Iron in PDB 8jjr: Cryo-Em Structure of Symbiodinium Photosystem I

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

Magnesium

(Mg)

216 atoms

Pages:

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

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Symbiodinium Photosystem I (pdb code 8jjr). 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 Symbiodinium Photosystem I, PDB code: 8jjr:
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 Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe838 b:16.8 occ:1.00 FE1 a:SF4838 0.0 16.8 1.0 S4 a:SF4838 2.3 16.8 1.0 S2 a:SF4838 2.3 16.8 1.0 S3 a:SF4838 2.3 16.8 1.0 FE2 a:SF4838 2.7 16.8 1.0 FE3 a:SF4838 2.7 16.8 1.0 FE4 a:SF4838 2.7 16.8 1.0 SG b:CYS510 2.8 14.2 1.0 CB b:CYS510 3.6 14.2 1.0 CA b:CYS510 3.8 14.2 1.0 N b:CYS510 3.8 14.2 1.0 S1 a:SF4838 3.9 16.8 1.0 SG b:CYS501 3.9 14.8 1.0 CD1 a:ILE655 4.0 13.7 1.0 CZ3 b:TRP604 4.3 12.5 1.0 C b:THR509 4.4 15.2 1.0 CG1 a:ILE655 4.7 13.7 1.0 CB b:CYS501 4.7 14.8 1.0 N b:THR509 4.7 15.2 1.0 O b:THR509 4.7 15.2 1.0 SG a:CYS492 4.7 13.7 1.0 CG2 a:ILE655 4.8 13.7 1.0 CE3 b:TRP604 4.9 12.5 1.0

Iron binding site 2 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe838 b:16.8 occ:1.00 FE2 a:SF4838 0.0 16.8 1.0 S3 a:SF4838 2.3 16.8 1.0 S4 a:SF4838 2.3 16.8 1.0 S1 a:SF4838 2.3 16.8 1.0 FE1 a:SF4838 2.7 16.8 1.0 FE4 a:SF4838 2.7 16.8 1.0 FE3 a:SF4838 2.7 16.8 1.0 SG a:CYS501 2.8 12.1 1.0 SG a:CYS492 3.6 13.7 1.0 CB a:CYS501 3.7 12.1 1.0 CE3 b:TRP604 3.8 12.5 1.0 S2 a:SF4838 3.9 16.8 1.0 CZ3 b:TRP604 3.9 12.5 1.0 CA a:CYS501 4.3 12.1 1.0 CD1 b:ILE641 4.6 13.1 1.0 NH2 a:ARG659 4.7 13.7 1.0 CB a:CYS492 4.7 13.7 1.0 N a:CYS501 4.9 12.1 1.0 SG b:CYS510 4.9 14.2 1.0 CD2 b:TRP604 4.9 12.5 1.0

Iron binding site 3 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe838 b:16.8 occ:1.00 FE3 a:SF4838 0.0 16.8 1.0 S2 a:SF4838 2.3 16.8 1.0 S4 a:SF4838 2.3 16.8 1.0 S1 a:SF4838 2.3 16.8 1.0 SG a:CYS492 2.7 13.7 1.0 FE1 a:SF4838 2.7 16.8 1.0 FE4 a:SF4838 2.7 16.8 1.0 FE2 a:SF4838 2.7 16.8 1.0 CB a:CYS492 3.0 13.7 1.0 S3 a:SF4838 3.9 16.8 1.0 CA a:CYS492 4.4 13.7 1.0 CD1 a:ILE655 4.6 13.7 1.0 N a:CYS492 4.7 13.7 1.0 CB b:PRO504 4.7 13.6 1.0 N b:PRO504 4.8 13.6 1.0 C a:PRO491 4.8 13.6 1.0 CD b:PRO504 4.9 13.6 1.0 O a:PRO491 4.9 13.6 1.0 CB a:PRO491 4.9 13.6 1.0 SG a:CYS501 4.9 12.1 1.0 CA b:PRO504 4.9 13.6 1.0

