Iron in PDB 6yxr: Dunaliella Minimal Photosystem I

All present enzymatic activity of Dunaliella Minimal Photosystem I:
1.97.1.12;

The structure of Dunaliella Minimal Photosystem I also contains other interesting chemical elements:

Magnesium

(Mg)

145 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the Dunaliella Minimal Photosystem I (pdb code 6yxr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Dunaliella Minimal Photosystem I, PDB code: 6yxr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:37.3 occ:1.00 FE1 A:SF43001 0.0 37.3 1.0 S4 A:SF43001 2.3 37.3 1.0 S3 A:SF43001 2.3 37.3 1.0 S2 A:SF43001 2.3 37.3 1.0 SG A:CYS575 2.3 36.5 1.0 FE2 A:SF43001 2.7 37.3 1.0 FE3 A:SF43001 2.7 37.3 1.0 FE4 A:SF43001 2.7 37.3 1.0 CB A:CYS575 3.3 36.5 1.0 S1 A:SF43001 3.9 37.3 1.0 CD1 A:ILE720 4.3 36.5 1.0 SG B:CYS569 4.4 36.5 1.0 CB A:CYS584 4.4 36.5 1.0 CA A:CYS575 4.6 36.5 1.0 SG A:CYS584 4.7 36.5 1.0 SG B:CYS560 4.7 36.5 1.0 N A:CYS575 4.7 36.5 1.0 C A:PRO574 5.0 36.5 1.0 CB A:PRO574 5.0 36.5 1.0 CA A:CYS584 5.0 36.5 1.0

Iron binding site 2 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:37.3 occ:1.00 FE2 A:SF43001 0.0 37.3 1.0 S3 A:SF43001 2.3 37.3 1.0 S4 A:SF43001 2.3 37.3 1.0 S1 A:SF43001 2.3 37.3 1.0 SG B:CYS560 2.5 36.5 1.0 FE1 A:SF43001 2.7 37.3 1.0 FE4 A:SF43001 2.7 37.3 1.0 FE3 A:SF43001 2.7 37.3 1.0 CB B:CYS560 3.3 36.5 1.0 S2 A:SF43001 3.9 37.3 1.0 SG A:CYS575 4.4 36.5 1.0 CA B:CYS560 4.6 36.5 1.0 CD1 B:ILE703 4.6 36.5 1.0 SG A:CYS584 4.6 36.5 1.0 CG A:PRO578 4.6 36.5 1.0 N B:CYS560 4.7 36.5 1.0 SG B:CYS569 4.8 36.5 1.0 CB B:CYS569 4.8 36.5 1.0 C B:PRO559 4.9 36.5 1.0 O B:PRO559 4.9 36.5 1.0 N B:GLY562 4.9 36.5 1.0 CA B:GLY562 5.0 36.5 1.0

Iron binding site 3 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:37.3 occ:1.00 FE3 A:SF43001 0.0 37.3 1.0 S1 A:SF43001 2.3 37.3 1.0 S2 A:SF43001 2.3 37.3 1.0 S4 A:SF43001 2.3 37.3 1.0 SG B:CYS569 2.5 36.5 1.0 CB B:CYS569 2.7 36.5 1.0 FE2 A:SF43001 2.7 37.3 1.0 FE4 A:SF43001 2.7 37.3 1.0 FE1 A:SF43001 2.7 37.3 1.0 CA B:CYS569 3.6 36.5 1.0 S3 A:SF43001 3.9 37.3 1.0 N B:CYS569 4.2 36.5 1.0 CD1 A:ILE720 4.5 36.5 1.0 CB B:CYS560 4.6 36.5 1.0 SG B:CYS560 4.6 36.5 1.0 C B:CYS569 4.9 36.5 1.0 CG2 A:ILE720 5.0 36.5 1.0

Iron binding site 4 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:37.3 occ:1.00 FE4 A:SF43001 0.0 37.3 1.0 S1 A:SF43001 2.3 37.3 1.0 S2 A:SF43001 2.3 37.3 1.0 S3 A:SF43001 2.3 37.3 1.0 SG A:CYS584 2.5 36.5 1.0 FE2 A:SF43001 2.7 37.3 1.0 FE3 A:SF43001 2.7 37.3 1.0 FE1 A:SF43001 2.7 37.3 1.0 CB A:CYS584 2.8 36.5 1.0 S4 A:SF43001 3.9 37.3 1.0 CA A:CYS584 4.0 36.5 1.0 CD1 B:ILE703 4.3 36.5 1.0 SG A:CYS575 4.5 36.5 1.0 N A:CYS584 4.5 36.5 1.0 CB A:CYS575 4.6 36.5 1.0 CE3 B:TRP668 5.0 36.5 1.0

