.0

Iron binding site 2 out of 6 in 8ez5

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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 2.09 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 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe101

b:51.0
occ:1.00
 FE E:HEM101 0.0 51.0 1.0
ND E:HEM101 2.0 45.3 1.0
NC E:HEM101 2.0 47.9 1.0
NA E:HEM101 2.0 52.2 1.0
NB E:HEM101 2.1 45.4 1.0
NE2 E:HIS23 2.1 54.4 1.0
NE2 F:HIS24 2.1 50.5 1.0
CD2 F:HIS24 2.7 46.2 1.0
C1D E:HEM101 3.0 50.4 1.0
C4D E:HEM101 3.0 53.6 1.0
C1A E:HEM101 3.0 52.1 1.0
CD2 E:HIS23 3.0 50.6 1.0
C4A E:HEM101 3.0 50.9 1.0
C4C E:HEM101 3.1 46.2 1.0
CE1 E:HIS23 3.1 54.9 1.0
C1B E:HEM101 3.1 51.0 1.0
C1C E:HEM101 3.1 46.5 1.0
C4B E:HEM101 3.1 46.1 1.0
CE1 F:HIS24 3.3 50.0 1.0
CHD E:HEM101 3.4 45.5 1.0
CHA E:HEM101 3.4 51.4 1.0
CHB E:HEM101 3.4 49.6 1.0
CHC E:HEM101 3.5 47.2 1.0
CG F:HIS24 4.0 50.0 1.0
C2D E:HEM101 4.2 47.6 1.0
C3D E:HEM101 4.2 49.1 1.0
ND1 E:HIS23 4.2 57.4 1.0
CG E:HIS23 4.2 57.0 1.0
ND1 F:HIS24 4.2 53.8 1.0
C2A E:HEM101 4.2 55.8 1.0
C3A E:HEM101 4.2 55.3 1.0
C3C E:HEM101 4.3 45.9 1.0
C2C E:HEM101 4.3 49.1 1.0
C2B E:HEM101 4.3 51.9 1.0
C3B E:HEM101 4.3 48.5 1.0
CD1 E:ILE22 4.5 56.5 0.1
NE1 F:TRP20 4.8 52.4 1.0
CZ2 F:TRP20 4.9 44.7 1.0

Iron binding site 3 out of 6 in 8ez5

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Iron binding site 3 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 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 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:33.8
occ:1.00
 FE V:HEC201 0.0 33.8 1.0
NA V:HEC201 2.0 29.4 1.0
NB V:HEC201 2.0 33.9 1.0
NE2 V:HIS92 2.0 39.0 1.0
NC V:HEC201 2.1 33.0 1.0
ND V:HEC201 2.1 30.6 1.0
NE2 V:HIS41 2.2 32.5 1.0
CD2 V:HIS41 2.9 32.9 1.0
CD2 V:HIS92 3.0 36.3 1.0
C4A V:HEC201 3.0 34.0 1.0
C1B V:HEC201 3.0 34.6 1.0
C1A V:HEC201 3.0 35.3 1.0
CE1 V:HIS92 3.1 32.3 1.0
C1C V:HEC201 3.1 38.8 1.0
C4D V:HEC201 3.1 32.6 1.0
C4B V:HEC201 3.1 34.9 1.0
C4C V:HEC201 3.1 29.1 1.0
C1D V:HEC201 3.1 35.2 1.0
CE1 V:HIS41 3.3 33.6 1.0
CHB V:HEC201 3.4 36.4 1.0
CHA V:HEC201 3.4 34.5 1.0
CHC V:HEC201 3.5 38.7 1.0
CHD V:HEC201 3.5 31.0 1.0
CG V:HIS92 4.1 39.5 1.0
ND1 V:HIS92 4.1 34.0 1.0
CG V:HIS41 4.2 35.2 1.0
C3A V:HEC201 4.2 39.3 1.0
C2A V:HEC201 4.3 32.6 1.0
C2B V:HEC201 4.3 34.6 1.0
C3B V:HEC201 4.3 32.2 1.0
ND1 V:HIS41 4.3 35.0 1.0
C2C V:HEC201 4.3 35.1 1.0
C3C V:HEC201 4.3 31.6 1.0
C3D V:HEC201 4.3 27.2 1.0
C2D V:HEC201 4.4 33.1 1.0
CE1 V:TYR75 4.9 37.1 1.0

Iron binding site 4 out of 6 in 8ez5

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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 2.09 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 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe603

b:38.1
occ:1.00
 NE2 a:HIS215 2.1 32.7 1.0
NE2 d:HIS214 2.1 32.6 1.0
O2 a:BCT606 2.2 34.2 1.0
NE2 d:HIS268 2.2 39.5 1.0
O3 a:BCT606 2.2 40.0 1.0
NE2 a:HIS272 2.3 44.3 1.0
C a:BCT606 2.4 44.4 1.0
CE1 a:HIS215 3.0 38.6 1.0
CE1 d:HIS214 3.0 33.9 1.0
CE1 a:HIS272 3.1 42.0 1.0
CE1 d:HIS268 3.1 34.0 1.0
CD2 a:HIS215 3.2 39.9 1.0
CD2 d:HIS214 3.2 30.5 1.0
CD2 d:HIS268 3.3 36.8 1.0
CD2 a:HIS272 3.4 33.4 1.0
O1 a:BCT606 3.9 49.7 1.0
ND1 a:HIS215 4.1 33.8 1.0
ND1 d:HIS214 4.2 36.9 1.0
CG a:HIS215 4.3 30.1 1.0
ND1 d:HIS268 4.3 34.1 1.0
ND1 a:HIS272 4.3 40.2 1.0
CG d:HIS214 4.3 36.3 1.0
CG d:HIS268 4.4 37.2 1.0
CG a:HIS272 4.4 38.8 1.0
CG2 a:VAL219 4.7 39.2 1.0
OH d:TYR244 5.0 43.1 1.0

