Iron in PDB 7y8a: 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)

236 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 7y8a). 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: 7y8a:
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 A:Fe849 b:76.7 occ:1.00 FE1 A:SF4849 0.0 76.7 1.0 S3 A:SF4849 2.1 64.3 1.0 S4 A:SF4849 2.1 59.7 1.0 S2 A:SF4849 2.1 71.2 1.0 SG B:CYS568 2.3 56.5 1.0 FE3 A:SF4849 2.9 61.0 1.0 FE4 A:SF4849 3.0 72.9 1.0 FE2 A:SF4849 3.0 65.0 1.0 CB B:CYS568 3.2 41.6 1.0 CA B:CYS568 3.7 37.7 1.0 S1 A:SF4849 3.7 52.8 1.0 CZ3 B:TRP667 3.7 43.3 1.0 N B:CYS568 4.1 38.5 1.0 CD1 A:ILE721 4.3 39.6 1.0 CE3 B:TRP667 4.5 48.3 1.0 CH2 B:TRP667 4.6 38.3 1.0 CG2 A:ILE721 4.8 40.5 1.0 C B:THR567 4.9 44.6 1.0 CB B:CYS559 5.0 31.3 1.0 NH2 A:ARG725 5.0 41.7 1.0 CG1 A:ILE721 5.0 38.0 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 A:Fe849 b:65.0 occ:1.00 FE2 A:SF4849 0.0 65.0 1.0 S3 A:SF4849 2.1 64.3 1.0 S1 A:SF4849 2.1 52.8 1.0 S4 A:SF4849 2.1 59.7 1.0 SG A:CYS584 2.4 54.7 1.0 FE3 A:SF4849 2.9 61.0 1.0 FE4 A:SF4849 3.0 72.9 1.0 FE1 A:SF4849 3.0 76.7 1.0 CB A:CYS584 3.2 40.6 1.0 S2 A:SF4849 3.7 71.2 1.0 CA A:CYS584 3.8 35.3 1.0 CE3 B:TRP667 3.9 48.3 1.0 CZ3 B:TRP667 4.1 43.3 1.0 CD1 B:ILE702 4.2 35.5 1.0 N A:CYS584 4.2 37.3 1.0 CB A:CYS575 4.7 34.9 1.0 CG1 B:ILE702 4.7 34.0 1.0 CG2 B:ILE702 4.8 50.3 1.0 CD2 B:TRP667 5.0 38.6 1.0 NH2 A:ARG725 5.0 41.7 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 A:Fe849 b:61.0 occ:1.00 FE3 A:SF4849 0.0 61.0 1.0 S4 A:SF4849 2.1 59.7 1.0 S2 A:SF4849 2.1 71.2 1.0 S1 A:SF4849 2.1 52.8 1.0 SG A:CYS575 2.6 57.1 1.0 CB A:CYS575 2.8 34.9 1.0 FE1 A:SF4849 2.9 76.7 1.0 FE2 A:SF4849 2.9 65.0 1.0 FE4 A:SF4849 3.0 72.9 1.0 S3 A:SF4849 3.6 64.3 1.0 CD1 A:ILE721 4.3 39.6 1.0 CA A:CYS575 4.3 32.7 1.0 SG B:CYS568 4.6 56.5 1.0 N A:CYS575 4.7 40.5 1.0 O A:PRO574 4.8 52.8 1.0 C A:PRO574 4.8 41.0 1.0 CA A:CYS584 4.9 35.3 1.0 NH2 A:ARG725 4.9 41.7 1.0 SG A:CYS584 4.9 54.7 1.0 N A:GLY577 5.0 39.4 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 A:Fe849 b:72.9 occ:1.00 FE4 A:SF4849 0.0 72.9 1.0 S1 A:SF4849 2.1 52.8 1.0 S3 A:SF4849 2.1 64.3 1.0 S2 A:SF4849 2.1 71.2 1.0 SG