Iron in PDB 5mdx: Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana

All present enzymatic activity of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana:
1.10.3.9;

The structure of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana also contains other interesting chemical elements:

Magnesium

(Mg)

308 atoms

The binding sites of Iron atom in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana (pdb code 5mdx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana, PDB code: 5mdx:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:0.1 occ:1.00 NE2 D:HIS269 2.1 0.5 1.0 NE2 A:HIS272 2.1 0.9 1.0 NE2 A:HIS215 2.2 0.5 1.0 NE2 D:HIS215 2.2 0.4 1.0 CD2 A:HIS272 2.7 0.9 1.0 CE1 D:HIS269 2.8 0.5 1.0 CE1 D:HIS215 2.8 0.4 1.0 CE1 A:HIS215 3.0 0.5 1.0 CD2 D:HIS269 3.3 0.5 1.0 CD2 A:HIS215 3.3 0.5 1.0 CE1 A:HIS272 3.3 0.9 1.0 CD2 D:HIS215 3.3 0.4 1.0 ND1 D:HIS215 4.0 0.4 1.0 ND1 D:HIS269 4.0 0.5 1.0 CG A:HIS272 4.0 0.9 1.0 ND1 A:HIS215 4.2 0.5 1.0 CG2 A:VAL219 4.2 0.3 1.0 ND1 A:HIS272 4.2 0.9 1.0 CG D:HIS269 4.2 0.5 1.0 CG D:HIS215 4.3 0.4 1.0 CG A:HIS215 4.3 0.5 1.0 OH D:TYR245 4.4 0.2 1.0 CG2 D:VAL219 4.6 0.4 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe101 b:0.1 occ:1.00 FE E:HEM101 0.0 0.1 1.0 ND E:HEM101 2.0 0.1 1.0 NA E:HEM101 2.0 0.1 1.0 NB E:HEM101 2.0 0.1 1.0 NE2 F:HIS18 2.1 0.6 1.0 NE2 E:HIS23 2.1 0.7 1.0 NC E:HEM101 2.1 0.1 1.0 CE1 F:HIS18 2.7 0.6 1.0 CE1 E:HIS23 2.9 0.7 1.0 C4D E:HEM101 3.0 0.1 1.0 C1A E:HEM101 3.0 0.1 1.0 C4A E:HEM101 3.0 0.1 1.0 C1B E:HEM101 3.0 0.1 1.0 C1D E:HEM101 3.0 0.1 1.0 C4B E:HEM101 3.1 0.1 1.0 C1C E:HEM101 3.1 0.1 1.0 C4C E:HEM101 3.1 0.1 1.0 CD2 E:HIS23 3.3 0.7 1.0 CD2 F:HIS18 3.4 0.6 1.0 CHA E:HEM101 3.4 0.1 1.0 CHB E:HEM101 3.4 0.1 1.0 CHD E:HEM101 3.5 0.1 1.0 CHC E:HEM101 3.5 0.1 1.0 ND1 F:HIS18 3.9 0.6 1.0 ND1 E:HIS23 4.1 0.7 1.0 NE1 F:TRP14 4.2 0.6 1.0 C3D E:HEM101 4.2 0.1 1.0 C2A E:HEM101 4.2 0.1 1.0 C3A E:HEM101 4.2 0.1 1.0 C2D E:HEM101 4.2 0.1 1.0 CG F:HIS18 4.2 0.6 1.0 C2B E:HEM101 4.3 0.1 1.0 CG E:HIS23 4.3 0.7 1.0 C3B E:HEM101 4.3 0.1 1.0 C2C E:HEM101 4.3 0.1 1.0 C3C E:HEM101 4.4 0.1 1.0 CD1 F:TRP14 4.6 0.6 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe401 b:0.1 occ:1.00 NE2 d:HIS215 2.2 0.9 1.0 NE2 a:HIS215 2.2 0.4 1.0 NE2 a:HIS272 2.3 0.8 1.0 NE2 d:HIS269 2.3 0.6 1.0 CE1 d:HIS215 2.9 0.9 1.0 CE1 a:HIS215 3.0 0.4 1.0 CD2 a:HIS272 3.0 0.8 1.0 CE1 d:HIS269 3.1 0.6 1.0 CD2 d:HIS215 3.2 0.9 1.0 CD2 a:HIS215 3.3 0.4 1.0 CD2 d:HIS269 3.4 0.6 1.0 CE1 a:HIS272 3.4 0.8 1.0 CG2 a:VAL219 3.9 0.5 1.0 ND1 d:HIS215 4.1 0.9 1.0 ND1 a:HIS215 4.2 0.4 1.0 CG d:HIS215 4.2 0.9 1.0 ND1 d:HIS269 4.3 0.6 1.0 CG a:HIS272 4.3 0.8 1.0 CG a:HIS215 4.4 0.4 1.0 ND1 a:HIS272 4.4 0.8 1.0 CG d:HIS269 4.4 0.6 1.0 CG2 d:VAL219 4.7 0.0 1.0 OH d:TYR245 4.7 0.1 1.0 CB a:VAL219 4.9 0.5 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ e:Fe101 b:0.1 occ:1.00 FE e:HEM101 0.0 0.1 1.0 ND e:HEM101 2.0 0.1 1.0 NC e:HEM101 2.0 0.1 1.0 NA e:HEM101 2.1 0.1 1.0 NB e:HEM101 2.1 0.1 1.0 NE2 e:HIS23 2.1 0.6 1.0 NE2 f:HIS18 2.1 0.1 1.0 CD2 e:HIS23 2.7 0.6 1.0 CD2 f:HIS18 2.8 0.1 1.0 C1D e:HEM101 3.0 0.1 1.0 C4C e:HEM101 3.0 0.1 1.0 C4D e:HEM101 3.0 0.1 1.0 C1C e:HEM101 3.0 0.1 1.0 C4A e:HEM101 3.1 0.1 1.0 C1A e:HEM101 3.1 0.1 1.0 C1B e:HEM101 3.1 0.1 1.0 C4B e:HEM101 3.1 0.1 1.0 CE1 f:HIS18 3.3 0.1 1.0 CE1 e:HIS23 3.3 0.6 1.0 CHD e:HEM101 3.4 0.1 1.0 CHC e:HEM101 3.4 0.1 1.0 CHA e:HEM101 3.4 0.1 1.0 CHB e:HEM101 3.4 0.1 1.0 CG e:HIS23 3.9 0.6 1.0 CG f:HIS18 4.1 0.1 1.0 C2D e:HEM101 4.2 0.1 1.0 C3D e:HEM101 4.2 0.1 1.0 ND1 e:HIS23 4.2 0.6 1.0 C2C e:HEM101 4.2 0.1 1.0 ND1 f:HIS18 4.2 0.1 1.0 C3C e:HEM101 4.2 0.1 1.0 NE1 f:TRP14 4.3 0.6 1.0 C3A e:HEM101 4.3 0.1 1.0 C2A e:HEM101 4.3 0.1 1.0 C2B e:HEM101 4.3 0.1 1.0 C3B e:HEM101 4.3 0.1 1.0

L.S.Van Bezouwen, S.Caffarri, R.S.Kale, R.Kouril, A.W.H.Thunnissen, G.T.Oostergetel, E.J.Boekema. Subunit and Chlorophyll Organization of the Plant Photosystem II Supercomplex. Nat Plants V. 3 17080 2017.
ISSN: ESSN 2055-0278
PubMed: 28604725
DOI: 10.1038/NPLANTS.2017.80