Iron in PDB 7y7b: Cryo-Em Structure of Cryptophyte Photosystem I

All present enzymatic activity of Cryo-Em Structure of Cryptophyte Photosystem I:
1.97.1.12;

The structure of Cryo-Em Structure of Cryptophyte Photosystem I also contains other interesting chemical elements:

Magnesium

(Mg)

274 atoms

Pages:

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

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Cryptophyte Photosystem I (pdb code 7y7b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Cryo-Em Structure of Cryptophyte Photosystem I, PDB code: 7y7b:
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 Cryo-Em Structure of Cryptophyte Photosystem I


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 Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:48.2 occ:1.00 FE1 B:SF4801 0.0 48.2 1.0 S3 B:SF4801 2.1 37.6 1.0 S4 B:SF4801 2.1 27.6 1.0 S2 B:SF4801 2.1 36.3 1.0 SG B:CYS568 2.3 23.1 1.0 FE3 B:SF4801 2.9 38.4 1.0 FE4 B:SF4801 2.9 43.8 1.0 FE2 B:SF4801 3.0 35.9 1.0 CB B:CYS568 3.2 18.7 1.0 S1 B:SF4801 3.6 25.2 1.0 CZ3 B:TRP667 3.7 16.1 1.0 CA B:CYS568 3.7 9.7 1.0 N B:CYS568 4.2 12.0 1.0 CD1 A:ILE721 4.3 11.1 1.0 CE3 B:TRP667 4.4 24.6 1.0 CH2 B:TRP667 4.5 20.3 1.0 CG2 A:ILE721 4.8 25.6 1.0 NH2 A:ARG725 4.9 20.0 1.0 CB B:CYS559 5.0 16.1 1.0 SG B:CYS559 5.0 42.3 1.0

Iron binding site 2 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:35.9 occ:1.00 FE2 B:SF4801 0.0 35.9 1.0 S3 B:SF4801 2.1 37.6 1.0 S1 B:SF4801 2.1 25.2 1.0 S4 B:SF4801 2.1 27.6 1.0 SG A:CYS584 2.4 31.6 1.0 FE3 B:SF4801 2.9 38.4 1.0 FE4 B:SF4801 3.0 43.8 1.0 FE1 B:SF4801 3.0 48.2 1.0 CB A:CYS584 3.1 17.3 1.0 S2 B:SF4801 3.7 36.3 1.0 CA A:CYS584 3.7 13.5 1.0 CE3 B:TRP667 3.9 24.6 1.0 N A:CYS584 4.1 13.0 1.0 CD1 B:ILE702 4.2 20.4 1.0 CZ3 B:TRP667 4.2 16.1 1.0 CG1 B:ILE702 4.7 20.6 1.0 CB A:CYS575 4.7 18.1 1.0 CG2 B:ILE702 4.8 27.3 1.0 CD2 B:TRP667 5.0 19.3 1.0 NH2 A:ARG725 5.0 20.0 1.0

Iron binding site 3 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:38.4 occ:1.00 FE3 B:SF4801 0.0 38.4 1.0 S4 B:SF4801 2.1 27.6 1.0 S2 B:SF4801 2.1 36.3 1.0 S1 B:SF4801 2.1 25.2 1.0 SG A:CYS575 2.6 37.5 1.0 CB A:CYS575 2.8 18.1 1.0 FE1 B:SF4801 2.9 48.2 1.0 FE2 B:SF4801 2.9 35.9 1.0 FE4 B:SF4801 3.0 43.8 1.0 S3 B:SF4801 3.7 37.6 1.0 CA A:CYS575 4.3 15.9 1.0 CD1 A:ILE721 4.3 11.1 1.0 SG B:CYS568 4.5 23.1 1.0 N A:CYS575 4.7 20.4 1.0 O A:PRO574 4.7 26.0 1.0 C A:PRO574 4.8 22.3 1.0 CA A:CYS584 4.8 13.5 1.0 NH2 A:ARG725 4.9 20.0 1.0 N A:GLY577 5.0 20.1 1.0 SG A:CYS584 5.0 31.6 1.0