B:CYS559 2.5 59.5 1.0 FE1 A:SF4849 3.0 76.7 1.0 FE2 A:SF4849 3.0 65.0 1.0 FE3 A:SF4849 3.0 61.0 1.0 CB B:CYS559 3.3 31.3 1.0 S4 A:SF4849 3.8 59.7 1.0 CD1 B:ILE702 4.5 35.5 1.0 N A:PRO578 4.7 29.8 1.0 CB A:PRO578 4.7 36.9 1.0 CA B:CYS559 4.7 45.3 1.0 N B:GLY561 4.7 50.6 1.0 CA B:GLY561 4.8 45.0 1.0 CD A:PRO578 4.8 38.2 1.0 CA A:PRO578 4.8 27.9 1.0 SG B:CYS568 5.0 56.5 1.0 C A:GLY577 5.0 40.0 1.0 SG A:CYS575 5.0 57.1 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:54.3 occ:1.00 FE1 C:SF4101 0.0 54.3 1.0 S3 C:SF4101 2.1 53.9 1.0 S4 C:SF4101 2.1 58.8 1.0 S2 C:SF4101 2.1 60.6 1.0 SG C:CYS51 2.5 47.0 1.0 FE2 C:SF4101 3.0 71.4 1.0 FE4 C:SF4101 3.0 65.8 1.0 FE3 C:SF4101 3.0 64.5 1.0 S1 C:SF4101 3.7 71.0 1.0 N C:CYS51 3.7 35.2 1.0 CB C:CYS51 3.8 49.4 1.0 CD C:PRO22 3.9 50.6 1.0 N C:LYS52 3.9 50.3 1.0 CG1 C:ILE49 4.0 55.5 1.0 CA C:CYS51 4.2 37.3 1.0 CG C:PRO22 4.3 55.0 1.0 N C:GLY50 4.3 43.1 1.0 N C:ARG53 4.3 41.4 1.0 C C:CYS51 4.4 44.2 1.0 C C:GLY50 4.5 42.7 1.0 CD1 C:ILE49 4.6 56.0 1.0 N C:ILE49 4.8 54.3 1.0 CA C:LYS52 4.8 42.5 1.0 SG C:CYS21 4.8 57.7 1.0 CA C:GLY50 4.8 38.0 1.0 CB C:ARG53 4.9 39.6 1.0 N C:CYS54 5.0 50.7 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:71.4 occ:1.00 FE2 C:SF4101 0.0 71.4 1.0 S1 C:SF4101 2.1 71.0 1.0 S3 C:SF4101 2.1 53.9 1.0 S4 C:SF4101 2.1 58.8 1.0 SG C:CYS21 2.4 57.7 1.0 FE1 C:SF4101 3.0 54.3 1.0 FE3 C:SF4101 3.0 64.5 1.0 FE4 C:SF4101 3.0 65.8 1.0 CB C:CYS21 3.1 49.3 1.0 S2 C:SF4101 3.7 60.6 1.0 CA C:CYS21 3.7 51.7 1.0 CB C:VAL25 4.0 52.6 1.0 CG2 C:VAL25 4.3 53.7 1.0 CD C:PRO22 4.3 50.6 1.0 C C:CYS21 4.5 50.8 1.0 CD1 C:LEU26 4.5 54.2 1.0 CG C:LEU26 4.7 51.3 1.0 N C:PRO22 4.7 42.4 1.0 CG1 C:VAL25 4.8 57.4 1.0 CB C:CYS54 4.8 50.7 1.0 N C:VAL25 4.9 56.9 1.0 N C:CYS21 4.9 50.3 1.0 N C:CYS23 5.0 57.8 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:64.5 occ:1.00 FE3 C:SF4101 0.0 64.5 1.0 S4 C:SF4101 2.1 58.8 1.0 S1 C:SF4101 2.1 71.0 1.0 S2 C:SF4101 2.1 60.6 1.0 SG C:CYS54 2.7 63.7 1.0 FE2 C:SF4101 3.0 71.4 1.0 CB C:CYS54 3.0 50.7 1.0 FE1 C:SF4101 3.0 54.3 1.0 FE4 C:SF4101 3.0 65.8 1.0 N C:CYS54 3.6 50.7 1.0 S3 C:SF4101 3.7 53.9 1.0 CG2 C:VAL67 3.9 49.3 1.0 CA C:CYS54 3.9 51.8 1.0 CA