Iron in PDB 8xls: Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335

Enzymatic activity of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335

All present enzymatic activity of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335:
1.97.1.12;

Other elements in 8xls:

The structure of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 also contains other interesting chemical elements:

Magnesium (Mg) 146 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 (pdb code 8xls). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335, PDB code: 8xls:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 8xls

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Iron binding site 1 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe846

b:19.8
occ:1.00
 FE1 A:SF4846 0.0 19.8 1.0
SG B:CYS567 2.3 28.5 1.0
S2 A:SF4846 2.3 18.9 1.0
S4 A:SF4846 2.3 19.4 1.0
S3 A:SF4846 2.3 20.9 1.0
FE3 A:SF4846 2.7 17.8 1.0
FE4 A:SF4846 2.7 19.6 1.0
FE2 A:SF4846 2.7 18.8 1.0
CB B:CYS567 3.2 26.2 1.0
CA B:CYS567 3.7 27.1 1.0
S1 A:SF4846 3.9 19.3 1.0
N B:CYS567 4.0 23.5 1.0
CZ3 B:TRP666 4.1 37.9 1.0
CD1 A:ILE721 4.2 28.0 1.0
SG B:CYS558 4.6 24.3 1.0
CB B:CYS558 4.6 28.2 1.0
SG A:CYS575 4.7 26.4 1.0
SG A:CYS584 4.8 22.9 1.0
CE3 B:TRP666 4.8 39.8 1.0
CG2 A:ILE721 4.8 22.2 1.0
CG1 A:ILE721 4.9 26.6 1.0
C B:THR566 4.9 26.8 1.0
NH2 A:ARG725 4.9 24.6 1.0

Iron binding site 2 out of 12 in 8xls

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Iron binding site 2 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe846

b:18.8
occ:1.00
 FE2 A:SF4846 0.0 18.8 1.0
SG A:CYS584 2.2 22.9 1.0
S3 A:SF4846 2.3 20.9 1.0
S4 A:SF4846 2.3 19.4 1.0
S1 A:SF4846 2.3 19.3 1.0
FE4 A:SF4846 2.7 19.6 1.0
FE1 A:SF4846 2.7 19.8 1.0
FE3 A:SF4846 2.7 17.8 1.0
CB A:CYS584 3.2 25.0 1.0
CA A:CYS584 3.9 25.0 1.0
S2 A:SF4846 3.9 18.9 1.0
CD1 B:ILE701 4.1 27.4 1.0
N A:CYS584 4.2 22.7 1.0
CE3 B:TRP666 4.2 39.8 1.0
CZ3 B:TRP666 4.4 37.9 1.0
CB A:CYS575 4.5 23.4 1.0
SG A:CYS575 4.5 26.4 1.0
SG B:CYS558 4.6 24.3 1.0
SG B:CYS567 4.8 28.5 1.0
CG1 B:ILE701 4.9 28.2 1.0

Iron binding site 3 out of 12 in 8xls

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Iron binding site 3 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe846

b:17.8
occ:1.00
 FE3 A:SF4846 0.0 17.8 1.0
SG A:CYS575 2.1 26.4 1.0
S2 A:SF4846 2.3 18.9 1.0
S4 A:SF4846 2.3 19.4 1.0
S1 A:SF4846 2.3 19.3 1.0
FE1 A:SF4846 2.7 19.8 1.0
FE4 A:SF4846 2.7 19.6 1.0
FE2 A:SF4846 2.7 18.8 1.0
CB A:CYS575 3.1 23.4 1.0
S3 A:SF4846 3.9 20.9 1.0
N B:PRO561 4.5 29.4 1.0
CD B:PRO561 4.5 25.4 1.0
CA A:CYS575 4.5 27.0 1.0
N A:GLY577 4.5 21.2 1.0
CD1 A:ILE721 4.6 28.0 1.0
CA A:GLY577 4.6 21.0 1.0
SG A:CYS584 4.6 22.9 1.0
CB B:PRO561 4.6 29.0 1.0
SG B:CYS558 4.7 24.3 1.0
SG B:CYS567 4.7 28.5 1.0
C B:GLY560 4.7 25.5 1.0
CA B:PRO561 4.8 31.4 1.0
C A:GLY577 4.9 22.9 1.0
N A:CYS575 4.9 26.9 1.0
CG B:PRO561 5.0 30.2 1.0
CA A:CYS584 5.0 25.0 1.0
CA B:GLY560 5.0 23.4 1.0
CB A:CYS584 5.0 25.0 1.0

