Iron in PDB 7dkz: Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex

Enzymatic activity of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex

All present enzymatic activity of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex:
1.97.1.12;

Protein crystallography data

The structure of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex, PDB code: 7dkz was solved by J.Wang, L.J.Yu, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.41 / 2.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 225.652, 168.952, 185.224, 90, 121.39, 90
R / Rfree (%) 18.9 / 22.7

Other elements in 7dkz:

The structure of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex also contains other interesting chemical elements:

Magnesium (Mg) 152 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex (pdb code 7dkz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex, PDB code: 7dkz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 7dkz

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Iron binding site 1 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe852

b:74.1
occ:1.00
 FE1 A:SF4852 0.0 74.1 1.0
S4 A:SF4852 2.2 67.3 1.0
S3 A:SF4852 2.2 55.6 1.0
S2 A:SF4852 2.2 62.2 1.0
SG B:CYS568 2.3 68.4 1.0
FE2 A:SF4852 2.9 66.3 1.0
FE3 A:SF4852 2.9 73.2 1.0
FE4 A:SF4852 3.0 70.5 1.0
CB B:CYS568 3.1 57.6 1.0
S1 A:SF4852 3.7 71.1 1.0
CA B:CYS568 3.7 65.3 1.0
N B:CYS568 3.9 67.3 1.0
CZ3 B:TRP667 4.1 75.9 1.0
CD1 A:ILE727 4.2 65.6 1.0
CG2 A:ILE727 4.6 51.7 1.0
CE3 B:TRP667 4.7 69.0 1.0
CG1 A:ILE727 4.8 64.0 1.0
CB B:CYS559 4.9 72.6 1.0
SG B:CYS559 5.0 71.5 1.0
C B:THR567 5.0 60.5 1.0

Iron binding site 2 out of 12 in 7dkz

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Iron binding site 2 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe852

b:66.3
occ:1.00
 FE2 A:SF4852 0.0 66.3 1.0
S1 A:SF4852 2.2 71.1 1.0
S3 A:SF4852 2.2 55.6 1.0
S4 A:SF4852 2.2 67.3 1.0
SG A:CYS590 2.4 65.6 1.0
FE1 A:SF4852 2.9 74.1 1.0
FE4 A:SF4852 2.9 70.5 1.0
FE3 A:SF4852 3.0 73.2 1.0
CB A:CYS590 3.1 66.2 1.0
S2 A:SF4852 3.8 62.2 1.0
CA A:CYS590 3.8 67.7 1.0
CE3 B:TRP667 4.0 69.0 1.0
CD1 B:ILE702 4.1 68.4 1.0
N A:CYS590 4.1 66.1 1.0
CZ3 B:TRP667 4.3 75.9 1.0
CB A:CYS581 4.7 73.5 1.0
SG A:CYS581 4.8 72.1 1.0
CG1 B:ILE702 4.9 65.9 1.0
CG2 B:ILE702 4.9 64.8 1.0
NH2 A:ARG731 5.0 60.7 1.0
SG B:CYS568 5.0 68.4 1.0

Iron binding site 3 out of 12 in 7dkz

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Iron binding site 3 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe852

b:73.2
occ:1.00
 FE3 A:SF4852 0.0 73.2 1.0
S2 A:SF4852 2.1 62.2 1.0
S1 A:SF4852 2.2 71.1 1.0
S4 A:SF4852 2.2 67.3 1.0
SG A:CYS581 2.4 72.1 1.0
FE4 A:SF4852 2.9 70.5 1.0
FE1 A:SF4852 2.9 74.1 1.0
FE2 A:SF4852 3.0 66.3 1.0
CB A:CYS581 3.3 73.5 1.0
S3 A:SF4852 3.8 55.6 1.0
N A:GLY583 4.2 64.4 1.0
CA A:GLY583 4.3 65.4 1.0
CD B:PRO562 4.4 58.7 1.0
N B:PRO562 4.5 61.8 1.0
CB B:PRO562 4.5 58.7 1.0
CD1 A:ILE727 4.7 65.6 1.0
CA A:CYS581 4.7 73.6 1.0
C A:GLY583 4.7 64.8 1.0
C B:GLY561 4.8 62.2 1.0
CA B:PRO562 4.8 57.7 1.0
CG B:PRO562 4.9 57.3 1.0
CA B:GLY561 4.9 55.7 1.0
SG A:CYS590 4.9 65.6 1.0
CA A:CYS590 5.0 67.7 1.0

Iron binding site 4 out of 12 in 7dkz

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Iron binding site 4 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe852

b:70.5
occ:1.00
 FE4 A:SF4852 0.0 70.5 1.0
S1 A:SF4852 2.1 71.1 1.0
S2 A:SF4852 2.2 62.2 1.0
S3 A:SF4852 2.2 55.6 1.0
SG B:CYS559 2.4 71.5 1.0
FE3 A:SF4852 2.9 73.2 1.0
FE2 A:SF4852 2.9 66.3 1.0
FE1 A:SF4852 3.0 74.1 1.0
CB B:CYS559 3.3 72.6 1.0
S4 A:SF4852 3.8 67.3 1.0
N B:GLY561 4.3 65.5 1.0
CD A:PRO584 4.4 61.2 1.0
CA B:GLY561 4.4 55.7 1.0
CD1 B:ILE702 4.4 68.4 1.0
N A:PRO584 4.6 61.0 1.0
CA B:CYS559 4.7 68.7 1.0
CB A:PRO584 4.7 64.9 1.0
CA A:PRO584 4.8 65.9 1.0
C A:GLY583 4.9 64.8 1.0
O B:PRO558 4.9 67.1 1.0
CA B:CYS568 4.9 65.3 1.0
C B:GLY561 4.9 62.2 1.0
SG A:CYS590 5.0 65.6 1.0
CG A:PRO584 5.0 60.4 1.0

Iron binding site 5 out of 12 in 7dkz

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Iron binding site 5 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:84.7
occ:1.00
 FE1 C:SF4101 0.0 84.7 1.0
S2 C:SF4101 2.2 85.4 1.0
S4 C:SF4101 2.2 69.5 1.0
S3 C:SF4101 2.2 75.2 1.0
SG C:CYS51 2.4 81.1 1.0
FE2 C:SF4101 2.9 82.1 1.0
FE3 C:SF4101 2.9 75.2 1.0
FE4 C:SF4101 3.0 77.0 1.0
N C:CYS51 3.4 70.1 1.0
N C:LYS52 3.5 70.6 1.0
CB C:CYS51 3.7 70.5 1.0
S1 C:SF4101 3.8 79.6 1.0
CD C:PRO22 3.9 77.8 1.0
CA C:CYS51 3.9 67.1 1.0
N C:GLY50 4.1 77.7 1.0
C C:CYS51 4.1 69.0 1.0
N C:ARG53 4.2 66.7 1.0
C C:GLY50 4.2 71.0 1.0
CA C:LYS52 4.3 74.1 1.0
CA C:GLY50 4.4 71.8 1.0
CG2 C:VAL49 4.5 72.7 1.0
CG C:PRO22 4.5 75.2 1.0
C C:LYS52 4.8 73.3 1.0
N C:VAL49 4.9 80.5 1.0
SG C:CYS21 5.0 77.6 1.0
CB C:ARG53 5.0 78.2 1.0
SG C:CYS54 5.0 71.1 1.0

Iron binding site 6 out of 12 in 7dkz

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Iron binding site 6 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:82.1
occ:1.00
 FE2 C:SF4101 0.0 82.1 1.0
S4 C:SF4101 2.2 69.5 1.0
S3 C:SF4101 2.2 75.2 1.0
S1 C:SF4101 2.2 79.6 1.0
SG C:CYS21 2.5 77.6 1.0
FE1 C:SF4101 2.9 84.7 1.0
FE3 C:SF4101 2.9 75.2 1.0
FE4 C:SF4101 2.9 77.0 1.0
CB C:CYS21 3.3 66.5 1.0
CG2 C:VAL25 3.7 82.2 1.0
S2 C:SF4101 3.7 85.4 1.0
CA C:CYS21 3.8 80.0 1.0
CD C:PRO22 3.9 77.8 1.0
CB C:VAL25 4.1 81.5 1.0
N C:PRO22 4.5 83.6 1.0
C C:CYS21 4.5 85.9 1.0
OG1 C:THR23 4.6 77.8 1.0
CD1 C:LEU26 4.6 68.3 1.0
N C:VAL25 4.9 73.9 1.0
SG C:CYS51 4.9 81.1 1.0
SG C:CYS54 4.9 71.1 1.0
N C:CYS21 5.0 78.9 1.0

Iron binding site 7 out of 12 in 7dkz

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Iron binding site 7 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:75.2
occ:1.00
 FE3 C:SF4101 0.0 75.2 1.0
S4 C:SF4101 2.2 69.5 1.0
S1 C:SF4101 2.2 79.6 1.0
S2 C:SF4101 2.2 85.4 1.0
SG C:CYS54 2.4 71.1 1.0
FE2 C:SF4101 2.9 82.1 1.0
FE1 C:SF4101 2.9 84.7 1.0
FE4 C:SF4101 3.0 77.0 1.0
CB C:CYS54 3.4 73.1 1.0
CG2 C:VAL67 3.7 68.7 1.0
S3 C:SF4101 3.8 75.2 1.0
N C:CYS54 4.1 67.8 1.0
CA C:LYS52 4.3 74.1 1.0
CA C:CYS54 4.3 71.7 1.0
N C:LYS52 4.4 70.6 1.0
CD1 C:LEU26 4.7 68.3 1.0
N C:ARG53 4.7 66.7 1.0
C C:LYS52 4.8 73.3 1.0
SG C:CYS51 5.0 81.1 1.0
CB C:VAL67 5.0 68.5 1.0

Iron binding site 8 out of 12 in 7dkz

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Iron binding site 8 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:77.0
occ:1.00
 FE4 C:SF4101 0.0 77.0 1.0
S3 C:SF4101 2.2 75.2 1.0
S2 C:SF4101 2.2 85.4 1.0
S1 C:SF4101 2.2 79.6 1.0
SG C:CYS48 2.5 76.5 1.0
FE2 C:SF4101 2.9 82.1 1.0
FE1 C:SF4101 3.0 84.7 1.0
FE3 C:SF4101 3.0 75.2 1.0
CB C:CYS48 3.3 72.5 1.0
CA C:CYS48 3.7 74.2 1.0
N C:GLY50 3.8 77.7 1.0
S4 C:SF4101 3.8 69.5 1.0
N C:VAL49 3.9 80.5 1.0
CG2 C:VAL25 4.0 82.2 1.0
C C:CYS48 4.1 78.2 1.0
CA C:GLY50 4.2 71.8 1.0
CG2 C:VAL5 4.4 77.2 1.0
CB C:VAL25 4.7 81.5 1.0
CG2 C:VAL67 4.7 68.7 1.0
C C:VAL49 4.8 83.7 1.0
CG1 C:VAL25 4.9 76.3 1.0
CG1 C:VAL67 4.9 64.0 1.0
N C:CYS51 5.0 70.1 1.0
CA C:VAL49 5.0 83.2 1.0

Iron binding site 9 out of 12 in 7dkz

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Iron binding site 9 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:84.0
occ:1.00
 FE1 C:SF4102 0.0 84.0 1.0
S4 C:SF4102 2.2 75.6 1.0
S3 C:SF4102 2.2 75.3 1.0
S2 C:SF4102 2.2 75.3 1.0
SG C:CYS58 2.5 80.7 1.0
FE4 C:SF4102 2.9 85.5 1.0
FE3 C:SF4102 2.9 90.0 1.0
FE2 C:SF4102 3.1 76.8 1.0
CB C:CYS58 3.2 84.0 1.0
CB C:SER64 3.7 75.7 1.0
S1 C:SF4102 3.7 84.7 1.0
CA C:CYS58 3.8 79.3 1.0
CD C:PRO59 4.2 75.0 1.0
OG C:SER64 4.3 74.1 1.0
CG1 C:VAL65 4.3 65.3 1.0
N C:VAL65 4.5 73.3 1.0
N C:SER64 4.5 70.2 1.0
CA C:SER64 4.5 77.8 1.0
C C:CYS58 4.6 73.1 1.0
OG1 C:THR60 4.7 30.0 1.0
C C:SER64 4.7 78.6 1.0
N C:PRO59 4.7 76.9 1.0
CG2 C:THR60 4.8 30.0 1.0
N C:CYS58 4.9 69.4 1.0
CB C:VAL65 4.9 67.0 1.0
CG C:PRO59 5.0 77.4 1.0

Iron binding site 10 out of 12 in 7dkz

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Iron binding site 10 out of 12 in the Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:76.8
occ:1.00
 FE2 C:SF4102 0.0 76.8 1.0
S1 C:SF4102 2.2 84.7 1.0
S3 C:SF4102 2.2 75.3 1.0
S4 C:SF4102 2.2 75.6 1.0
SG C:CYS17 2.5 79.7 1.0
FE4 C:SF4102 3.0 85.5 1.0
FE3 C:SF4102 3.0 90.0 1.0
FE1 C:SF4102 3.1 84.0 1.0
CB C:CYS17 3.2 67.3 1.0
S2 C:SF4102 3.9 75.3 1.0
N C:CYS17 3.9 70.5 1.0
CB C:ALA40 3.9 72.4 1.0
CA C:CYS17 4.2 69.3 1.0
CG1 C:VAL65 4.5 65.3 1.0
CB C:VAL65 4.7 67.0 1.0
N C:GLN16 4.8 83.2 1.0
C C:THR15 5.0 78.2 1.0
N C:VAL18 5.0 77.3 1.0

Reference:

W.Wang, J.R.Shen. Structure of Plant Photosystem I-Light Harvesting Complex I Supercomplex at 2.4 A Resolution To Be Published.
Page generated: Sat Apr 3 15:54:44 2021

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