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Iron in PDB 5tis: Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex

Enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex

All present enzymatic activity of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis was solved by I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, C.De Lichtenberg, L.V.Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.-C.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Braeuer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Watermann, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.28 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.870, 223.140, 310.710, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.1

Other elements in 5tis:

The structure of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex also contains other interesting chemical elements:

Magnesium (Mg) 70 atoms
Manganese (Mn) 8 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex (pdb code 5tis). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex, PDB code: 5tis:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5tis

Go back to Iron Binding Sites List in 5tis
Iron binding site 1 out of 6 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:36.6
occ:1.00
NE2 A:HIS215 2.2 40.8 1.0
O1 A:BCT605 2.2 42.2 1.0
NE2 D:HIS214 2.2 40.0 1.0
O2 A:BCT605 2.2 44.3 1.0
NE2 A:HIS272 2.2 44.7 1.0
NE2 D:HIS268 2.2 41.2 1.0
C A:BCT605 2.4 43.4 1.0
CE1 A:HIS215 3.0 38.6 1.0
CE1 A:HIS272 3.1 41.2 1.0
CE1 D:HIS268 3.1 39.0 1.0
CE1 D:HIS214 3.1 35.0 1.0
CD2 D:HIS214 3.2 34.5 1.0
CD2 A:HIS215 3.3 40.2 1.0
CD2 A:HIS272 3.3 37.4 1.0
CD2 D:HIS268 3.3 38.1 1.0
O3 A:BCT605 3.9 53.1 1.0
ND1 A:HIS215 4.2 35.7 1.0
ND1 D:HIS214 4.2 35.0 1.0
ND1 A:HIS272 4.2 38.0 1.0
ND1 D:HIS268 4.2 38.6 1.0
CG A:HIS215 4.3 36.6 1.0
CG D:HIS214 4.3 35.6 1.0
CG A:HIS272 4.4 39.6 1.0
CG D:HIS268 4.4 37.4 1.0
CG2 A:VAL219 4.9 36.0 1.0
OH D:TYR244 4.9 46.5 1.0
CG2 D:VAL218 5.0 36.1 1.0

Iron binding site 2 out of 6 in 5tis

Go back to Iron Binding Sites List in 5tis
Iron binding site 2 out of 6 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe101

b:51.9
occ:1.00
FE E:HEM101 0.0 51.9 1.0
ND E:HEM101 2.0 47.1 1.0
NA E:HEM101 2.1 52.3 1.0
NC E:HEM101 2.1 51.9 1.0
NB E:HEM101 2.1 44.3 1.0
NE2 E:HIS23 2.1 54.4 1.0
NE2 F:HIS24 2.2 50.4 1.0
CD2 F:HIS24 2.9 48.1 1.0
C4D E:HEM101 3.0 51.6 1.0
C1D E:HEM101 3.0 50.7 1.0
C1A E:HEM101 3.0 54.6 1.0
CD2 E:HIS23 3.0 53.9 1.0
C4A E:HEM101 3.0 48.1 1.0
C1C E:HEM101 3.1 47.1 1.0
C1B E:HEM101 3.1 52.3 1.0
C4C E:HEM101 3.1 44.0 1.0
C4B E:HEM101 3.1 48.8 1.0
CE1 E:HIS23 3.2 55.0 1.0
CE1 F:HIS24 3.3 47.9 1.0
CHA E:HEM101 3.4 47.3 1.0
CHD E:HEM101 3.4 47.3 1.0
CHB E:HEM101 3.4 49.0 1.0
CHC E:HEM101 3.5 51.5 1.0
CG F:HIS24 4.1 53.1 1.0
C3D E:HEM101 4.2 50.5 1.0
C2D E:HEM101 4.2 43.8 1.0
CG E:HIS23 4.2 58.6 1.0
ND1 E:HIS23 4.2 58.6 1.0
C2A E:HEM101 4.2 57.1 1.0
C3A E:HEM101 4.2 51.2 1.0
ND1 F:HIS24 4.3 53.1 1.0
C2C E:HEM101 4.3 51.8 1.0
C2B E:HEM101 4.3 47.8 1.0
C3C E:HEM101 4.3 43.9 1.0
C3B E:HEM101 4.3 47.5 1.0
CE1 E:TYR19 4.9 59.0 1.0

