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Iron in PDB 5kai: NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution

Enzymatic activity of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution

All present enzymatic activity of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution:
1.10.3.9;

Protein crystallography data

The structure of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution, PDB code: 5kai 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) 43.57 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.911, 224.268, 330.996, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 30

Other elements in 5kai:

The structure of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 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 NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution (pdb code 5kai). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution, PDB code: 5kai:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5kai

Go back to Iron Binding Sites List in 5kai
Iron binding site 1 out of 6 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:60.2
occ:1.00
 O1 A:BCT615 2.2 54.4 1.0
NE2 A:HIS215 2.2 52.2 1.0
NE2 D:HIS214 2.2 53.0 1.0
NE2 A:HIS272 2.2 58.0 1.0
O2 A:BCT615 2.2 46.1 1.0
NE2 D:HIS268 2.2 53.4 1.0
C A:BCT615 2.4 49.3 1.0
CE1 A:HIS215 2.9 54.6 1.0
CE1 D:HIS268 3.0 50.6 1.0
CE1 D:HIS214 3.1 50.7 1.0
CE1 A:HIS272 3.1 57.8 1.0
CD2 D:HIS214 3.2 48.0 1.0
CD2 A:HIS272 3.2 59.7 1.0
CD2 D:HIS268 3.3 51.4 1.0
CD2 A:HIS215 3.4 52.5 1.0
O3 A:BCT615 3.8 52.0 1.0
ND1 A:HIS215 4.1 52.5 1.0
ND1 D:HIS268 4.2 47.2 1.0
ND1 D:HIS214 4.2 43.9 1.0
ND1 A:HIS272 4.3 57.0 1.0
CG D:HIS214 4.3 47.7 1.0
CG A:HIS272 4.4 56.5 1.0
CG A:HIS215 4.4 55.0 1.0
CG D:HIS268 4.4 47.4 1.0
OH D:TYR244 4.7 55.1 1.0
CG2 D:VAL218 4.9 52.0 1.0
CG2 A:VAL219 4.9 50.3 1.0

Iron binding site 2 out of 6 in 5kai

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Iron binding site 2 out of 6 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe102

b:71.2
occ:1.00
 FE E:HEM102 0.0 71.2 1.0
NB E:HEM102 2.1 66.0 1.0
NA E:HEM102 2.1 73.9 1.0
NC E:HEM102 2.1 69.8 1.0
ND E:HEM102 2.1 73.6 1.0
NE2 F:HIS24 2.2 68.3 1.0
NE2 E:HIS23 2.2 74.3 1.0
C1A E:HEM102 3.0 69.1 1.0
C4D E:HEM102 3.0 65.9 1.0
C1C E:HEM102 3.0 64.3 1.0
C4A E:HEM102 3.1 70.5 1.0
C4B E:HEM102 3.1 65.8 1.0
CE1 F:HIS24 3.1 67.3 1.0
C1D E:HEM102 3.1 67.6 1.0
CE1 E:HIS23 3.1 72.5 1.0
C1B E:HEM102 3.1 64.3 1.0
C4C E:HEM102 3.1 65.6 1.0
CD2 F:HIS24 3.1 68.9 1.0
CD2 E:HIS23 3.2 70.1 1.0
CHA E:HEM102 3.4 67.1 1.0
CHC E:HEM102 3.4 59.7 1.0
CHB E:HEM102 3.5 62.4 1.0
CHD E:HEM102 3.5 57.9 1.0
ND1 F:HIS24 4.1 63.2 1.0
CG F:HIS24 4.2 69.7 1.0
ND1 E:HIS23 4.2 73.9 1.0
C2A E:HEM102 4.2 69.3 1.0
C3A E:HEM102 4.2 72.1 1.0
C3D E:HEM102 4.2 66.3 1.0
C2D E:HEM102 4.2 67.1 1.0
C2C E:HEM102 4.3 59.4 1.0
CG E:HIS23 4.3 72.2 1.0
C3B E:HEM102 4.3 65.7 1.0
C2B E:HEM102 4.3 61.8 1.0
C3C E:HEM102 4.3 58.6 1.0
CE1 E:TYR19 4.9 70.8 1.0
NE1 F:TRP20 4.9 70.2 1.0