Iron binding site 4 out of 12 in 8xls

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Iron binding site 4 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe846

b:19.6
occ:1.00
 FE4 A:SF4846 0.0 19.6 1.0
SG B:CYS558 2.1 24.3 1.0
S2 A:SF4846 2.3 18.9 1.0
S1 A:SF4846 2.3 19.3 1.0
S3 A:SF4846 2.3 20.9 1.0
FE3 A:SF4846 2.7 17.8 1.0
FE1 A:SF4846 2.7 19.8 1.0
FE2 A:SF4846 2.7 18.8 1.0
CB B:CYS558 3.0 28.2 1.0
S4 A:SF4846 3.9 19.4 1.0
N B:GLY560 4.3 24.7 1.0
CA B:GLY560 4.4 23.4 1.0
CA B:CYS558 4.4 30.2 1.0
N A:PRO578 4.6 23.5 1.0
CB A:PRO578 4.6 24.7 1.0
CD1 B:ILE701 4.6 27.4 1.0
CD A:PRO578 4.6 23.5 1.0
SG A:CYS584 4.7 22.9 1.0
SG A:CYS575 4.7 26.4 1.0
C B:GLY560 4.7 25.5 1.0
SG B:CYS567 4.8 28.5 1.0
CA B:CYS567 4.9 27.1 1.0
CA A:PRO578 4.9 24.9 1.0
N B:CYS558 4.9 31.5 1.0
C A:GLY577 5.0 22.9 1.0
C B:CYS558 5.0 32.7 1.0
CG A:PRO578 5.0 23.5 1.0
O B:GLY560 5.0 24.7 1.0

Iron binding site 5 out of 12 in 8xls

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Iron binding site 5 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:28.7
occ:1.00
 FE1 C:SF4101 0.0 28.7 1.0
S2 C:SF4101 2.3 23.7 1.0
S4 C:SF4101 2.3 28.8 1.0
S3 C:SF4101 2.3 27.9 1.0
SG C:CYS51 2.4 31.2 1.0
FE3 C:SF4101 2.7 23.0 1.0
FE4 C:SF4101 2.7 24.6 1.0
FE2 C:SF4101 2.7 24.3 1.0
N C:CYS51 3.4 25.1 1.0
N C:LYS52 3.5 26.9 1.0
CB C:CYS51 3.7 27.7 1.0
S1 C:SF4101 3.9 22.8 1.0
CA C:CYS51 3.9 25.9 1.0
CD C:PRO22 3.9 32.7 1.0
C C:CYS51 4.1 28.4 1.0
N C:GLY50 4.2 26.7 1.0
N C:ARG53 4.2 24.3 1.0
C C:GLY50 4.2 25.9 1.0
CA C:LYS52 4.4 26.0 1.0
CG C:PRO22 4.4 31.1 1.0
CA C:GLY50 4.5 24.0 1.0
CG2 C:VAL49 4.5 36.6 1.0
SG C:CYS48 4.7 27.4 1.0
SG C:CYS54 4.7 27.6 1.0
C C:LYS52 4.8 26.4 1.0
SG C:CYS21 4.8 29.0 1.0
N C:CYS54 4.9 28.6 1.0
N C:VAL49 4.9 28.8 1.0
CB C:ARG53 5.0 30.5 1.0

Iron binding site 6 out of 12 in 8xls

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Iron binding site 6 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:24.3
occ:1.00
 FE2 C:SF4101 0.0 24.3 1.0
S4 C:SF4101 2.3 28.8 1.0
S3 C:SF4101 2.3 27.9 1.0
S1 C:SF4101 2.3 22.8 1.0
SG C:CYS21 2.3 29.0 1.0
FE3 C:SF4101 2.7 23.0 1.0
FE4 C:SF4101 2.7 24.6 1.0
FE1 C:SF4101 2.7 28.7 1.0
CB C:CYS21 3.4 24.6 1.0
CA C:CYS21 3.8 28.8 1.0
CD C:PRO22 3.8 32.7 1.0
S2 C:SF4101 3.9 23.7 1.0
CG2 C:VAL25 4.0 35.7 1.0
CB C:VAL25 4.2 32.5 1.0
OG1 C:THR23 4.3 36.5 1.0
N C:PRO22 4.4 32.7 1.0
C C:CYS21 4.5 29.9 1.0
SG C:CYS51 4.7 31.2 1.0
CG C:PRO22 4.8 31.1 1.0
SG C:CYS48 4.8 27.4 1.0
SG C:CYS54 4.9 27.6 1.0
N C:THR23 4.9 31.7 1.0
N C:VAL25 4.9 34.1 1.0
N C:CYS21 4.9 30.4 1.0
CG C:LEU26 5.0 38.9 1.0

Iron binding site 7 out of 12 in 8xls

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Iron binding site 7 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:23.0
occ:1.00
 FE3 C:SF4101 0.0 23.0 1.0
S1 C:SF4101 2.3 22.8 1.0
S2 C:SF4101 2.3 23.7 1.0
S4 C:SF4101 2.3 28.8 1.0
SG C:CYS54 2.4 27.6 1.0
FE2 C:SF4101 2.7 24.3 1.0
FE1 C:SF4101 2.7 28.7 1.0
FE4 C:SF4101 2.7 24.6 1.0
CB C:CYS54 3.3 27.8 1.0
CG2 C:VAL67 3.9 32.8 1.0
S3 C:SF4101 3.9 27.9 1.0
N C:CYS54 4.0 28.6 1.0
CA C:CYS54 4.3 29.5 1.0
N C:LYS52 4.5 26.9 1.0
CA C:LYS52 4.5 26.0 1.0
SG C:CYS48 4.7 27.4 1.0
N C:ARG53 4.7 24.3 1.0
SG C:CYS21 4.8 29.0 1.0
SG C:CYS51 4.8 31.2 1.0
CD1 C:LEU26 4.8 37.9 1.0
C C:LYS52 4.9 26.4 1.0

