Iron in PDB 8am5: Rcii/Psi Complex, Class 3

All present enzymatic activity of Rcii/Psi Complex, Class 3:
1.10.3.9; 1.97.1.12;

The structure of Rcii/Psi Complex, Class 3 also contains other interesting chemical elements:

Magnesium

(Mg)

102 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iron atom in the Rcii/Psi Complex, Class 3 (pdb code 8am5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the Rcii/Psi Complex, Class 3, PDB code: 8am5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:175.1 occ:1.00 NE2 A:HIS215 2.1 160.9 1.0 NE2 D:HIS214 2.1 158.5 1.0 NE2 D:HIS268 2.4 166.7 1.0 NE2 A:HIS272 2.4 159.5 1.0 CD2 A:HIS215 2.8 159.9 1.0 CE1 D:HIS214 2.8 157.2 1.0 CE1 A:HIS215 3.2 160.1 1.0 CE1 D:HIS268 3.3 166.0 1.0 CD2 D:HIS214 3.3 154.7 1.0 CE1 A:HIS272 3.3 155.1 1.0 CD2 A:HIS272 3.3 158.2 1.0 CD2 D:HIS268 3.4 167.4 1.0 CG A:HIS215 4.0 159.1 1.0 ND1 D:HIS214 4.0 156.5 1.0 ND1 A:HIS215 4.2 160.1 1.0 CG D:HIS214 4.3 154.4 1.0 ND1 A:HIS272 4.4 153.9 1.0 ND1 D:HIS268 4.4 165.8 1.0 CG2 D:VAL218 4.5 153.9 1.0 CG A:HIS272 4.5 156.1 1.0 CG D:HIS268 4.5 166.4 1.0 CG2 A:VAL219 4.5 176.3 1.0

Iron binding site 2 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe101 b:200.7 occ:1.00 FE E:HEM101 0.0 200.7 1.0 NC E:HEM101 2.1 189.7 1.0 ND E:HEM101 2.1 191.2 1.0 NB E:HEM101 2.1 189.3 1.0 NE2 E:HIS23 2.1 194.0 1.0 NA E:HEM101 2.1 191.0 1.0 CD2 E:HIS23 2.4 194.0 1.0 NE2 F:HIS23 2.7 197.3 1.0 C4B E:HEM101 3.0 187.9 1.0 C1C E:HEM101 3.0 187.5 1.0 C1B E:HEM101 3.0 188.7 1.0 C4C E:HEM101 3.1 189.3 1.0 C1D E:HEM101 3.1 189.7 1.0 C4A E:HEM101 3.1 189.1 1.0 C1A E:HEM101 3.1 191.0 1.0 C4D E:HEM101 3.1 190.8 1.0 CE1 E:HIS23 3.4 191.8 1.0 CHC E:HEM101 3.4 187.4 1.0 CHD E:HEM101 3.4 189.3 1.0 CHB E:HEM101 3.4 188.1 1.0 CHA E:HEM101 3.5 191.1 1.0 CE1 F:HIS23 3.5 197.5 1.0 CD2 F:HIS23 3.7 197.0 1.0 CG E:HIS23 3.7 193.4 1.0 ND1 E:HIS23 4.1 191.8 1.0 C2B E:HEM101 4.2 188.1 1.0 C3B E:HEM101 4.2 188.2 1.0 C2C E:HEM101 4.2 188.1 1.0 C3C E:HEM101 4.3 188.5 1.0 C2D E:HEM101 4.3 189.1 1.0 C3A E:HEM101 4.3 189.4 1.0 C2A E:HEM101 4.3 190.8 1.0 C3D E:HEM101 4.3 189.9 1.0 CG2 E:ILE22 4.6 184.0 1.0 ND1 F:HIS23 4.6 198.6 1.0 CG F:HIS23 4.7 198.3 1.0 CB E:HIS23 5.0 193.3 1.0

Iron binding site 3 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe845 b:76.2 occ:1.00 FE1 a:SF4845 0.0 76.2 1.0 SG b:CYS565 2.3 49.9 1.0 S4 a:SF4845 2.3 67.7 1.0 S2 a:SF4845 2.3 27.3 1.0 S3 a:SF4845 2.3 55.4 1.0 FE4 a:SF4845 2.7 65.3 1.0 FE3 a:SF4845 2.7 65.3 1.0 FE2 a:SF4845 2.7 58.3 1.0 CB b:CYS565 3.5 37.3 1.0 S1 a:SF4845 3.9 63.2 1.0 CA b:CYS565 3.9 37.2 1.0 CD1 a:ILE720 4.2 46.7 1.0 CZ3 b:TRP664 4.2 38.1 1.0 N b:CYS565 4.3 42.5 1.0 CG2 a:ILE720 4.7 48.1 1.0 SG b:CYS556 4.7 64.8 1.0 CB b:CYS556 4.8 33.3 1.0 SG a:CYS574 4.9 46.0 1.0 SG a:CYS583 4.9 55.8 1.0 CE3 b:TRP664 4.9 43.9 1.0 CG1 a:ILE720 5.0 39.8 1.0 CH2 b:TRP664 5.0 32.4 1.0 C b:THR564 5.0 43.1 1.0

Iron binding site 4 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe845 b:58.3 occ:1.00 FE2 a:SF4845 0.0 58.3 1.0 SG a:CYS583 2.3 55.8 1.0 S1 a:SF4845 2.3 63.2 1.0 S4 a:SF4845 2.3 67.7 1.0 S3 a:SF4845 2.3 55.4 1.0 FE3 a:SF4845 2.7 65.3 1.0 FE1 a:SF4845 2.7 76.2 1.0 FE4 a:SF4845 2.7 65.3 1.0 CB a:CYS583 3.2 47.0 1.0 S2 a:SF4845 3.9 27.3 1.0 CA a:CYS583 3.9 45.2 1.0 CE3 b:TRP664 4.2 43.9 1.0 N a:CYS583 4.3 55.5 1.0 CD1 b:ILE699 4.3 44.7 1.0 CZ3 b:TRP664 4.3 38.1 1.0 CB a:CYS574 4.4 44.8 1.0 SG a:CYS574 4.6 46.0 1.0 SG b:CYS556 4.7 64.8 1.0 SG b:CYS565 4.8 49.9 1.0

Iron binding site 5 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe845 b:65.3 occ:1.00 FE3 a:SF4845 0.0 65.3 1.0 SG a:CYS574 2.2 46.0 1.0 S2 a:SF4845 2.3 27.3 1.0 S1 a:SF4845 2.3 63.2 1.0 S4 a:SF4845 2.3 67.7 1.0 FE1 a:SF4845 2.7 76.2 1.0 FE4 a:SF4845 2.7 65.3 1.0 FE2 a:SF4845 2.7 58.3 1.0 CB a:CYS574 2.9 44.8 1.0 S3 a:SF4845 3.9 55.4 1.0 CA a:CYS574 4.4 47.0 1.0 N a:GLY576 4.5 59.7 1.0 N b:PRO559 4.5 38.4 1.0 CD b:PRO559 4.6 40.9 1.0 CA a:GLY576 4.6 54.5 1.0 SG a:CYS583 4.6 55.8 1.0 SG b:CYS565 4.7 49.9 1.0 CD1 a:ILE720 4.7 46.7 1.0 CB b:PRO559 4.7 43.0 1.0 SG b:CYS556 4.8 64.8 1.0 C b:GLY558 4.8 43.4 1.0 CA b:PRO559 4.9 40.1 1.0 N a:CYS574 4.9 53.1 1.0 C a:GLY576 4.9 47.9 1.0

Iron binding site 6 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ a:Fe845 b:65.3 occ:1.00 FE4 a:SF4845 0.0 65.3 1.0 SG b:CYS556 2.2 64.8 1.0 S2 a:SF4845 2.3 27.3 1.0 S1 a:SF4845 2.3 63.2 1.0 S3 a:SF4845 2.3 55.4 1.0 FE1 a:SF4845 2.7 76.2 1.0 FE3 a:SF4845 2.7 65.3 1.0 FE2 a:SF4845 2.7 58.3 1.0 CB b:CYS556 3.1 33.3 1.0 S4 a:SF4845 3.9 67.7 1.0 CA b:CYS556 4.6 33.5 1.0 SG a:CYS583 4.6 55.8 1.0 CD1 b:ILE699 4.6 44.7 1.0 CD a:PRO577 4.7 34.2 1.0 N b:GLY558 4.7 46.1 1.0 SG b:CYS565 4.7 49.9 1.0 CA b:GLY558 4.7 36.5 1.0 SG a:CYS574 4.7 46.0 1.0 N a:PRO577 4.8 27.0 1.0 C b:GLY558 4.9 43.4 1.0

Iron binding site 7 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe101 b:73.8 occ:1.00 FE1 c:SF4101 0.0 73.8 1.0 SG c:CYS51 2.3 62.4 1.0 S4 c:SF4101 2.3 72.3 1.0 S2 c:SF4101 2.3 82.3 1.0 S3 c:SF4101 2.3 51.4 1.0 FE2 c:SF4101 2.7 64.4 1.0 FE4 c:SF4101 2.7 68.9 1.0 FE3 c:SF4101 2.7 66.2 1.0 N c:CYS51 3.5 51.4 1.0 CB c:CYS51 3.7 50.5 1.0 N c:LYS52 3.8 51.1 1.0 S1 c:SF4101 3.9 51.6 1.0 CA c:CYS51 4.0 50.4 1.0 CD c:PRO22 4.1 54.8 1.0 C c:CYS51 4.2 54.1 1.0 N c:ARG53 4.3 44.4 1.0 N c:GLY50 4.4 46.4 1.0 C c:GLY50 4.5 44.1 1.0 CG2 c:VAL49 4.6 54.6 1.0 SG c:CYS48 4.7 67.0 1.0 CA c:GLY50 4.7 40.8 1.0 SG c:CYS54 4.7 47.2 1.0 CG c:PRO22 4.8 49.1 1.0 CA c:LYS52 4.8 40.4 1.0 SG c:CYS21 4.8 65.5 1.0 CB c:ARG53 4.9 45.5 1.0 N c:CYS54 4.9 40.8 1.0

Iron binding site 8 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe101 b:64.4 occ:1.00 FE2 c:SF4101 0.0 64.4 1.0 SG c:CYS21 2.3 65.5 1.0 S3 c:SF4101 2.3 51.4 1.0 S1 c:SF4101 2.3 51.6 1.0 S4 c:SF4101 2.3 72.3 1.0 FE1 c:SF4101 2.7 73.8 1.0 FE4 c:SF4101 2.7 68.9 1.0 FE3 c:SF4101 2.7 66.2 1.0 CB c:CYS21 3.4 48.4 1.0 CA c:CYS21 3.8 43.3 1.0 S2 c:SF4101 3.9 82.3 1.0 CD c:PRO22 4.0 54.8 1.0 CB c:VAL25 4.2 59.2 1.0 CG2 c:VAL25 4.4 53.0 1.0 N c:PRO22 4.5 51.3 1.0 C c:CYS21 4.5 53.7 1.0 SG c:CYS51 4.6 62.4 1.0 SG c:CYS54 4.8 47.2 1.0 CG c:LEU26 4.8 56.6 1.0 SG c:CYS48 4.8 67.0 1.0 N c:LEU23 4.9 55.8 1.0 N c:VAL25 4.9 64.0 1.0 CD1 c:LEU26 5.0 53.9 1.0 N c:CYS21 5.0 47.9 1.0 CB c:CYS54 5.0 48.0 1.0

Iron binding site 9 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe101 b:66.2 occ:1.00 FE3 c:SF4101 0.0 66.2 1.0 SG c:CYS54 2.3 47.2 1.0 S4 c:SF4101 2.3 72.3 1.0 S1 c:SF4101 2.3 51.6 1.0 S2 c:SF4101 2.3 82.3 1.0 FE4 c:SF4101 2.7 68.9 1.0 FE2 c:SF4101 2.7 64.4 1.0 FE1 c:SF4101 2.7 73.8 1.0 CB c:CYS54 3.2 48.0 1.0 N c:CYS54 3.8 40.8 1.0 S3 c:SF4101 3.9 51.4 1.0 CG2 c:VAL67 4.1 52.5 1.0 CA c:CYS54 4.1 40.9 1.0 N c:LYS52 4.5 51.1 1.0 N c:ARG53 4.6 44.4 1.0 SG c:CYS21 4.7 65.5 1.0 CA c:LYS52 4.7 40.4 1.0 SG c:CYS48 4.8 67.0 1.0 SG c:CYS51 4.8 62.4 1.0 CD1 c:LEU26 4.9 53.9 1.0 C c:LYS52 4.9 45.4 1.0 C c:ARG53 5.0 52.3 1.0

Iron binding site 10 out of 14 in the Rcii/Psi Complex, Class 3


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, Class 3 within 5.0Å range: probe atom residue distance (Å) B Occ c:Fe101 b:68.9 occ:1.00 FE4 c:SF4101 0.0 68.9 1.0 SG c:CYS48 2.3 67.0 1.0 S3 c:SF4101 2.3 51.4 1.0 S1 c:SF4101 2.3 51.6 1.0 S2 c:SF4101 2.3 82.3 1.0 FE1 c:SF4101 2.7 73.8 1.0 FE3 c:SF4101 2.7 66.2 1.0 FE2 c:SF4101 2.7 64.4 1.0 CB c:CYS48 3.3 53.5 1.0 S4 c:SF4101 3.9 72.3 1.0 N c:GLY50 3.9 46.4 1.0 CA c:CYS48 3.9 56.6 1.0 N c:VAL49 4.1 47.6 1.0 CA c:GLY50 4.4 40.8 1.0 C c:CYS48 4.5 61.4 1.0 CG2 c:VAL5 4.5 53.3 1.0 CG2 c:VAL67 4.6 52.5 1.0 CG2 c:VAL25 4.7 53.0 1.0 N c:CYS51 4.7 51.4 1.0 SG c:CYS54 4.8 47.2 1.0 SG c:CYS51 4.8 62.4 1.0 SG c:CYS21 4.8 65.5 1.0 CB c:VAL25 4.9 59.2 1.0 C c:VAL49 5.0 55.0 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