Iron binding site 3 out of 6 in 5kai

Go back to Iron Binding Sites List in 5kai
Iron binding site 3 out of 6 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe201

b:61.5
occ:1.00
 FE V:HEM201 0.0 61.5 1.0
NB V:HEM201 2.0 53.6 1.0
ND V:HEM201 2.0 50.7 1.0
NA V:HEM201 2.1 55.0 1.0
NC V:HEM201 2.1 50.7 1.0
NE2 V:HIS41 2.2 51.8 1.0
NE2 V:HIS92 2.2 52.3 1.0
CE1 V:HIS41 3.0 48.1 1.0
C4B V:HEM201 3.1 56.9 1.0
C4D V:HEM201 3.1 51.7 1.0
C1C V:HEM201 3.1 51.3 1.0
C1D V:HEM201 3.1 42.8 1.0
C1B V:HEM201 3.1 54.8 1.0
C1A V:HEM201 3.1 55.2 1.0
C4A V:HEM201 3.1 53.2 1.0
CD2 V:HIS92 3.1 53.4 1.0
C4C V:HEM201 3.1 45.1 1.0
CD2 V:HIS41 3.1 48.0 1.0
CE1 V:HIS92 3.2 52.0 1.0
CHC V:HEM201 3.4 54.8 1.0
CHA V:HEM201 3.4 51.7 1.0
CHB V:HEM201 3.4 51.1 1.0
CHD V:HEM201 3.4 41.8 1.0
ND1 V:HIS41 4.1 54.1 1.0
CG V:HIS41 4.2 52.7 1.0
CG V:HIS92 4.3 50.0 1.0
ND1 V:HIS92 4.3 52.6 1.0
C2D V:HEM201 4.3 44.6 1.0
C3D V:HEM201 4.3 50.0 1.0
C3B V:HEM201 4.3 55.5 1.0
C2B V:HEM201 4.3 55.1 1.0
C2C V:HEM201 4.3 51.0 1.0
C2A V:HEM201 4.3 53.6 1.0
C3A V:HEM201 4.3 49.8 1.0
C3C V:HEM201 4.3 50.7 1.0

Iron binding site 4 out of 6 in 5kai

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Iron binding site 4 out of 6 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe703

b:60.5
occ:1.00
 O2 a:BCT706 2.1 59.7 1.0
NE2 d:HIS214 2.2 46.0 1.0
NE2 a:HIS215 2.2 53.2 1.0
O1 a:BCT706 2.2 50.7 1.0
NE2 a:HIS272 2.2 60.8 1.0
NE2 d:HIS268 2.2 55.3 1.0
C a:BCT706 2.3 56.1 1.0
CE1 a:HIS215 2.9 52.9 1.0
CE1 d:HIS214 3.0 49.5 1.0
CE1 a:HIS272 3.1 55.4 1.0
CE1 d:HIS268 3.1 50.7 1.0
CD2 a:HIS272 3.2 56.3 1.0
CD2 d:HIS268 3.2 53.4 1.0
CD2 d:HIS214 3.3 45.3 1.0
CD2 a:HIS215 3.3 53.9 1.0
O3 a:BCT706 3.7 56.3 1.0
ND1 a:HIS215 4.1 58.1 1.0
ND1 d:HIS214 4.2 45.1 1.0
ND1 a:HIS272 4.3 50.1 1.0
ND1 d:HIS268 4.3 47.8 1.0
CG a:HIS272 4.3 55.0 1.0
CG d:HIS268 4.3 48.9 1.0
CG d:HIS214 4.3 45.3 1.0
CG a:HIS215 4.4 55.1 1.0
OH d:TYR244 4.7 47.0 1.0
CG2 a:VAL219 4.7 54.1 1.0
CG2 d:VAL218 4.9 45.6 1.0