Iron binding site 5 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:37.1 occ:1.00 FE1 C:SF43002 0.0 37.1 1.0 S3 C:SF43002 2.3 37.1 1.0 S2 C:SF43002 2.3 37.1 1.0 S4 C:SF43002 2.3 37.1 1.0 CB C:CYS21 2.4 36.6 1.0 FE3 C:SF43002 2.7 37.1 1.0 FE4 C:SF43002 2.7 37.1 1.0 FE2 C:SF43002 2.7 37.1 1.0 SG C:CYS21 3.2 36.6 1.0 CA C:CYS21 3.3 36.6 1.0 S1 C:SF43002 3.9 37.1 1.0 C C:CYS21 4.2 36.6 1.0 SG C:CYS51 4.4 36.5 1.0 N C:CYS21 4.5 36.6 1.0 SG C:CYS54 4.5 36.5 1.0 CB C:CYS54 4.7 36.5 1.0 O C:CYS21 4.7 36.6 1.0 CB C:VAL25 4.8 36.5 1.0 CD C:PRO22 4.9 36.5 1.0 N C:PRO22 4.9 36.5 1.0

Iron binding site 6 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:37.1 occ:1.00 FE2 C:SF43002 0.0 37.1 1.0 S4 C:SF43002 2.3 37.1 1.0 S1 C:SF43002 2.3 37.1 1.0 S3 C:SF43002 2.3 37.1 1.0 SG C:CYS54 2.5 36.5 1.0 FE3 C:SF43002 2.7 37.1 1.0 FE1 C:SF43002 2.7 37.1 1.0 FE4 C:SF43002 2.7 37.1 1.0 CG2 C:VAL67 3.3 36.5 1.0 CB C:CYS54 3.6 36.5 1.0 S2 C:SF43002 3.9 37.1 1.0 N C:CYS54 4.3 36.5 1.0 N C:LYS52 4.4 36.5 1.0 CA C:LYS52 4.4 36.5 1.0 SG C:CYS21 4.5 36.6 1.0 SG C:CYS48 4.5 36.5 1.0 CB C:VAL67 4.6 36.5 1.0 CA C:CYS54 4.6 36.5 1.0 CB C:CYS21 4.6 36.6 1.0 SG C:CYS51 4.7 36.5 1.0 N C:ARG53 4.7 36.5 1.0 CG1 C:VAL67 4.7 36.5 1.0 C C:LYS52 4.9 36.5 1.0 CG2 C:VAL5 5.0 36.5 1.0

Iron binding site 7 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:37.1 occ:1.00 FE3 C:SF43002 0.0 37.1 1.0 S1 C:SF43002 2.3 37.1 1.0 S4 C:SF43002 2.3 37.1 1.0 S2 C:SF43002 2.3 37.1 1.0 SG C:CYS51 2.5 36.5 1.0 FE1 C:SF43002 2.7 37.1 1.0 FE2 C:SF43002 2.7 37.1 1.0 FE4 C:SF43002 2.7 37.1 1.0 N C:CYS51 3.2 36.5 1.0 N C:LYS52 3.3 36.5 1.0 CB C:CYS51 3.4 36.5 1.0 CA C:CYS51 3.7 36.5 1.0 S3 C:SF43002 3.9 37.1 1.0 C C:CYS51 4.0 36.5 1.0 C C:GLY50 4.2 36.5 1.0 N C:ARG53 4.2 36.5 1.0 CA C:LYS52 4.3 36.5 1.0 N C:GLY50 4.3 36.5 1.0 CG1 C:VAL49 4.4 36.5 1.0 CA C:GLY50 4.5 36.5 1.0 SG C:CYS48 4.6 36.5 1.0 C C:LYS52 4.7 36.5 1.0 SG C:CYS54 4.7 36.5 1.0 CB C:CYS21 4.8 36.6 1.0 N C:VAL49 5.0 36.5 1.0