Iron binding site 8 out of 12 in 8xls

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Iron binding site 8 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:24.6
occ:1.00
 FE4 C:SF4101 0.0 24.6 1.0
SG C:CYS48 2.2 27.4 1.0
S1 C:SF4101 2.3 22.8 1.0
S3 C:SF4101 2.3 27.9 1.0
S2 C:SF4101 2.3 23.7 1.0
FE2 C:SF4101 2.7 24.3 1.0
FE1 C:SF4101 2.7 28.7 1.0
FE3 C:SF4101 2.7 23.0 1.0
CB C:CYS48 3.3 27.1 1.0
CA C:CYS48 3.7 28.2 1.0
N C:GLY50 3.8 26.7 1.0
S4 C:SF4101 3.9 28.8 1.0
N C:VAL49 4.0 28.8 1.0
C C:CYS48 4.2 30.2 1.0
CA C:GLY50 4.3 24.0 1.0
CG2 C:VAL25 4.3 35.7 1.0
CG2 C:VAL5 4.5 30.4 1.0
CG2 C:VAL67 4.7 32.8 1.0
N C:CYS51 4.7 25.1 1.0
CB C:VAL25 4.8 32.5 1.0
SG C:CYS21 4.8 29.0 1.0
C C:VAL49 4.9 30.1 1.0
CG1 C:VAL67 4.9 30.3 1.0
C C:GLY50 4.9 25.9 1.0
SG C:CYS54 5.0 27.6 1.0

Iron binding site 9 out of 12 in 8xls

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Iron binding site 9 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:28.9
occ:1.00
 FE1 C:SF4102 0.0 28.9 1.0
S2 C:SF4102 2.3 30.8 1.0
S4 C:SF4102 2.3 29.4 1.0
S3 C:SF4102 2.3 29.4 1.0
SG C:CYS58 2.4 33.0 1.0
FE3 C:SF4102 2.7 27.8 1.0
FE4 C:SF4102 2.7 26.0 1.0
FE2 C:SF4102 2.7 30.0 1.0
CB C:CYS58 3.2 28.2 1.0
CA C:CYS58 3.7 31.7 1.0
S1 C:SF4102 3.9 29.9 1.0
CD C:PRO59 3.9 38.5 1.0
CB C:SER64 4.0 28.0 1.0
CG1 C:VAL65 4.3 24.9 1.0
N C:PRO59 4.5 36.6 1.0
C C:CYS58 4.5 34.3 1.0
SG C:CYS14 4.5 36.5 1.0
OG C:SER64 4.6 29.4 1.0
N C:VAL65 4.6 31.0 1.0
SG C:CYS17 4.8 32.6 1.0
N C:SER64 4.8 36.5 1.0
CA C:SER64 4.8 32.0 1.0
CB C:CYS17 4.9 28.8 1.0
N C:CYS58 4.9 29.2 1.0
CG2 C:THR60 4.9 31.9 1.0
C C:SER64 4.9 31.0 1.0
SG C:CYS11 4.9 29.5 1.0
CB C:VAL65 4.9 27.9 1.0

Iron binding site 10 out of 12 in 8xls

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Iron binding site 10 out of 12 in the Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Psi-Fcpi of the Diatom Thalassiosira Pseudonana CCMP1335 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:30.0
occ:1.00
 FE2 C:SF4102 0.0 30.0 1.0
SG C:CYS17 2.3 32.6 1.0
S3 C:SF4102 2.3 29.4 1.0
S4 C:SF4102 2.3 29.4 1.0
S1 C:SF4102 2.3 29.9 1.0
FE4 C:SF4102 2.7 26.0 1.0
FE1 C:SF4102 2.7 28.9 1.0
FE3 C:SF4102 2.7 27.8 1.0
CB C:CYS17 3.2 28.8 1.0
N C:CYS17 3.8 30.2 1.0
S2 C:SF4102 3.9 30.8 1.0
CB C:ALA40 3.9 33.7 1.0
CA C:CYS17 4.1 30.1 1.0
SG C:CYS11 4.6 29.5 1.0
CG1 C:VAL65 4.7 24.9 1.0
SG C:CYS14 4.7 36.5 1.0
N C:GLN16 4.7 33.3 0.5
N C:GLN16 4.7 33.3 0.6
N C:THR15 4.9 34.9 1.0
CB C:VAL65 5.0 27.9 1.0
SG C:CYS58 5.0 33.0 1.0
N C:VAL18 5.0 32.1 1.0

Reference:

K.Kato, Y.Nakajima, J.Xing, M.Kumazawa, H.Ogawa, J.R.Shen, K.Ifuku, R.Nagao. Structural Basis For Molecular Assembly of Fucoxanthin Chlorophyll A/C-Binding Proteins in A Diatom Photosystem I Supercomplex Elife 2024.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.99858.2
Page generated: Wed Nov 13 09:55:54 2024

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