Iron binding site 4 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe801 b:43.8 occ:1.00 FE4 B:SF4801 0.0 43.8 1.0 S1 B:SF4801 2.1 25.2 1.0 S3 B:SF4801 2.1 37.6 1.0 S2 B:SF4801 2.1 36.3 1.0 SG B:CYS559 2.4 42.3 1.0 FE1 B:SF4801 2.9 48.2 1.0 FE2 B:SF4801 3.0 35.9 1.0 FE3 B:SF4801 3.0 38.4 1.0 CB B:CYS559 3.3 16.1 1.0 S4 B:SF4801 3.8 27.6 1.0 CD1 B:ILE702 4.4 20.4 1.0 N A:PRO578 4.7 18.4 1.0 CB A:PRO578 4.7 18.8 1.0 N B:GLY561 4.7 23.6 1.0 CA B:CYS559 4.7 19.1 1.0 CA A:PRO578 4.8 14.2 1.0 CA B:GLY561 4.8 25.1 1.0 CD A:PRO578 4.9 25.6 1.0 SG B:CYS568 4.9 23.1 1.0 C A:GLY577 4.9 23.6 1.0 SG A:CYS575 5.0 37.5 1.0

Iron binding site 5 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:42.6 occ:1.00 FE1 C:SF4101 0.0 42.6 1.0 S3 C:SF4101 2.1 43.2 1.0 S2 C:SF4101 2.1 37.7 1.0 S4 C:SF4101 2.1 42.6 1.0 SG C:CYS51 2.5 33.8 1.0 FE2 C:SF4101 3.0 57.3 1.0 FE4 C:SF4101 3.0 45.3 1.0 FE3 C:SF4101 3.0 49.4 1.0 S1 C:SF4101 3.7 46.3 1.0 N C:CYS51 3.7 27.9 1.0 CB C:CYS51 3.8 30.7 1.0 N C:LYS52 3.9 31.2 1.0 CD C:PRO22 3.9 35.4 1.0 CG1 C:ILE49 4.0 29.5 1.0 CA C:CYS51 4.2 25.5 1.0 N C:GLY50 4.3 19.8 1.0 CG C:PRO22 4.4 37.2 1.0 N C:ARG53 4.4 25.2 1.0 C C:CYS51 4.5 29.6 1.0 CD1 C:ILE49 4.5 31.8 1.0 C C:GLY50 4.6 29.5 1.0 SG C:CYS21 4.7 41.6 1.0 N C:ILE49 4.8 32.1 1.0 CA C:LYS52 4.8 23.6 1.0 CA C:GLY50 4.8 22.1 1.0 CB C:ARG53 4.9 23.5 1.0

Iron binding site 6 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:57.3 occ:1.00 FE2 C:SF4101 0.0 57.3 1.0 S1 C:SF4101 2.1 46.3 1.0 S3 C:SF4101 2.1 43.2 1.0 S4 C:SF4101 2.1 42.6 1.0 SG C:CYS21 2.4 41.6 1.0 FE1 C:SF4101 3.0 42.6 1.0 FE3 C:SF4101 3.0 49.4 1.0 FE4 C:SF4101 3.0 45.3 1.0 CB C:CYS21 3.1 33.2 1.0 S2 C:SF4101 3.7 37.7 1.0 CA C:CYS21 3.8 35.3 1.0 CB C:VAL25 4.0 42.1 1.0 CG2 C:VAL25 4.3 41.5 1.0 CD C:PRO22 4.4 35.4 1.0 C C:CYS21 4.5 34.0 1.0 CD1 C:LEU26 4.6 43.6 1.0 CG C:LEU26 4.7 44.3 1.0 N C:PRO22 4.8 30.8 1.0 CG1 C:VAL25 4.8 44.8 1.0 CB C:CYS54 4.9 36.5 1.0 N C:VAL25 4.9 41.2 1.0 N C:CYS21 4.9 31.9 1.0 N C:CYS23 5.0 41.2 1.0

Iron binding site 7 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:49.4 occ:1.00 FE3 C:SF4101 0.0 49.4 1.0 S4 C:SF4101 2.1 42.6 1.0 S1 C:SF4101 2.1 46.3 1.0 S2 C:SF4101 2.1 37.7 1.0 SG C:CYS54 2.7 42.0 1.0 FE2 C:SF4101 3.0 57.3 1.0 FE1 C:SF4101 3.0 42.6 1.0 FE4 C:SF4101 3.0 45.3 1.0 CB C:CYS54 3.1 36.5 1.0 N C:CYS54 3.6 34.3 1.0 S3 C:SF4101 3.7 43.2 1.0 CG2 C:VAL67 3.9 34.3 1.0 CA C:CYS54 4.0 32.0 1.0 CA C:LYS52 4.3 23.6 1.0 N C:LYS52 4.4 31.2 1.0 N C:ARG53 4.4 25.2 1.0 C C:LYS52 4.6 23.3 1.0 CD1 C:LEU26 4.6 43.6 1.0 SG C:CYS51 4.8 33.8 1.0 C C:ARG53 4.8 31.8 1.0 N C:GLU55 4.8 34.0 1.0 C C:CYS54 4.9 32.0 1.0

