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Iron in PDB 5kaf: Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf was solved by I.D.Young, M.Ibrahim, R.Chatterjee, S.Gul, S.Koroidov, A.S.Brewster, R.Tran, R.Alonso-Mori, F.Fuller, T.Kroll, T.Michels-Clark, H.Laksmono, R.G.Sierra, C.A.Stan, C.Saracini, M.A.Bean, I.Seuffert, D.Sokaras, T.-C.Weng, 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.Waterman, G.Evans, 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) 43.12 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.731, 223.815, 330.818, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 30.3

Other elements in 5kaf:

The structure of Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution 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 Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A Resolution (pdb code 5kaf). 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 Photosystem II in the Dark State at 3.0 A Resolution, PDB code: 5kaf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5kaf

Go back to Iron Binding Sites List in 5kaf
Iron binding site 1 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:46.8
occ:1.00
O1 A:BCT620 2.1 44.9 1.0
NE2 A:HIS215 2.2 39.6 1.0
NE2 D:HIS214 2.2 40.4 1.0
O2 A:BCT620 2.2 36.4 1.0
NE2 A:HIS272 2.2 47.3 1.0
NE2 D:HIS268 2.2 44.9 1.0
C A:BCT620 2.3 37.9 1.0
CE1 A:HIS215 2.9 48.4 1.0
CE1 D:HIS214 3.1 40.0 1.0
CE1 D:HIS268 3.1 39.5 1.0
CE1 A:HIS272 3.1 44.8 1.0
CD2 D:HIS214 3.2 42.9 1.0
CD2 D:HIS268 3.2 43.4 1.0
CD2 A:HIS272 3.2 42.1 1.0
CD2 A:HIS215 3.3 44.9 1.0
O3 A:BCT620 3.8 26.8 1.0
ND1 A:HIS215 4.2 47.0 1.0
ND1 D:HIS268 4.2 35.0 1.0
ND1 D:HIS214 4.2 39.3 1.0
ND1 A:HIS272 4.2 43.1 1.0
CG D:HIS214 4.3 37.0 1.0
CG D:HIS268 4.3 39.7 1.0
CG A:HIS272 4.3 45.9 1.0
CG A:HIS215 4.4 43.0 1.0
OH D:TYR244 4.7 37.4 1.0
CG2 A:VAL219 4.8 44.4 1.0
CG2 D:VAL218 5.0 39.8 1.0

Iron binding site 2 out of 6 in 5kaf

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Iron binding site 2 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe101

b:65.6
occ:1.00
FE E:HEM101 0.0 65.6 1.0
NC E:HEM101 2.1 51.2 1.0
ND E:HEM101 2.1 60.1 1.0
NA E:HEM101 2.1 58.0 1.0
NB E:HEM101 2.1 56.4 1.0
NE2 F:HIS24 2.2 62.1 1.0
NE2 E:HIS23 2.2 58.4 1.0
CE1 F:HIS24 2.8 61.3 1.0
C1A E:HEM101 3.0 55.6 1.0
C4A E:HEM101 3.0 50.9 1.0
C4D E:HEM101 3.0 54.8 1.0
CD2 E:HIS23 3.1 61.7 1.0
C1D E:HEM101 3.1 62.6 1.0
C1C E:HEM101 3.1 49.6 1.0
C4B E:HEM101 3.1 53.6 1.0
C4C E:HEM101 3.1 57.0 1.0
C1B E:HEM101 3.1 56.4 1.0
CE1 E:HIS23 3.2 56.9 1.0
CD2 F:HIS24 3.3 58.6 1.0
CHA E:HEM101 3.4 52.1 1.0
CHC E:HEM101 3.4 55.9 1.0
CHB E:HEM101 3.4 47.4 1.0
CHD E:HEM101 3.4 54.9 1.0
ND1 F:HIS24 4.0 61.0 1.0
CG E:HIS23 4.2 59.1 1.0
C2A E:HEM101 4.2 61.1 1.0
ND1 E:HIS23 4.2 57.1 1.0
C3A E:HEM101 4.2 55.7 1.0
CG F:HIS24 4.2 60.3 1.0
C3D E:HEM101 4.3 54.6 1.0
C2D E:HEM101 4.3 56.4 1.0
C2C E:HEM101 4.3 49.5 1.0
C3C E:HEM101 4.3 60.2 1.0
C2B E:HEM101 4.3 53.9 1.0
C3B E:HEM101 4.3 53.4 1.0
CE1 E:TYR19 4.9 53.3 1.0