Iron binding site 5 out of 6 in 8ez5

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Iron binding site 5 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 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 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:60.6
occ:1.00
 FE f:HEM101 0.0 60.6 1.0
NC f:HEM101 2.0 55.4 1.0
ND f:HEM101 2.0 55.8 1.0
NE2 e:HIS23 2.1 63.8 1.0
NB f:HEM101 2.1 58.1 1.0
NA f:HEM101 2.1 57.7 1.0
NE2 f:HIS24 2.1 61.6 1.0
C1D f:HEM101 2.9 57.5 1.0
C4C f:HEM101 3.0 59.9 1.0
C4D f:HEM101 3.0 54.7 1.0
CE1 e:HIS23 3.0 62.5 1.0
C1C f:HEM101 3.1 57.4 1.0
CD2 f:HIS24 3.1 53.2 1.0
C4A f:HEM101 3.1 59.3 1.0
C1B f:HEM101 3.1 60.2 1.0
C1A f:HEM101 3.1 62.2 1.0
CE1 f:HIS24 3.1 55.7 1.0
CD2 e:HIS23 3.1 64.2 1.0
C4B f:HEM101 3.1 60.4 1.0
CHD f:HEM101 3.3 56.5 1.0
CHB f:HEM101 3.4 60.4 1.0
CHA f:HEM101 3.4 61.8 1.0
CHC f:HEM101 3.5 63.9 1.0
C2D f:HEM101 4.1 55.7 1.0
C3D f:HEM101 4.1 54.3 1.0
ND1 e:HIS23 4.2 66.7 1.0
C3C f:HEM101 4.2 59.9 1.0
ND1 f:HIS24 4.2 55.4 1.0
CG f:HIS24 4.2 52.6 1.0
CG e:HIS23 4.2 63.4 1.0
C2C f:HEM101 4.2 58.4 1.0
C3A f:HEM101 4.3 65.7 1.0
C2A f:HEM101 4.3 62.2 1.0
C2B f:HEM101 4.3 61.7 1.0
C3B f:HEM101 4.3 52.4 1.0
NE1 f:TRP20 4.9 63.0 1.0
CZ2 f:TRP20 4.9 54.0 1.0
CE1 e:TYR19 5.0 64.0 1.0

Iron binding site 6 out of 6 in 8ez5

Go back to Iron Binding Sites List in 8ez5
Iron binding site 6 out of 6 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 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 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:36.9
occ:1.00
 FE v:HEC201 0.0 36.9 1.0
NC v:HEC201 2.0 36.8 1.0
ND v:HEC201 2.0 36.9 1.0
NB v:HEC201 2.0 37.1 1.0
NE2 v:HIS41 2.1 36.6 1.0
NA v:HEC201 2.1 39.1 1.0
NE2 v:HIS92 2.1 40.8 1.0
CD2 v:HIS92 3.0 37.4 1.0
C1D v:HEC201 3.0 31.3 1.0
C4C v:HEC201 3.0 37.9 1.0
CD2 v:HIS41 3.0 36.6 1.0
C1C v:HEC201 3.0 37.8 1.0
C4D v:HEC201 3.0 37.9 1.0
C4B v:HEC201 3.0 38.2 1.0
C1B v:HEC201 3.1 36.4 1.0
CE1 v:HIS41 3.1 37.6 1.0
C1A v:HEC201 3.2 37.2 1.0
C4A v:HEC201 3.2 37.7 1.0
CE1 v:HIS92 3.2 36.5 1.0
CHD v:HEC201 3.3 33.9 1.0
CHC v:HEC201 3.4 36.8 1.0
CHA v:HEC201 3.5 34.7 1.0
CHB v:HEC201 3.5 38.4 1.0
CG v:HIS41 4.2 36.4 1.0
CG v:HIS92 4.2 38.4 1.0
ND1 v:HIS41 4.2 40.0 1.0
C2D v:HEC201 4.2 31.8 1.0
C3C v:HEC201 4.2 41.3 1.0
C3D v:HEC201 4.2 34.5 1.0
C2C v:HEC201 4.3 40.4 1.0
ND1 v:HIS92 4.3 43.7 1.0
C3B v:HEC201 4.3 38.3 1.0
C2B v:HEC201 4.3 39.8 1.0
C2A v:HEC201 4.4 41.7 1.0
C3A v:HEC201 4.4 42.4 1.0
CE1 v:TYR75 5.0 39.1 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 02:29:03 2024

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