Iron binding site 8 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:45.3 occ:1.00 FE4 C:SF4101 0.0 45.3 1.0 S2 C:SF4101 2.1 37.7 1.0 S3 C:SF4101 2.1 43.2 1.0 S1 C:SF4101 2.1 46.3 1.0 SG C:CYS48 2.7 32.5 1.0 FE1 C:SF4101 3.0 42.6 1.0 FE2 C:SF4101 3.0 57.3 1.0 FE3 C:SF4101 3.0 49.4 1.0 CB C:CYS48 3.2 32.4 1.0 CA C:CYS48 3.7 34.5 1.0 S4 C:SF4101 3.7 42.6 1.0 N C:ILE49 4.1 32.1 1.0 N C:GLY50 4.2 19.8 1.0 CG2 C:VAL5 4.2 38.7 1.0 C C:CYS48 4.3 34.1 1.0 CG2 C:VAL25 4.5 41.5 1.0 CB C:VAL25 4.6 42.1 1.0 CG1 C:VAL25 4.6 44.8 1.0 CG1 C:VAL67 4.7 35.6 1.0 CA C:GLY50 4.7 22.1 1.0 CG2 C:VAL67 4.8 34.3 1.0 N C:CYS48 4.9 35.2 1.0

Iron binding site 9 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe102 b:65.4 occ:1.00 FE1 C:SF4102 0.0 65.4 1.0 S3 C:SF4102 2.1 53.9 1.0 S4 C:SF4102 2.1 58.5 1.0 S2 C:SF4102 2.1 65.0 1.0 FE3 C:SF4102 3.0 50.2 1.0 SG C:CYS58 3.0 45.2 1.0 FE2 C:SF4102 3.0 52.5 1.0 FE4 C:SF4102 3.0 72.1 1.0 CB C:SER64 3.7 41.9 1.0 S1 C:SF4102 3.7 48.4 1.0 CB C:CYS58 3.7 41.0 1.0 CD C:PRO59 4.1 39.5 1.0 CA C:CYS58 4.1 39.5 1.0 OG C:SER64 4.3 50.0 1.0 CG1 C:VAL65 4.3 32.0 1.0 N C:SER64 4.4 44.2 1.0 N C:VAL65 4.5 36.6 1.0 CA C:SER64 4.5 38.1 1.0 CB C:CYS17 4.6 38.8 1.0 SG C:CYS11 4.7 65.4 1.0 C C:SER64 4.7 41.3 1.0 O C:ALA57 4.7 55.4 1.0 CB C:VAL65 4.8 31.1 1.0 CG2 C:THR60 4.8 40.4 1.0 N C:PRO59 4.9 37.4 1.0 C C:CYS58 4.9 43.6 1.0 SG C:CYS14 5.0 56.5 1.0

Iron binding site 10 out of 12 in the Cryo-Em Structure of Cryptophyte Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Cryptophyte Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe102 b:52.5 occ:1.00 FE2 C:SF4102 0.0 52.5 1.0 S1 C:SF4102 2.1 48.4 1.0 S4 C:SF4102 2.1 58.5 1.0 S3 C:SF4102 2.1 53.9 1.0 SG C:CYS17 2.5 49.5 1.0 CB C:CYS17 2.7 38.8 1.0 FE4 C:SF4102 3.0 72.1 1.0 FE1 C:SF4102 3.0 65.4 1.0 FE3 C:SF4102 3.0 50.2 1.0 N C:CYS17 3.6 43.8 1.0 S2 C:SF4102 3.7 65.0 1.0 CA C:CYS17 3.8 38.6 1.0 CB C:ALA40 4.1 52.2 1.0 SG C:CYS14 4.5 56.5 1.0 N C:THR15 4.5 48.0 1.0 N C:VAL18 4.6 48.2 1.0 N C:GLN16 4.6 47.2 1.0 C C:CYS17 4.7 45.2 1.0 CA C:THR15 4.7 46.2 1.0 C C:THR15 4.7 47.8 1.0 O C:ALA57 4.8 55.4 1.0 C C:GLN16 4.8 47.9 1.0 SG C:CYS11 5.0 65.4 1.0

L.S.Zhao, P.Wang, K.Li, Q.B.Zhang, F.Y.He, C.Y.Li, H.N.Su, X.L.Chen, L.N.Liu, Y.Z.Zhang. Structural Basis and Evolution of the Photosystem I-Light-Harvesting Supercomplex of Cryptophyte Algae Plant Cell 2023.
ISSN: ESSN 1532-298X
DOI: 10.1093/PLCELL/KOAD087