Iron in PDB 8asp: Rcii/Psi Complex, Focused Refinement of Psi

All present enzymatic activity of Rcii/Psi Complex, Focused Refinement of Psi:
1.97.1.12;

The structure of Rcii/Psi Complex, Focused Refinement of Psi also contains other interesting chemical elements:

Magnesium

(Mg)

96 atoms

Pages:

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

Binding sites:

The binding sites of Iron atom in the Rcii/Psi Complex, Focused Refinement of Psi (pdb code 8asp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Rcii/Psi Complex, Focused Refinement of Psi, PDB code: 8asp:
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 Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ b:Fe802 b:79.0 occ:1.00 FE1 b:SF4802 0.0 79.0 1.0 SG b:CYS565 2.3 51.9 1.0 S2 b:SF4802 2.3 35.1 1.0 S4 b:SF4802 2.3 74.0 1.0 S3 b:SF4802 2.3 69.8 1.0 FE3 b:SF4802 2.7 63.0 1.0 FE4 b:SF4802 2.7 60.6 1.0 FE2 b:SF4802 2.7 69.8 1.0 CB b:CYS565 3.7 51.0 1.0 CA b:CYS565 3.9 41.0 1.0 S1 b:SF4802 3.9 63.3 1.0 O b:GLY563 4.0 67.1 1.0 CD1 a:ILE720 4.1 42.1 1.0 N b:CYS565 4.2 39.9 1.0 CZ3 b:TRP664 4.3 38.7 1.0 CB b:CYS556 4.7 40.8 1.0 SG b:CYS556 4.8 65.3 1.0 SG a:CYS574 4.8 43.7 1.0 CG2 a:ILE720 4.8 44.4 1.0 SG a:CYS583 4.9 56.9 1.0 OG1 b:THR564 4.9 68.7 1.0 CG1 a:ILE720 4.9 42.8 1.0

Iron binding site 2 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ b:Fe802 b:69.8 occ:1.00 FE2 b:SF4802 0.0 69.8 1.0 SG a:CYS583 2.2 56.9 1.0 S3 b:SF4802 2.3 69.8 1.0 S4 b:SF4802 2.3 74.0 1.0 S1 b:SF4802 2.3 63.3 1.0 FE3 b:SF4802 2.7 63.0 1.0 FE4 b:SF4802 2.7 60.6 1.0 FE1 b:SF4802 2.7 79.0 1.0 CB a:CYS583 3.5 49.2 1.0 S2 b:SF4802 3.9 35.1 1.0 CA a:CYS583 4.1 50.6 1.0 CE3 b:TRP664 4.3 47.0 1.0 CD1 b:ILE699 4.3 41.7 1.0 CZ3 b:TRP664 4.3 38.7 1.0 CB a:CYS574 4.5 49.3 1.0 N a:CYS583 4.6 58.5 1.0 SG a:CYS574 4.6 43.7 1.0 SG b:CYS556 4.7 65.3 1.0 SG b:CYS565 4.8 51.9 1.0

Iron binding site 3 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ b:Fe802 b:63.0 occ:1.00 FE3 b:SF4802 0.0 63.0 1.0 SG a:CYS574 2.2 43.7 1.0 S2 b:SF4802 2.3 35.1 1.0 S1 b:SF4802 2.3 63.3 1.0 S4 b:SF4802 2.3 74.0 1.0 FE2 b:SF4802 2.7 69.8 1.0 FE4 b:SF4802 2.7 60.6 1.0 FE1 b:SF4802 2.7 79.0 1.0 CB a:CYS574 3.1 49.3 1.0 S3 b:SF4802 3.9 69.8 1.0 N b:PRO559 4.5 44.6 1.0 CA a:CYS574 4.5 41.2 1.0 CD b:PRO559 4.5 40.8 1.0 SG a:CYS583 4.6 56.9 1.0 CB b:PRO559 4.7 49.2 1.0 CD1 a:ILE720 4.7 42.1 1.0 SG b:CYS565 4.7 51.9 1.0 C b:GLY558 4.7 48.5 1.0 SG b:CYS556 4.8 65.3 1.0 CA b:PRO559 4.8 47.9 1.0 N a:CYS574 4.9 46.7 1.0 CA a:GLY576 4.9 52.7 1.0 CG b:PRO559 5.0 45.9 1.0 N a:GLY576 5.0 59.0 1.0 C a:GLY576 5.0 47.0 1.0