Iron binding site 3 out of 6 in 5kaf

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Iron binding site 3 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:54.2
occ:1.00
FE V:HEM201 0.0 54.2 1.0
ND V:HEM201 2.0 45.7 1.0
NB V:HEM201 2.0 50.2 1.0
NA V:HEM201 2.1 44.9 1.0
NC V:HEM201 2.1 49.0 1.0
NE2 V:HIS41 2.2 47.9 1.0
NE2 V:HIS92 2.2 47.4 1.0
CE1 V:HIS92 3.0 47.2 1.0
C4D V:HEM201 3.1 41.3 1.0
C1C V:HEM201 3.1 47.4 1.0
C4B V:HEM201 3.1 49.4 1.0
C1D V:HEM201 3.1 43.8 1.0
C1A V:HEM201 3.1 44.7 1.0
C1B V:HEM201 3.1 48.2 1.0
C4A V:HEM201 3.1 44.2 1.0
C4C V:HEM201 3.1 40.7 1.0
CE1 V:HIS41 3.1 51.5 1.0
CD2 V:HIS41 3.1 49.9 1.0
CD2 V:HIS92 3.3 45.5 1.0
CHC V:HEM201 3.4 45.1 1.0
CHA V:HEM201 3.4 44.8 1.0
CHD V:HEM201 3.4 38.2 1.0
CHB V:HEM201 3.4 48.5 1.0
ND1 V:HIS92 4.2 47.6 1.0
ND1 V:HIS41 4.2 58.5 1.0
CG V:HIS41 4.3 51.0 1.0
C3D V:HEM201 4.3 41.9 1.0
C2D V:HEM201 4.3 41.4 1.0
C2C V:HEM201 4.3 46.0 1.0
C3B V:HEM201 4.3 49.0 1.0
C2B V:HEM201 4.3 41.3 1.0
C2A V:HEM201 4.3 39.2 1.0
C3A V:HEM201 4.3 37.3 1.0
C3C V:HEM201 4.3 50.2 1.0
CG V:HIS92 4.3 47.1 1.0
CE1 V:TYR75 4.9 40.1 1.0

Iron binding site 4 out of 6 in 5kaf

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Iron binding site 4 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe602

b:62.8
occ:1.00
O1 a:BCT605 2.2 49.2 1.0
O2 a:BCT605 2.2 47.2 1.0
NE2 d:HIS214 2.2 42.1 1.0
NE2 a:HIS215 2.2 44.3 1.0
NE2 a:HIS272 2.2 48.0 1.0
NE2 d:HIS268 2.2 36.8 1.0
C a:BCT605 2.3 50.4 1.0
CE1 a:HIS215 3.0 45.7 1.0
CE1 d:HIS268 3.0 36.8 1.0
CE1 a:HIS272 3.0 49.1 1.0
CE1 d:HIS214 3.0 40.2 1.0
CD2 d:HIS214 3.3 39.9 1.0
CD2 a:HIS215 3.3 43.4 1.0
CD2 a:HIS272 3.3 40.5 1.0
CD2 d:HIS268 3.3 42.9 1.0
O3 a:BCT605 3.7 44.1 1.0
ND1 a:HIS215 4.2 42.0 1.0
ND1 d:HIS268 4.2 35.7 1.0
ND1 a:HIS272 4.2 44.5 1.0
ND1 d:HIS214 4.2 34.5 1.0
CG d:HIS214 4.3 38.0 1.0
CG a:HIS215 4.4 40.0 1.0
CG a:HIS272 4.4 38.0 1.0
CG d:HIS268 4.4 39.7 1.0
CG2 a:VAL219 4.6 42.9 1.0
OH d:TYR244 4.7 39.7 1.0