Iron binding site 3 out of 6 in 5tis

Go back to Iron Binding Sites List in 5tis
Iron binding site 3 out of 6 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:36.9
occ:1.00
FE V:HEM201 0.0 36.9 1.0
NB V:HEM201 2.0 35.4 1.0
NA V:HEM201 2.0 43.1 1.0
NC V:HEM201 2.0 34.9 1.0
ND V:HEM201 2.1 40.3 1.0
NE2 V:HIS41 2.1 36.5 1.0
NE2 V:HIS92 2.2 40.0 1.0
CD2 V:HIS92 3.0 36.7 1.0
CD2 V:HIS41 3.0 30.5 1.0
C1D V:HEM201 3.1 33.4 1.0
C1B V:HEM201 3.1 33.7 1.0
C4A V:HEM201 3.1 41.9 1.0
C4D V:HEM201 3.1 38.1 1.0
C1C V:HEM201 3.1 39.0 1.0
C4C V:HEM201 3.1 37.4 1.0
C4B V:HEM201 3.1 39.5 1.0
C1A V:HEM201 3.1 38.2 1.0
CE1 V:HIS41 3.2 33.5 1.0
CE1 V:HIS92 3.2 39.9 1.0
CHD V:HEM201 3.4 32.9 1.0
CHB V:HEM201 3.4 37.6 1.0
CHC V:HEM201 3.4 38.3 1.0
CHA V:HEM201 3.4 39.5 1.0
CG V:HIS92 4.2 41.9 1.0
CG V:HIS41 4.2 38.5 1.0
C2D V:HEM201 4.3 36.1 1.0
C3D V:HEM201 4.3 33.5 1.0
ND1 V:HIS92 4.3 42.1 1.0
ND1 V:HIS41 4.3 37.7 1.0
C3A V:HEM201 4.3 40.6 1.0
C2B V:HEM201 4.3 35.6 1.0
C2C V:HEM201 4.3 36.3 1.0
C2A V:HEM201 4.3 37.5 1.0
C3C V:HEM201 4.3 35.9 1.0
C3B V:HEM201 4.3 36.1 1.0
CE2 V:TYR75 4.9 38.8 1.0
OH V:TYR75 5.0 34.1 1.0

Iron binding site 4 out of 6 in 5tis

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Iron binding site 4 out of 6 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe602

b:43.9
occ:1.00
NE2 a:HIS215 2.1 39.8 1.0
O1 a:BCT605 2.2 37.1 1.0
O2 a:BCT605 2.2 46.7 0.8
NE2 d:HIS214 2.2 39.3 1.0
NE2 d:HIS268 2.2 45.0 1.0
NE2 a:HIS272 2.2 50.2 1.0
C a:BCT605 2.4 45.2 1.0
CE1 a:HIS215 2.9 43.8 1.0
CE1 d:HIS268 3.0 43.8 1.0
CE1 a:HIS272 3.0 47.1 1.0
CE1 d:HIS214 3.2 36.7 1.0
CD2 d:HIS214 3.2 36.9 1.0
CD2 a:HIS215 3.3 41.6 1.0
CD2 a:HIS272 3.3 43.9 1.0
CD2 d:HIS268 3.3 37.4 1.0
O3 a:BCT605 3.9 53.0 0.8
ND1 a:HIS215 4.1 44.1 1.0
ND1 d:HIS268 4.2 39.2 1.0
ND1 a:HIS272 4.2 46.4 1.0
ND1 d:HIS214 4.3 37.5 1.0
CG d:HIS214 4.3 38.7 1.0
CG a:HIS215 4.3 42.9 1.0
CG a:HIS272 4.4 43.3 1.0
CG d:HIS268 4.4 46.5 1.0
CG2 a:VAL219 4.8 36.4 1.0
OH d:TYR244 4.9 44.7 1.0
CG2 d:VAL218 5.0 36.2 1.0

Iron binding site 5 out of 6 in 5tis

Go back to Iron Binding Sites List in 5tis
Iron binding site 5 out of 6 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe101