Iron binding site 8 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:37.1 occ:1.00 FE4 C:SF43002 0.0 37.1 1.0 S2 C:SF43002 2.3 37.1 1.0 S3 C:SF43002 2.3 37.1 1.0 S1 C:SF43002 2.3 37.1 1.0 SG C:CYS48 2.5 36.5 1.0 FE3 C:SF43002 2.7 37.1 1.0 FE1 C:SF43002 2.7 37.1 1.0 FE2 C:SF43002 2.7 37.1 1.0 CB C:CYS48 3.6 36.5 1.0 CA C:CYS48 3.8 36.5 1.0 S4 C:SF43002 3.9 37.1 1.0 N C:VAL49 4.2 36.5 1.0 N C:GLY50 4.3 36.5 1.0 CB C:VAL25 4.4 36.5 1.0 C C:CYS48 4.4 36.5 1.0 CG2 C:VAL25 4.4 36.5 1.0 CG1 C:VAL25 4.6 36.5 1.0 CG2 C:VAL5 4.7 36.5 1.0 CA C:GLY50 4.9 36.5 1.0 CG2 C:VAL67 4.9 36.5 1.0 N C:CYS51 5.0 36.5 1.0

Iron binding site 9 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3003 b:39.9 occ:1.00 FE1 C:SF43003 0.0 39.9 1.0 SG C:CYS14 2.1 38.0 1.0 S4 C:SF43003 2.3 39.9 1.0 S2 C:SF43003 2.3 39.9 1.0 S3 C:SF43003 2.3 39.9 1.0 FE3 C:SF43003 2.7 39.9 1.0 FE4 C:SF43003 2.7 39.9 1.0 FE2 C:SF43003 2.7 39.9 1.0 CB C:CYS14 3.1 38.0 1.0 N C:CYS14 3.4 38.0 1.0 CA C:CYS14 3.7 38.0 1.0 S1 C:SF43003 3.9 39.9 1.0 N C:THR15 4.1 37.2 1.0 CD C:PRO59 4.1 36.5 1.0 C C:CYS14 4.3 38.0 1.0 SG C:CYS17 4.4 36.8 1.0 N C:GLY13 4.5 38.2 1.0 C C:GLY13 4.6 38.2 1.0 CG1 C:ILE12 4.6 37.8 1.0 N C:GLN16 4.7 36.6 1.0 SG C:CYS11 4.7 37.9 1.0 N C:ILE12 4.8 37.8 1.0 CG C:PRO59 4.9 36.5 1.0 CA C:GLY13 4.9 38.2 1.0

Iron binding site 10 out of 12 in the Dunaliella Minimal Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Dunaliella Minimal Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3003 b:39.9 occ:1.00 FE2 C:SF43003 0.0 39.9 1.0 SG C:CYS11 2.2 37.9 1.0 S1 C:SF43003 2.3 39.9 1.0 S3 C:SF43003 2.3 39.9 1.0 S4 C:SF43003 2.3 39.9 1.0 FE4 C:SF43003 2.7 39.9 1.0 FE3 C:SF43003 2.7 39.9 1.0 FE1 C:SF43003 2.7 39.9 1.0 CB C:CYS11 2.9 37.9 1.0 CA C:CYS11 3.0 37.9 1.0 N C:ILE12 3.1 37.8 1.0 C C:CYS11 3.5 37.9 1.0 N C:GLY13 3.6 38.2 1.0 S2 C:SF43003 3.9 39.9 1.0 OG C:SER64 3.9 36.7 1.0 CA C:ILE12 4.2 37.8 1.0 C C:ILE12 4.4 37.8 1.0 N C:CYS11 4.4 37.9 1.0 N C:CYS14 4.4 38.0 1.0 CA C:GLY13 4.5 38.2 1.0 CG1 C:ILE12 4.5 37.8 1.0 O C:CYS11 4.7 37.9 1.0 SG C:CYS14 4.8 38.0 1.0 CB C:SER64 5.0 36.7 1.0

I.Caspy, T.Malavath, D.Klaiman, M.Fadeeva, Y.Shkolnisky, N.Nelson. Structure and Energy Transfer Pathways of the Dunaliella Salina Photosystem I Supercomplex. Biochim Biophys Acta V.1861 48253 2020BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 32569661
DOI: 10.1016/J.BBABIO.2020.148253