Iron binding site 4 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe838 b:16.8 occ:1.00 FE4 a:SF4838 0.0 16.8 1.0 S1 a:SF4838 2.3 16.8 1.0 S2 a:SF4838 2.3 16.8 1.0 S3 a:SF4838 2.3 16.8 1.0 FE2 a:SF4838 2.7 16.8 1.0 FE3 a:SF4838 2.7 16.8 1.0 FE1 a:SF4838 2.7 16.8 1.0 CB b:CYS501 3.0 14.8 1.0 SG b:CYS501 3.1 14.8 1.0 S4 a:SF4838 3.9 16.8 1.0 CA b:CYS501 4.6 14.8 1.0 N b:GLY503 4.6 13.1 1.0 CD1 b:ILE641 4.7 13.1 1.0 N a:PRO495 4.7 14.3 1.0 CA b:GLY503 4.8 13.1 1.0 C b:GLY503 4.8 13.1 1.0 CD a:PRO495 4.8 14.3 1.0 SG a:CYS501 4.9 12.1 1.0 CB a:PRO495 4.9 14.3 1.0 CA a:PRO495 4.9 14.3 1.0 C a:GLY494 5.0 13.3 1.0 O b:THR509 5.0 15.2 1.0

Iron binding site 5 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe201 b:15.9 occ:1.00 FE1 c:SF4201 0.0 15.9 1.0 S2 c:SF4201 2.3 15.9 1.0 S3 c:SF4201 2.3 15.9 1.0 S4 c:SF4201 2.3 15.9 1.0 SG c:CYS125 2.6 14.0 1.0 FE4 c:SF4201 2.7 15.9 1.0 FE2 c:SF4201 2.7 15.9 1.0 FE3 c:SF4201 2.7 15.9 1.0 N c:CYS125 3.6 14.0 1.0 CD c:PRO96 3.6 15.0 1.0 CB c:CYS125 3.7 14.0 1.0 N c:LYS126 3.8 15.1 1.0 S1 c:SF4201 3.9 15.9 1.0 CG c:PRO96 4.0 15.0 1.0 CA c:CYS125 4.1 14.0 1.0 N c:ARG127 4.2 15.2 1.0 C c:CYS125 4.2 14.0 1.0 CG2 c:VAL123 4.3 14.7 1.0 N c:GLY124 4.4 14.2 1.0 C c:GLY124 4.6 14.2 1.0 CA c:LYS126 4.7 15.1 1.0 CB c:ARG127 4.8 15.2 1.0 CA c:GLY124 4.8 14.2 1.0 N c:CYS128 4.9 15.3 1.0 C c:LYS126 4.9 15.1 1.0 N c:VAL123 5.0 14.7 1.0

Iron binding site 6 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe201 b:15.9 occ:1.00 FE2 c:SF4201 0.0 15.9 1.0 S1 c:SF4201 2.3 15.9 1.0 S4 c:SF4201 2.3 15.9 1.0 S3 c:SF4201 2.3 15.9 1.0 FE4 c:SF4201 2.7 15.9 1.0 FE1 c:SF4201 2.7 15.9 1.0 FE3 c:SF4201 2.7 15.9 1.0 SG c:CYS95 2.8 15.4 1.0 CD c:PRO96 3.5 15.0 1.0 S2 c:SF4201 3.9 15.9 1.0 CA c:CYS95 3.9 15.4 1.0 CB c:CYS95 3.9 15.4 1.0 CB c:VAL99 4.2 15.0 1.0 CD1 c:LEU100 4.3 15.4 1.0 CG2 c:VAL99 4.3 15.0 1.0 N c:PRO96 4.4 15.0 1.0 CG c:PRO96 4.5 15.0 1.0 C c:CYS95 4.6 15.4 1.0 N c:VAL99 4.9 15.0 1.0 CG1 c:VAL99 5.0 15.0 1.0

Iron binding site 7 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe201 b:15.9 occ:1.00 FE3 c:SF4201 0.0 15.9 1.0 S1 c:SF4201 2.3 15.9 1.0 S2 c:SF4201 2.3 15.9 1.0 S4 c:SF4201 2.3 15.9 1.0 FE4 c:SF4201 2.7 15.9 1.0 FE2 c:SF4201 2.7 15.9 1.0 FE1 c:SF4201 2.7 15.9 1.0 SG c:CYS128 2.9 15.3 1.0 CB c:CYS128 3.5 15.3 1.0 CG2 c:VAL141 3.8 15.7 1.0 S3 c:SF4201 3.9 15.9 1.0 N c:CYS128 4.0 15.3 1.0 CA c:CYS128 4.4 15.3 1.0 N c:LYS126 4.5 15.1 1.0 N c:ARG127 4.5 15.2 1.0 CA c:LYS126 4.6 15.1 1.0 CD1 c:LEU100 4.6 15.4 1.0 SG c:CYS125 4.9 14.0 1.0 C c:LYS126 5.0 15.1 1.0