Iron binding site 4 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ b:Fe802 b:60.6 occ:1.00 FE4 b:SF4802 0.0 60.6 1.0 SG b:CYS556 2.2 65.3 1.0 S2 b:SF4802 2.3 35.1 1.0 S1 b:SF4802 2.3 63.3 1.0 S3 b:SF4802 2.3 69.8 1.0 FE2 b:SF4802 2.7 69.8 1.0 FE3 b:SF4802 2.7 63.0 1.0 FE1 b:SF4802 2.7 79.0 1.0 CB b:CYS556 3.1 40.8 1.0 S4 b:SF4802 3.9 74.0 1.0 N b:GLY558 4.5 52.2 1.0 CA b:CYS556 4.5 39.5 1.0 OG1 b:THR564 4.5 68.7 1.0 CA b:GLY558 4.6 44.1 1.0 SG a:CYS583 4.7 56.9 1.0 SG b:CYS565 4.7 51.9 1.0 CD1 b:ILE699 4.8 41.7 1.0 SG a:CYS574 4.8 43.7 1.0 C b:GLY558 4.8 48.5 1.0 N a:PRO577 4.8 33.8 1.0 CD a:PRO577 4.9 46.7 1.0 CB a:PRO577 4.9 45.2 1.0 O b:GLY563 5.0 67.1 1.0 N b:CYS565 5.0 39.9 1.0 N b:CYS556 5.0 48.6 1.0

Iron binding site 5 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe101 b:69.1 occ:1.00 FE1 c:SF4101 0.0 69.1 1.0 SG c:CYS51 2.3 71.0 1.0 S4 c:SF4101 2.3 73.6 1.0 S2 c:SF4101 2.3 80.2 1.0 S3 c:SF4101 2.3 63.5 1.0 FE4 c:SF4101 2.7 83.5 1.0 FE2 c:SF4101 2.7 67.2 1.0 FE3 c:SF4101 2.7 79.0 1.0 N c:CYS51 3.4 51.3 1.0 CB c:CYS51 3.7 48.3 1.0 N c:LYS52 3.7 48.9 1.0 S1 c:SF4101 3.9 58.4 1.0 CA c:CYS51 3.9 46.8 1.0 C c:CYS51 4.1 50.5 1.0 CD c:PRO22 4.2 57.3 1.0 N c:ARG53 4.2 41.2 1.0 N c:GLY50 4.4 50.5 1.0 C c:GLY50 4.4 45.3 1.0 CG2 c:VAL49 4.6 59.6 1.0 CA c:GLY50 4.6 40.7 1.0 CA c:LYS52 4.7 41.5 1.0 SG c:CYS48 4.7 68.0 1.0 SG c:CYS21 4.7 62.9 1.0 SG c:CYS54 4.7 60.1 1.0 CB c:ARG53 4.8 48.0 1.0 CG c:PRO22 4.8 50.1 1.0 N c:CYS54 4.9 43.4 1.0 C c:LYS52 4.9 44.0 1.0

Iron binding site 6 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe101 b:67.2 occ:1.00 FE2 c:SF4101 0.0 67.2 1.0 SG c:CYS21 2.3 62.9 1.0 S3 c:SF4101 2.3 63.5 1.0 S4 c:SF4101 2.3 73.6 1.0 S1 c:SF4101 2.3 58.4 1.0 FE1 c:SF4101 2.7 69.1 1.0 FE3 c:SF4101 2.7 79.0 1.0 FE4 c:SF4101 2.7 83.5 1.0 CB c:CYS21 3.3 51.0 1.0 CA c:CYS21 3.9 47.6 1.0 S2 c:SF4101 3.9 80.2 1.0 CB c:VAL25 4.1 56.9 1.0 CD c:PRO22 4.1 57.3 1.0 CG2 c:VAL25 4.2 53.5 1.0 SG c:CYS51 4.6 71.0 1.0 C c:CYS21 4.6 53.8 1.0 N c:PRO22 4.6 57.0 1.0 CD1 c:LEU26 4.6 59.2 1.0 CG c:LEU26 4.7 56.4 1.0 SG c:CYS54 4.7 60.1 1.0 SG c:CYS48 4.8 68.0 1.0 CG1 c:VAL25 5.0 51.9 1.0 N c:LEU23 5.0 56.0 1.0 N c:VAL25 5.0 68.6 1.0

Iron binding site 7 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe101 b:79.0 occ:1.00 FE3 c:SF4101 0.0 79.0 1.0 SG c:CYS54 2.3 60.1 1.0 S4 c:SF4101 2.3 73.6 1.0 S1 c:SF4101 2.3 58.4 1.0 S2 c:SF4101 2.3 80.2 1.0 FE2 c:SF4101 2.7 67.2 1.0 FE4 c:SF4101 2.7 83.5 1.0 FE1 c:SF4101 2.7 69.1 1.0 CB c:CYS54 3.3 47.0 1.0 N c:CYS54 3.9 43.4 1.0 S3 c:SF4101 3.9 63.5 1.0 CG2 c:VAL67 4.1 55.0 1.0 CA c:CYS54 4.2 41.3 1.0 N c:LYS52 4.5 48.9 1.0 N c:ARG53 4.6 41.2 1.0 CA c:LYS52 4.7 41.5 1.0 CD1 c:LEU26 4.7 59.2 1.0 SG c:CYS21 4.7 62.9 1.0 SG c:CYS48 4.8 68.0 1.0 SG c:CYS51 4.8 71.0 1.0 C c:LYS52 4.9 44.0 1.0

