Iron in PDB 8htu: Cryo-Em Structure of Pppsi-L

All present enzymatic activity of Cryo-Em Structure of Pppsi-L:
1.97.1.12;

The structure of Cryo-Em Structure of Pppsi-L also contains other interesting chemical elements:

Magnesium

(Mg)

270 atoms

Pages:

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

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Pppsi-L (pdb code 8htu). 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 Pppsi-L, PDB code: 8htu:
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 Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe853 b:16.6 occ:1.00 FE1 A:SF4853 0.0 16.6 1.0 SG B:CYS559 2.1 16.1 1.0 S3 A:SF4853 2.2 16.6 1.0 S2 A:SF4853 2.2 16.6 1.0 S4 A:SF4853 2.3 16.6 1.0 FE4 A:SF4853 2.7 16.6 1.0 FE2 A:SF4853 2.7 16.6 1.0 FE3 A:SF4853 2.7 16.6 1.0 CB B:CYS559 3.0 16.1 1.0 S1 A:SF4853 3.8 16.6 1.0 CA B:CYS559 4.5 16.1 1.0 SG A:CYS573 4.5 15.0 1.0 SG B:CYS568 4.5 15.2 1.0 N B:GLY561 4.5 15.9 1.0 SG A:CYS582 4.6 15.5 1.0 CA B:GLY561 4.6 15.9 1.0 CD1 B:ILE702 4.7 15.9 1.0 C B:GLY561 4.8 15.9 1.0 N A:PRO576 4.8 16.4 1.0 CD A:PRO576 5.0 16.4 1.0 N B:CYS559 5.0 16.1 1.0 C A:GLY575 5.0 15.9 1.0

Iron binding site 2 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe853 b:16.6 occ:1.00 FE2 A:SF4853 0.0 16.6 1.0 SG A:CYS582 2.1 15.5 1.0 S4 A:SF4853 2.2 16.6 1.0 S1 A:SF4853 2.2 16.6 1.0 S3 A:SF4853 2.3 16.6 1.0 FE3 A:SF4853 2.7 16.6 1.0 FE1 A:SF4853 2.7 16.6 1.0 FE4 A:SF4853 2.7 16.6 1.0 CB A:CYS582 3.4 15.5 1.0 S2 A:SF4853 3.8 16.6 1.0 CA A:CYS582 3.9 15.5 1.0 CD1 B:ILE702 4.2 15.9 1.0 CE3 B:TRP667 4.2 15.1 1.0 N A:CYS582 4.4 15.5 1.0 CZ3 B:TRP667 4.4 15.1 1.0 SG A:CYS573 4.5 15.0 1.0 CB A:CYS573 4.5 15.0 1.0 SG B:CYS559 4.6 16.1 1.0 SG B:CYS568 4.6 15.2 1.0 CG2 B:ILE702 4.9 15.9 1.0 CG1 B:ILE702 5.0 15.9 1.0

Iron binding site 3 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe853 b:16.6 occ:1.00 FE3 A:SF4853 0.0 16.6 1.0 SG B:CYS568 2.1 15.2 1.0 S1 A:SF4853 2.2 16.6 1.0 S4 A:SF4853 2.2 16.6 1.0 S2 A:SF4853 2.3 16.6 1.0 FE2 A:SF4853 2.7 16.6 1.0 FE4 A:SF4853 2.7 16.6 1.0 FE1 A:SF4853 2.7 16.6 1.0 CB B:CYS568 3.5 15.2 1.0 S3 A:SF4853 3.8 16.6 1.0 CZ3 B:TRP667 3.8 15.1 1.0 CA B:CYS568 4.0 15.2 1.0 CD1 A:ILE719 4.1 13.5 1.0 N B:CYS568 4.3 15.2 1.0 CE3 B:TRP667 4.5 15.1 1.0 SG B:CYS559 4.6 16.1 1.0 SG A:CYS582 4.6 15.5 1.0 CB B:CYS559 4.6 16.1 1.0 CG2 A:ILE719 4.7 13.5 1.0 SG A:CYS573 4.7 15.0 1.0 CH2 B:TRP667 4.8 15.1 1.0 CG1 A:ILE719 4.8 13.5 1.0 C B:THR567 5.0 16.2 1.0