Iron binding site 5 out of 6 in 5kai

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Iron binding site 5 out of 6 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe102

b:91.0
occ:1.00
 FE e:HEM102 0.0 91.0 1.0
NC e:HEM102 2.1 74.9 1.0
ND e:HEM102 2.1 70.9 1.0
NA e:HEM102 2.1 73.2 1.0
NB e:HEM102 2.1 68.3 1.0
NE2 f:HIS24 2.2 73.0 1.0
NE2 e:HIS23 2.2 77.0 1.0
CE1 e:HIS23 2.9 73.3 1.0
C1A e:HEM102 3.0 73.7 1.0
C4D e:HEM102 3.0 76.8 1.0
C1C e:HEM102 3.1 73.6 1.0
C1D e:HEM102 3.1 65.7 1.0
C4A e:HEM102 3.1 75.8 1.0
C4B e:HEM102 3.1 69.8 1.0
CE1 f:HIS24 3.1 72.6 1.0
C4C e:HEM102 3.1 72.6 1.0
C1B e:HEM102 3.1 70.8 1.0
CD2 f:HIS24 3.2 74.3 1.0
CD2 e:HIS23 3.3 76.1 1.0
CHA e:HEM102 3.4 79.6 1.0
CHC e:HEM102 3.4 75.5 1.0
CHD e:HEM102 3.4 68.2 1.0
CHB e:HEM102 3.5 75.0 1.0
ND1 e:HIS23 4.1 76.6 1.0
ND1 f:HIS24 4.2 74.0 1.0
C2A e:HEM102 4.2 71.6 1.0
C3D e:HEM102 4.2 70.0 1.0
C2D e:HEM102 4.2 71.3 1.0
C3A e:HEM102 4.2 71.3 1.0
CG f:HIS24 4.3 69.1 1.0
C2C e:HEM102 4.3 69.7 1.0
C3C e:HEM102 4.3 73.8 1.0
C2B e:HEM102 4.3 64.5 1.0
C3B e:HEM102 4.3 63.2 1.0
CG e:HIS23 4.3 76.3 1.0
CE1 e:TYR19 4.8 78.0 1.0
NE1 f:TRP20 4.9 80.0 1.0

Iron binding site 6 out of 6 in 5kai

Go back to Iron Binding Sites List in 5kai
Iron binding site 6 out of 6 in the NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of NH3-Bound Rt Xfel Structure of Photosystem II 500 Ms After the 2ND Illumination (2F) at 2.8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe201

b:72.8
occ:1.00
 FE v:HEM201 0.0 72.8 1.0
ND v:HEM201 2.0 60.8 1.0
NB v:HEM201 2.0 63.2 1.0
NA v:HEM201 2.1 65.1 1.0
NC v:HEM201 2.1 57.3 1.0
NE2 v:HIS41 2.2 49.4 1.0
NE2 v:HIS92 2.2 58.5 1.0
CE1 v:HIS92 3.0 61.5 1.0
C1D v:HEM201 3.1 58.5 1.0
C4D v:HEM201 3.1 61.1 1.0
C1C v:HEM201 3.1 54.7 1.0
CE1 v:HIS41 3.1 56.0 1.0
C4B v:HEM201 3.1 59.9 1.0
C1A v:HEM201 3.1 60.0 1.0
C1B v:HEM201 3.1 61.7 1.0
C4A v:HEM201 3.1 63.2 1.0
C4C v:HEM201 3.1 57.4 1.0
CD2 v:HIS41 3.1 53.8 1.0
CD2 v:HIS92 3.2 56.6 1.0
CHD v:HEM201 3.4 57.1 1.0
CHC v:HEM201 3.4 57.1 1.0
CHA v:HEM201 3.4 56.8 1.0
CHB v:HEM201 3.4 60.9 1.0
ND1 v:HIS41 4.1 58.7 1.0
ND1 v:HIS92 4.2 62.6 1.0
CG v:HIS41 4.2 57.6 1.0
C2D v:HEM201 4.3 55.7 1.0
C3D v:HEM201 4.3 58.2 1.0
C2C v:HEM201 4.3 57.6 1.0
C2A v:HEM201 4.3 61.7 1.0
C3A v:HEM201 4.3 58.2 1.0
C2B v:HEM201 4.3 54.0 1.0
C3B v:HEM201 4.3 57.0 1.0
C3C v:HEM201 4.3 55.2 1.0
CG v:HIS92 4.3 62.2 1.0
CE2 v:TYR75 4.9 60.2 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 03:10:28 2024

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