Iron binding site 8 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe101 b:83.5 occ:1.00 FE4 c:SF4101 0.0 83.5 1.0 SG c:CYS48 2.3 68.0 1.0 S3 c:SF4101 2.3 63.5 1.0 S1 c:SF4101 2.3 58.4 1.0 S2 c:SF4101 2.3 80.2 1.0 FE1 c:SF4101 2.7 69.1 1.0 FE3 c:SF4101 2.7 79.0 1.0 FE2 c:SF4101 2.7 67.2 1.0 CB c:CYS48 3.4 57.5 1.0 S4 c:SF4101 3.9 73.6 1.0 CA c:CYS48 3.9 57.2 1.0 N c:GLY50 4.0 50.5 1.0 N c:VAL49 4.1 53.0 1.0 CA c:GLY50 4.4 40.7 1.0 C c:CYS48 4.5 59.7 1.0 CG2 c:VAL5 4.6 53.1 1.0 CG2 c:VAL25 4.6 53.5 1.0 N c:CYS51 4.7 51.3 1.0 CB c:VAL25 4.8 56.9 1.0 SG c:CYS51 4.8 71.0 1.0 SG c:CYS21 4.8 62.9 1.0 SG c:CYS54 4.8 60.1 1.0 CG1 c:VAL25 4.9 51.9 1.0 CG2 c:VAL67 4.9 55.0 1.0

Iron binding site 9 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe102 b:80.5 occ:1.00 FE1 c:SF4102 0.0 80.5 1.0 SG c:CYS58 2.3 78.7 1.0 S4 c:SF4102 2.3 82.2 1.0 S3 c:SF4102 2.3 64.8 1.0 S2 c:SF4102 2.3 66.6 1.0 FE3 c:SF4102 2.7 71.3 1.0 FE2 c:SF4102 2.7 87.0 1.0 FE4 c:SF4102 2.7 79.0 1.0 CB c:CYS58 3.4 58.2 1.0 CA c:CYS58 3.8 56.5 1.0 S1 c:SF4102 3.9 57.5 1.0 CD c:PRO59 4.0 52.8 1.0 CG2 c:ILE65 4.1 44.6 1.0 CB c:SER64 4.2 50.1 1.0 SG c:CYS14 4.6 77.6 1.0 C c:CYS58 4.7 61.5 1.0 N c:PRO59 4.7 54.7 1.0 SG c:CYS17 4.8 73.1 1.0 N c:ILE65 4.8 44.7 1.0 N c:SER64 4.8 51.5 1.0 N c:CYS58 4.9 52.5 1.0 SG c:CYS11 4.9 82.2 1.0 CG2 c:THR60 4.9 62.5 1.0 OG c:SER64 4.9 70.1 1.0 CB c:CYS17 4.9 64.4 1.0 CA c:SER64 4.9 44.9 1.0 CB c:ILE65 5.0 44.2 1.0

Iron binding site 10 out of 12 in the Rcii/Psi Complex, Focused Refinement of Psi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Rcii/Psi Complex, Focused Refinement of Psi within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe102 b:87.0 occ:1.00 FE2 c:SF4102 0.0 87.0 1.0 SG c:CYS17 2.3 73.1 1.0 S4 c:SF4102 2.3 82.2 1.0 S1 c:SF4102 2.3 57.5 1.0 S3 c:SF4102 2.3 64.8 1.0 FE4 c:SF4102 2.7 79.0 1.0 FE3 c:SF4102 2.7 71.3 1.0 FE1 c:SF4102 2.7 80.5 1.0 CB c:CYS17 3.1 64.4 1.0 N c:CYS17 3.8 54.6 1.0 S2 c:SF4102 3.9 66.6 1.0 CA c:CYS17 4.1 59.0 1.0 CB c:ALA40 4.2 55.2 1.0 CG2 c:ILE65 4.6 44.6 1.0 SG c:CYS11 4.7 82.2 1.0 N c:GLN16 4.7 60.0 1.0 SG c:CYS14 4.7 77.6 1.0 N c:THR15 4.7 53.3 1.0 SG c:CYS58 4.8 78.7 1.0 CA c:THR15 4.9 59.1 1.0 C c:GLN16 5.0 55.6 1.0

Z.Zhao, I.Vercellino, J.Knoppova, R.Sobotka, J.W.Murray, P.J.Nixon, L.A.Sazanov, J.Komenda. The YCF48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster During Photosystem II Biogenesis. Nat Commun V. 14 4681 2023.
ISSN: ESSN 2041-1723
PubMed: 37542031
DOI: 10.1038/S41467-023-40388-6