Iron binding site 4 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe853 b:16.6 occ:1.00 FE4 A:SF4853 0.0 16.6 1.0 SG A:CYS573 2.1 15.0 1.0 S2 A:SF4853 2.2 16.6 1.0 S3 A:SF4853 2.2 16.6 1.0 S1 A:SF4853 2.3 16.6 1.0 FE1 A:SF4853 2.7 16.6 1.0 FE3 A:SF4853 2.7 16.6 1.0 FE2 A:SF4853 2.7 16.6 1.0 CB A:CYS573 3.0 15.0 1.0 S4 A:SF4853 3.8 16.6 1.0 CA A:CYS573 4.4 15.0 1.0 SG A:CYS582 4.5 15.5 1.0 SG B:CYS559 4.6 16.1 1.0 SG B:CYS568 4.6 15.2 1.0 CD1 A:ILE719 4.6 13.5 1.0 N B:PRO562 4.7 15.6 1.0 CD B:PRO562 4.8 15.6 1.0 N A:GLY575 4.8 15.9 1.0 N A:CYS573 4.8 15.0 1.0 CB B:PRO562 4.8 15.6 1.0 CA A:GLY575 4.9 15.9 1.0 C A:GLY575 4.9 15.9 1.0 C B:GLY561 4.9 15.9 1.0 O A:GLY575 5.0 15.9 1.0

Iron binding site 5 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:19.6 occ:1.00 FE1 C:SF4101 0.0 19.6 1.0 SG C:CYS21 2.1 18.4 1.0 S3 C:SF4101 2.2 19.6 1.0 S2 C:SF4101 2.2 19.6 1.0 S4 C:SF4101 2.3 19.6 1.0 FE4 C:SF4101 2.7 19.6 1.0 FE3 C:SF4101 2.7 19.6 1.0 FE2 C:SF4101 2.7 19.6 1.0 CB C:CYS21 3.4 18.4 1.0 S1 C:SF4101 3.8 19.6 1.0 CA C:CYS21 3.9 18.4 1.0 CD C:PRO22 4.1 19.7 1.0 CB C:VAL25 4.2 20.8 1.0 SG C:CYS54 4.4 17.9 1.0 OG1 C:THR23 4.4 20.9 1.0 CG2 C:VAL25 4.5 20.8 1.0 SG C:CYS51 4.5 17.9 1.0 C C:CYS21 4.7 18.4 1.0 N C:PRO22 4.7 19.7 1.0 SG C:CYS48 4.7 19.9 1.0 CB C:CYS54 4.7 17.9 1.0 CG C:LEU26 4.7 20.6 1.0 CD1 C:LEU26 4.8 20.6 1.0

Iron binding site 6 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:19.6 occ:1.00 FE2 C:SF4101 0.0 19.6 1.0 SG C:CYS54 2.1 17.9 1.0 S1 C:SF4101 2.2 19.6 1.0 S4 C:SF4101 2.2 19.6 1.0 S3 C:SF4101 2.3 19.6 1.0 FE3 C:SF4101 2.7 19.6 1.0 FE1 C:SF4101 2.7 19.6 1.0 FE4 C:SF4101 2.7 19.6 1.0 CB C:CYS54 3.3 17.9 1.0 CG2 C:VAL67 3.8 19.0 1.0 S2 C:SF4101 3.8 19.6 1.0 N C:CYS54 3.9 17.9 1.0 N C:LYS52 4.2 17.8 1.0 CA C:LYS52 4.2 17.8 1.0 CA C:CYS54 4.2 17.9 1.0 N C:ARG53 4.5 18.0 1.0 SG C:CYS51 4.5 17.9 1.0 SG C:CYS48 4.6 19.9 1.0 C C:LYS52 4.7 17.8 1.0 SG C:CYS21 4.7 18.4 1.0 CD1 C:LEU26 4.9 20.6 1.0

Iron binding site 7 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:19.6 occ:1.00 FE3 C:SF4101 0.0 19.6 1.0 SG C:CYS51 2.1 17.9 1.0 S1 C:SF4101 2.2 19.6 1.0 S4 C:SF4101 2.2 19.6 1.0 S2 C:SF4101 2.3 19.6 1.0 FE2 C:SF4101 2.7 19.6 1.0 FE1 C:SF4101 2.7 19.6 1.0 FE4 C:SF4101 2.7 19.6 1.0 N C:CYS51 3.5 17.9 1.0 N C:LYS52 3.6 17.8 1.0 CB C:CYS51 3.6 17.9 1.0 S3 C:SF4101 3.8 19.6 1.0 CA C:CYS51 4.0 17.9 1.0 CD C:PRO22 4.0 19.7 1.0 C C:CYS51 4.2 17.9 1.0 N C:ARG53 4.2 18.0 1.0 N C:GLY50 4.4 18.1 1.0 CG2 C:VAL49 4.4 19.5 1.0 C C:GLY50 4.5 18.1 1.0 SG C:CYS48 4.5 19.9 1.0 CA C:LYS52 4.5 17.8 1.0 SG C:CYS21 4.5 18.4 1.0 SG C:CYS54 4.6 17.9 1.0 CG C:PRO22 4.6 19.7 1.0 CA C:GLY50 4.8 18.1 1.0 C C:LYS52 4.8 17.8 1.0 N C:CYS54 4.9 17.9 1.0 CB C:ARG53 5.0 18.0 1.0