b:57.8
occ:1.00
FE e:HEM101 0.0 57.8 1.0
NC e:HEM101 2.0 47.2 1.0
ND e:HEM101 2.1 53.7 1.0
NB e:HEM101 2.1 60.1 1.0
NA e:HEM101 2.1 56.3 1.0
NE2 f:HIS24 2.2 64.2 1.0
NE2 e:HIS23 2.2 63.4 1.0
C1D e:HEM101 3.0 57.7 1.0
C1C e:HEM101 3.0 51.7 1.0
C4D e:HEM101 3.0 57.4 1.0
C4C e:HEM101 3.1 53.9 1.0
C1A e:HEM101 3.1 64.5 1.0
C4A e:HEM101 3.1 60.7 1.0
C1B e:HEM101 3.1 59.4 1.0
C4B e:HEM101 3.1 58.1 1.0
CE1 e:HIS23 3.1 60.7 1.0
CE1 f:HIS24 3.1 58.7 1.0
CD2 f:HIS24 3.1 48.8 1.0
CD2 e:HIS23 3.2 62.2 1.0
CHD e:HEM101 3.4 56.7 1.0
CHC e:HEM101 3.4 52.4 1.0
CHA e:HEM101 3.4 60.9 1.0
CHB e:HEM101 3.5 60.0 1.0
ND1 f:HIS24 4.2 53.7 1.0
CG f:HIS24 4.2 55.0 1.0
ND1 e:HIS23 4.2 64.3 1.0
C2D e:HEM101 4.2 56.3 1.0
C3D e:HEM101 4.2 58.6 1.0
C2A e:HEM101 4.2 64.5 1.0
C3A e:HEM101 4.2 68.6 1.0
C2C e:HEM101 4.3 55.5 1.0
CG e:HIS23 4.3 61.1 1.0
C3C e:HEM101 4.3 54.9 1.0
C2B e:HEM101 4.3 61.2 1.0
C3B e:HEM101 4.3 54.2 1.0
CE1 e:TYR19 4.9 70.1 1.0
NE1 f:TRP20 5.0 63.8 1.0

Iron binding site 6 out of 6 in 5tis

Go back to Iron Binding Sites List in 5tis
Iron binding site 6 out of 6 in the Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Room Temperature Xfel Structure of the Native, Doubly-Illuminated Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:38.9
occ:1.00
FE v:HEM201 0.0 38.9 1.0
NC v:HEM201 2.0 43.2 1.0
ND v:HEM201 2.0 37.5 1.0
NA v:HEM201 2.0 36.9 1.0
NB v:HEM201 2.1 41.7 1.0
NE2 v:HIS41 2.1 36.6 1.0
NE2 v:HIS92 2.2 40.3 1.0
CD2 v:HIS41 3.0 44.1 1.0
CE1 v:HIS92 3.0 40.2 1.0
C4D v:HEM201 3.0 41.9 1.0
C1D v:HEM201 3.0 37.5 1.0
C1C v:HEM201 3.1 43.2 1.0
C4C v:HEM201 3.1 37.0 1.0
C1A v:HEM201 3.1 39.5 1.0
C4B v:HEM201 3.1 41.9 1.0
C4A v:HEM201 3.1 38.6 1.0
C1B v:HEM201 3.1 40.5 1.0
CD2 v:HIS92 3.2 44.0 1.0
CE1 v:HIS41 3.2 41.1 1.0
CHD v:HEM201 3.4 37.6 1.0
CHC v:HEM201 3.4 40.9 1.0
CHA v:HEM201 3.4 37.3 1.0
CHB v:HEM201 3.4 39.2 1.0
ND1 v:HIS92 4.1 40.1 1.0
CG v:HIS41 4.2 39.7 1.0
C3D v:HEM201 4.2 39.0 1.0
C2D v:HEM201 4.2 31.9 1.0
ND1 v:HIS41 4.3 37.7 1.0
CG v:HIS92 4.3 42.3 1.0
C2C v:HEM201 4.3 41.2 1.0
C3C v:HEM201 4.3 43.7 1.0
C2A v:HEM201 4.3 40.6 1.0
C3A v:HEM201 4.3 44.5 1.0
C2B v:HEM201 4.3 43.7 1.0
C3B v:HEM201 4.3 40.0 1.0
CE2 v:TYR75 4.9 41.4 1.0

Reference:

I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, F.D.Fuller, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, R.Hussein, M.Zhang, L.Douthit, M.Kubin, C.De Lichtenberg, L.Vo Pham, H.Nilsson, M.H.Cheah, D.Shevela, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.C.Weng, E.Pastor, C.Weninger, T.Fransson, L.Lassalle, P.Brauer, P.Aller, P.T.Docker, B.Andi, A.M.Orville, J.M.Glownia, S.Nelson, M.Sikorski, D.Zhu, M.S.Hunter, T.J.Lane, A.Aquila, J.E.Koglin, J.Robinson, M.Liang, S.Boutet, A.Y.Lyubimov, M.Uervirojnangkoorn, N.W.Moriarty, D.Liebschner, P.V.Afonine, D.G.Waterman, G.Evans, P.Wernet, H.Dobbek, W.I.Weis, A.T.Brunger, P.H.Zwart, P.D.Adams, A.Zouni, J.Messinger, U.Bergmann, N.K.Sauter, J.Kern, V.K.Yachandra, J.Yano. Structure of Photosystem II and Substrate Binding at Room Temperature. Nature V. 540 453 2016.
ISSN: ESSN 1476-4687
PubMed: 27871088
DOI: 10.1038/NATURE20161
Page generated: Sun Dec 13 16:12:40 2020

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