Iron binding site 8 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe201 b:15.9 occ:1.00 FE4 c:SF4201 0.0 15.9 1.0 S3 c:SF4201 2.3 15.9 1.0 S1 c:SF4201 2.3 15.9 1.0 S2 c:SF4201 2.3 15.9 1.0 FE2 c:SF4201 2.7 15.9 1.0 FE3 c:SF4201 2.7 15.9 1.0 FE1 c:SF4201 2.7 15.9 1.0 SG c:CYS122 2.8 14.2 1.0 CB c:CYS122 3.3 14.2 1.0 CA c:CYS122 3.5 14.2 1.0 N c:VAL123 3.8 14.7 1.0 N c:GLY124 3.8 14.2 1.0 S4 c:SF4201 3.9 15.9 1.0 C c:CYS122 4.0 14.2 1.0 CA c:GLY124 4.5 14.2 1.0 CG2 c:VAL79 4.5 15.6 1.0 CG2 c:VAL99 4.6 15.0 1.0 N c:CYS125 4.7 14.0 1.0 CG2 c:VAL141 4.8 15.7 1.0 C c:VAL123 4.8 14.7 1.0 N c:CYS122 4.8 14.2 1.0 CA c:VAL123 4.8 14.7 1.0 CG2 c:VAL123 4.9 14.7 1.0 CB c:VAL99 4.9 15.0 1.0 CG1 c:VAL141 5.0 15.7 1.0

Iron binding site 9 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe202 b:19.2 occ:1.00 FE1 c:SF4202 0.0 19.2 1.0 S4 c:SF4202 2.3 19.2 1.0 S2 c:SF4202 2.3 19.2 1.0 S3 c:SF4202 2.3 19.2 1.0 FE3 c:SF4202 2.7 19.2 1.0 FE2 c:SF4202 2.7 19.2 1.0 FE4 c:SF4202 2.7 19.2 1.0 SG c:CYS88 2.9 14.8 1.0 N c:CYS88 3.4 14.8 1.0 S1 c:SF4202 3.9 19.2 1.0 CB c:CYS88 3.9 14.8 1.0 N c:GLY87 4.0 15.1 1.0 CD c:PRO133 4.1 16.7 1.0 CA c:CYS88 4.1 14.8 1.0 N c:THR89 4.2 14.8 1.0 CG1 c:ILE86 4.2 15.5 1.0 C c:GLY87 4.4 15.1 1.0 CA c:GLY87 4.5 15.1 1.0 N c:ILE86 4.5 15.5 1.0 C c:CYS88 4.5 14.8 1.0 CG c:PRO133 4.7 16.7 1.0 SG c:CYS85 4.8 17.9 1.0 C c:ILE86 4.8 15.5 1.0 N c:LEU90 4.8 13.9 1.0 CD1 c:ILE86 4.9 15.5 1.0

Iron binding site 10 out of 12 in the Cryo-Em Structure of Symbiodinium 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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe202 b:19.2 occ:1.00 FE2 c:SF4202 0.0 19.2 1.0 S3 c:SF4202 2.3 19.2 1.0 S1 c:SF4202 2.3 19.2 1.0 S4 c:SF4202 2.3 19.2 1.0 FE1 c:SF4202 2.7 19.2 1.0 FE3 c:SF4202 2.7 19.2 1.0 FE4 c:SF4202 2.7 19.2 1.0 SG c:CYS91 2.9 14.8 1.0 CB c:CYS91 3.2 14.8 1.0 N c:CYS91 3.8 14.8 1.0 S2 c:SF4202 3.9 19.2 1.0 CB c:ALA114 3.9 15.5 1.0 CA c:CYS91 4.2 14.8 1.0 N c:THR89 4.6 14.8 1.0 N c:LEU90 4.6 13.9 1.0 SG c:CYS88 4.7 14.8 1.0 CA c:THR89 4.9 14.8 1.0 C c:THR89 4.9 14.8 1.0 C c:LEU90 5.0 13.9 1.0

L.S.Zhao, N.Wang, K.Li, C.Y.Li, J.P.Guo, F.Y.He, G.M.Liu, X.L.Chen, J.Gao, L.N.Liu, Y.Z.Zhang. Architecture of Symbiotic Dinoflagellate Photosystem I-Light-Harvesting Supercomplex in Symbiodinium. Nat Commun V. 15 2392 2024.
ISSN: ESSN 2041-1723
PubMed: 38493166
DOI: 10.1038/S41467-024-46791-X