Iron binding site 8 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:19.6 occ:1.00 FE4 C:SF4101 0.0 19.6 1.0 SG C:CYS48 2.1 19.9 1.0 S3 C:SF4101 2.2 19.6 1.0 S2 C:SF4101 2.2 19.6 1.0 S1 C:SF4101 2.3 19.6 1.0 FE1 C:SF4101 2.7 19.6 1.0 FE3 C:SF4101 2.7 19.6 1.0 FE2 C:SF4101 2.7 19.6 1.0 CB C:CYS48 3.3 19.9 1.0 S4 C:SF4101 3.8 19.6 1.0 CA C:CYS48 3.9 19.9 1.0 N C:GLY50 4.1 18.1 1.0 N C:VAL49 4.2 19.5 1.0 C C:CYS48 4.4 19.9 1.0 CG2 C:VAL5 4.5 20.4 1.0 SG C:CYS21 4.6 18.4 1.0 CG2 C:VAL25 4.6 20.8 1.0 CA C:GLY50 4.7 18.1 1.0 SG C:CYS51 4.7 17.9 1.0 CG2 C:VAL67 4.7 19.0 1.0 SG C:CYS54 4.8 17.9 1.0 CB C:VAL25 4.8 20.8 1.0 N C:CYS51 4.8 17.9 1.0 CG1 C:VAL67 4.9 19.0 1.0 CG1 C:VAL25 4.9 20.8 1.0

Iron binding site 9 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe102 b:22.4 occ:1.00 FE1 C:SF4102 0.0 22.4 1.0 SG C:CYS58 2.1 19.2 1.0 S2 C:SF4102 2.2 22.4 1.0 S3 C:SF4102 2.2 22.4 1.0 S4 C:SF4102 2.3 22.4 1.0 FE4 C:SF4102 2.7 22.4 1.0 FE3 C:SF4102 2.7 22.4 1.0 FE2 C:SF4102 2.7 22.4 1.0 CB C:CYS58 3.3 19.2 1.0 CA C:CYS58 3.7 19.2 1.0 S1 C:SF4102 3.8 22.4 1.0 CD C:PRO59 4.1 19.8 1.0 CB C:SER64 4.2 20.3 1.0 SG C:CYS14 4.4 20.9 1.0 SG C:CYS17 4.6 20.1 1.0 CG1 C:VAL65 4.6 19.6 1.0 C C:CYS58 4.6 19.2 1.0 CB C:CYS17 4.7 20.1 1.0 N C:PRO59 4.7 19.8 1.0 SG C:CYS11 4.7 21.4 1.0 OG C:SER64 4.8 20.3 1.0 N C:VAL65 4.8 19.6 1.0 N C:CYS58 4.8 19.2 1.0 CG2 C:THR60 4.9 20.9 1.0 N C:SER64 5.0 20.3 1.0

Iron binding site 10 out of 12 in the Cryo-Em Structure of Pppsi-L


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 Pppsi-L within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe102 b:22.4 occ:1.00 FE2 C:SF4102 0.0 22.4 1.0 SG C:CYS14 2.1 20.9 1.0 S1 C:SF4102 2.2 22.4 1.0 S4 C:SF4102 2.2 22.4 1.0 S3 C:SF4102 2.3 22.4 1.0 FE3 C:SF4102 2.7 22.4 1.0 FE1 C:SF4102 2.7 22.4 1.0 FE4 C:SF4102 2.7 22.4 1.0 N C:CYS14 3.4 20.9 1.0 CB C:CYS14 3.5 20.9 1.0 N C:THR15 3.7 21.7 1.0 S2 C:SF4102 3.8 22.4 1.0 CA C:CYS14 3.8 20.9 1.0 C C:CYS14 4.1 20.9 1.0 N C:GLN16 4.1 20.0 1.0 CD C:PRO59 4.3 19.8 1.0 SG C:CYS11 4.4 21.4 1.0 N C:GLY13 4.5 22.6 1.0 C C:GLY13 4.5 22.6 1.0 SG C:CYS58 4.6 19.2 1.0 CA C:THR15 4.6 21.7 1.0 N C:CYS17 4.6 20.1 1.0 CG1 C:ILE12 4.6 22.1 1.0 SG C:CYS17 4.6 20.1 1.0 CA C:GLY13 4.7 22.6 1.0 C C:THR15 4.8 21.7 1.0 CB C:GLN16 4.8 20.0 1.0 CA C:GLN16 5.0 20.0 1.0

H.Sun, H.Shang, X.Pan, M.Li. Structural Insights Into the Assembly and Energy Transfer of the LHCB9-Dependent Photosystem I From Moss Physcomitrium Patens. Nat.Plants 2023.
ISSN: ESSN 2055-0278
PubMed: 37474782
DOI: 10.1038/S41477-023-01463-4