Iron binding site 5 out of 6 in 5kaf

Go back to Iron Binding Sites List in 5kaf
Iron binding site 5 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe101

b:66.4
occ:1.00
FE e:HEM101 0.0 66.4 1.0
NC e:HEM101 2.1 68.3 1.0
NA e:HEM101 2.1 64.9 1.0
ND e:HEM101 2.1 66.3 1.0
NB e:HEM101 2.1 62.5 1.0
NE2 e:HIS23 2.2 69.7 1.0
NE2 f:HIS24 2.2 68.5 1.0
CD2 f:HIS24 3.0 58.8 1.0
CD2 e:HIS23 3.0 65.3 1.0
C1A e:HEM101 3.0 60.9 1.0
C4D e:HEM101 3.1 65.3 1.0
C4A e:HEM101 3.1 62.5 1.0
C1C e:HEM101 3.1 67.0 1.0
C4B e:HEM101 3.1 62.4 1.0
C1D e:HEM101 3.1 62.4 1.0
C1B e:HEM101 3.1 60.8 1.0
C4C e:HEM101 3.1 64.6 1.0
CE1 f:HIS24 3.2 61.6 1.0
CE1 e:HIS23 3.2 72.3 1.0
CHA e:HEM101 3.4 61.8 1.0
CHC e:HEM101 3.4 66.2 1.0
CHB e:HEM101 3.4 60.9 1.0
CHD e:HEM101 3.5 59.3 1.0
CG f:HIS24 4.2 53.9 1.0
ND1 f:HIS24 4.2 55.7 1.0
CG e:HIS23 4.2 67.0 1.0
ND1 e:HIS23 4.2 69.1 1.0
C2A e:HEM101 4.2 62.8 1.0
C3A e:HEM101 4.2 67.7 1.0
C3D e:HEM101 4.3 62.5 1.0
C2D e:HEM101 4.3 63.0 1.0
C2C e:HEM101 4.3 66.5 1.0
C3B e:HEM101 4.3 53.3 1.0
C2B e:HEM101 4.3 57.2 1.0
C3C e:HEM101 4.3 67.4 1.0
CE1 e:TYR19 4.8 68.6 1.0

Iron binding site 6 out of 6 in 5kaf

Go back to Iron Binding Sites List in 5kaf
Iron binding site 6 out of 6 in the Rt Xfel Structure of Photosystem II in the Dark State at 3.0 A 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 Photosystem II in the Dark State at 3.0 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:49.6
occ:1.00
FE v:HEM201 0.0 49.6 1.0
ND v:HEM201 2.0 40.1 1.0
NC v:HEM201 2.1 42.5 1.0
NA v:HEM201 2.1 46.5 1.0
NB v:HEM201 2.1 43.1 1.0
NE2 v:HIS41 2.2 40.1 1.0
NE2 v:HIS92 2.2 41.9 1.0
C1D v:HEM201 3.1 39.5 1.0
C4D v:HEM201 3.1 39.1 1.0
CE1 v:HIS92 3.1 41.7 1.0
C1C v:HEM201 3.1 41.5 1.0
C4B v:HEM201 3.1 40.2 1.0
C1A v:HEM201 3.1 42.7 1.0
C4C v:HEM201 3.1 41.6 1.0
C4A v:HEM201 3.1 40.3 1.0
C1B v:HEM201 3.1 41.8 1.0
CD2 v:HIS41 3.1 41.2 1.0
CE1 v:HIS41 3.1 36.6 1.0
CD2 v:HIS92 3.3 44.1 1.0
CHD v:HEM201 3.4 41.5 1.0
CHC v:HEM201 3.4 42.8 1.0
CHA v:HEM201 3.4 34.3 1.0
CHB v:HEM201 3.5 40.0 1.0
ND1 v:HIS41 4.2 42.9 1.0
ND1 v:HIS92 4.2 48.7 1.0
CG v:HIS41 4.2 41.8 1.0
C2D v:HEM201 4.3 35.3 1.0
C3D v:HEM201 4.3 40.6 1.0
C2C v:HEM201 4.3 41.4 1.0
C2A v:HEM201 4.3 41.7 1.0
C3B v:HEM201 4.3 35.0 1.0
C3A v:HEM201 4.3 45.4 1.0
C2B v:HEM201 4.3 36.2 1.0
C3C v:HEM201 4.3 43.1 1.0
CG v:HIS92 4.3 47.7 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 03:07:57 2024

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