C:LYS52 4.3 42.5 1.0 N C:ARG53 4.4 41.4 1.0 N C:LYS52 4.4 50.3 1.0 CD1 C:LEU26 4.6 54.2 1.0 C C:LYS52 4.6 43.0 1.0 C C:ARG53 4.8 50.3 1.0 N C:GLU55 4.8 53.9 1.0 SG C:CYS51 4.8 47.0 1.0 C C:CYS54 4.9 50.3 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:65.8 occ:1.00 FE4 C:SF4101 0.0 65.8 1.0 S2 C:SF4101 2.1 60.6 1.0 S3 C:SF4101 2.1 53.9 1.0 S1 C:SF4101 2.1 71.0 1.0 SG C:CYS48 2.7 64.1 1.0 FE1 C:SF4101 3.0 54.3 1.0 FE2 C:SF4101 3.0 71.4 1.0 FE3 C:SF4101 3.0 64.5 1.0 CB C:CYS48 3.2 47.6 1.0 CA C:CYS48 3.7 48.4 1.0 S4 C:SF4101 3.7 58.8 1.0 N C:ILE49 4.0 54.3 1.0 N C:GLY50 4.1 43.1 1.0 CG2 C:VAL5 4.2 56.8 1.0 C C:CYS48 4.3 52.5 1.0 CG2 C:VAL25 4.5 53.7 1.0 CB C:VAL25 4.6 52.6 1.0 CG1 C:VAL25 4.6 57.4 1.0 CA C:GLY50 4.7 38.0 1.0 CG1 C:VAL67 4.7 51.7 1.0 CG2 C:VAL67 4.8 49.3 1.0 N C:CYS48 4.9 54.5 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:91.0 occ:1.00 FE1 C:SF4102 0.0 91.0 1.0 S3 C:SF4102 2.1 79.8 1.0 S4 C:SF4102 2.1 83.0 1.0 S2 C:SF4102 2.1 87.2 1.0 SG C:CYS58 3.0 73.6 1.0 FE3 C:SF4102 3.0 82.4 1.0 FE2 C:SF4102 3.0 79.1 1.0 FE4 C:SF4102 3.0 80.9 1.0 S1 C:SF4102 3.7 67.2 1.0 CB C:SER64 3.7 51.3 1.0 CB C:CYS58 3.8 60.5 1.0 CD C:PRO59 4.2 55.9 1.0 CA C:CYS58 4.2 58.4 1.0 CG1 C:VAL65 4.3 48.0 1.0 OG C:SER64 4.4 58.6 1.0 N C:SER64 4.4 51.9 1.0 N C:VAL65 4.5 46.9 1.0 CA C:SER64 4.5 46.8 1.0 CB C:CYS17 4.7 54.5 1.0 C C:SER64 4.7 50.5 1.0 O C:ALA57 4.8 74.3 1.0 CB C:VAL65 4.8 46.0 1.0 CG2 C:THR60 4.8 59.9 1.0 N C:PRO59 4.9 55.2 1.0 C C:CYS58 4.9 67.0 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:79.1 occ:1.00 FE2 C:SF4102 0.0 79.1 1.0 S1 C:SF4102 2.1 67.2 1.0 S4 C:SF4102 2.1 83.0 1.0 S3 C:SF4102 2.1 79.8 1.0 SG C:CYS17 2.5 68.2 1.0 CB C:CYS17 2.7 54.5 1.0 FE4 C:SF4102 3.0 80.9 1.0 FE1 C:SF4102 3.0 91.0 1.0 FE3 C:SF4102 3.0 82.4 1.0 N C:CYS17 3.6 56.2 1.0 S2 C:SF4102 3.7 87.2 1.0 CA C:CYS17 3.8 53.0 1.0 CB C:ALA40 4.1 64.8 1.0 N C:THR15 4.6 61.6 1.0 SG C:CYS14 4.7 74.2 1.0 N C:VAL18 4.7 61.6 1.0 C C:CYS17 4.7 56.9 1.0 N C:GLN16 4.7 56.1 1.0 CA C:THR15 4.8 57.5 1.0 C C:THR15 4.8 59.0 1.0 O C:ALA57 4.9 74.3 1.0 C C:GLN16 4.9 55.5 1.0 CG1 C:VAL65 4.9 48.0 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