Atomistry » Iron » PDB 5tis-5ufj » 5tis
Atomistry »
  Iron »
    PDB 5tis-5ufj »
      5tis »

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

Go back to Iron Binding Sites List in 5tis
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: Tue Aug 6 09:41:16 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy