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

Enzymatic activity of Rcii/Psi Complex, Class 3

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

Other elements in 8am5:

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

Magnesium (Mg) 102 atoms

Iron Binding Sites:

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 8am5

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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 8am5

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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 8am5

Go back to Iron Binding Sites List in 8am5
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 8am5

Go back to Iron Binding Sites List in 8am5
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 8am5

Go back to Iron Binding Sites List in 8am5
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 8am5

Go back to Iron Binding Sites List in 8am5
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 8am5

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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 8am5

Go back to Iron Binding Sites List in 8am5
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 8am5

Go back to Iron Binding Sites List in 8am5
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 8am5

Go back to Iron Binding Sites List in 8am5
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

Reference:

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
Page generated: Fri Aug 9 17:54:34 2024

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