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Iron in PDB 4y28: The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.

Enzymatic activity of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.

All present enzymatic activity of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.:
1.97.1.12;

Protein crystallography data

The structure of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution., PDB code: 4y28 was solved by Y.Mazor, A.Brovikov, N.Nelson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.65 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.000, 201.900, 213.200, 90.00, 90.00, 90.00
R / Rfree (%) 25.9 / 26.8

Other elements in 4y28:

The structure of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. also contains other interesting chemical elements:

Magnesium (Mg) 156 atoms
Calcium (Ca) 1 atom

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. (pdb code 4y28). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution., PDB code: 4y28:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 4y28

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Iron binding site 1 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:99.9
occ:1.00
 FE1 A:SF43001 0.0 99.9 1.0
S4 A:SF43001 2.2 74.0 1.0
S3 A:SF43001 2.2 81.7 1.0
S2 A:SF43001 2.2 69.0 1.0
SG A:CYS581 2.6 80.4 1.0
FE2 A:SF43001 3.0 97.5 1.0
FE3 A:SF43001 3.1 97.0 1.0
FE4 A:SF43001 3.1 96.2 1.0
CB A:CYS581 3.2 77.0 1.0
S1 A:SF43001 3.8 95.1 1.0
N A:GLY583 4.1 69.8 1.0
CA A:GLY583 4.2 61.1 1.0
C A:GLY583 4.4 67.5 1.0
CG B:PRO562 4.5 56.6 1.0
O A:GLY583 4.5 65.8 1.0
CA A:CYS581 4.7 77.5 1.0
CD1 A:ILE727 4.8 55.0 1.0
N B:PRO562 4.8 77.5 1.0
CB A:CYS590 4.8 52.3 1.0
CD B:PRO562 4.9 69.3 1.0
C B:GLY561 4.9 90.7 1.0
CB B:PRO562 4.9 57.4 1.0
N A:PRO584 4.9 71.9 1.0
CA A:CYS590 4.9 67.7 1.0

Iron binding site 2 out of 12 in 4y28

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Iron binding site 2 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:97.5
occ:1.00
 FE2 A:SF43001 0.0 97.5 1.0
S1 A:SF43001 2.2 95.1 1.0
S3 A:SF43001 2.2 81.7 1.0
S4 A:SF43001 2.2 74.0 1.0
SG B:CYS559 2.6 71.6 1.0
FE1 A:SF43001 3.0 99.9 1.0
CB B:CYS559 3.1 69.9 1.0
FE4 A:SF43001 3.1 96.2 1.0
FE3 A:SF43001 3.1 97.0 1.0
S2 A:SF43001 3.8 69.0 1.0
CD1 B:ILE702 4.3 53.6 1.0
N B:GLY561 4.4 65.6 1.0
CA B:CYS559 4.5 71.7 1.0
CB A:PRO584 4.5 61.3 1.0
CA B:GLY561 4.6 80.4 1.0
N A:PRO584 4.6 71.9 1.0
CD A:PRO584 4.6 64.9 1.0
O B:PRO558 4.8 65.0 1.0
CA B:CYS568 4.8 66.9 1.0
CA A:PRO584 4.8 69.3 1.0
C B:GLY561 4.9 90.7 1.0
CB B:CYS568 4.9 67.0 1.0
O B:GLY561 4.9 0.1 1.0
CG A:PRO584 4.9 54.6 1.0
C A:GLY583 5.0 67.5 1.0
N B:CYS559 5.0 62.3 1.0
N B:ASP560 5.0 68.4 1.0

Iron binding site 3 out of 12 in 4y28

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Iron binding site 3 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:97.0
occ:1.00
 FE3 A:SF43001 0.0 97.0 1.0
S2 A:SF43001 2.2 69.0 1.0
S1 A:SF43001 2.2 95.1 1.0
S4 A:SF43001 2.2 74.0 1.0
SG B:CYS568 2.7 75.3 1.0
FE1 A:SF43001 3.1 99.9 1.0
FE4 A:SF43001 3.1 96.2 1.0
FE2 A:SF43001 3.1 97.5 1.0
CB B:CYS568 3.1 67.0 1.0
S3 A:SF43001 3.8 81.7 1.0
CD1 A:ILE727 3.9 55.0 1.0
CZ3 B:TRP667 3.9 61.6 1.0
CA B:CYS568 4.0 66.9 1.0
N B:CYS568 4.2 67.6 1.0
CG2 A:ILE727 4.5 53.2 1.0
CE3 B:TRP667 4.5 63.1 1.0
CG1 A:ILE727 4.7 57.7 1.0
CH2 B:TRP667 4.8 65.2 1.0
NH2 A:ARG731 4.9 79.3 1.0

Iron binding site 4 out of 12 in 4y28

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Iron binding site 4 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3001

b:96.2
occ:1.00
 FE4 A:SF43001 0.0 96.2 1.0
S1 A:SF43001 2.2 95.1 1.0
S2 A:SF43001 2.2 69.0 1.0
S3 A:SF43001 2.2 81.7 1.0
SG A:CYS590 2.8 94.4 1.0
CB A:CYS590 3.0 52.3 1.0
FE3 A:SF43001 3.1 97.0 1.0
FE1 A:SF43001 3.1 99.9 1.0
FE2 A:SF43001 3.1 97.5 1.0
CD1 B:ILE702 3.8 53.6 1.0
S4 A:SF43001 3.8 74.0 1.0
CA A:CYS590 3.9 67.7 1.0
CE3 B:TRP667 4.0 63.1 1.0
N A:CYS590 4.2 72.3 1.0
CZ3 B:TRP667 4.3 61.6 1.0
CG1 B:ILE702 4.6 59.7 1.0
CG2 B:ILE702 4.8 62.7 1.0
CB A:CYS581 5.0 77.0 1.0

Iron binding site 5 out of 12 in 4y28

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Iron binding site 5 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:0.1
occ:1.00
 FE1 C:SF43002 0.0 0.1 1.0
S4 C:SF43002 2.1 97.1 1.0
S2 C:SF43002 2.1 73.9 1.0
S3 C:SF43002 2.1 77.7 1.0
FE3 C:SF43002 2.8 0.4 1.0
FE4 C:SF43002 2.9 0.5 1.0
SG C:CYS21 2.9 0.1 1.0
FE2 C:SF43002 3.0 0.1 1.0
CB C:CYS21 3.3 80.9 1.0
S1 C:SF43002 3.4 0.1 1.0
CG2 C:VAL25 3.8 73.0 1.0
CA C:CYS21 3.9 79.8 1.0
CB C:VAL25 3.9 80.3 1.0
CD C:PRO22 4.0 77.7 1.0
CD2 C:LEU26 4.2 86.2 1.0
OG1 C:THR23 4.2 75.6 1.0
N C:PRO22 4.6 76.1 1.0
C C:CYS21 4.7 82.4 1.0
N C:VAL25 4.7 82.1 1.0
CG1 C:VAL25 4.9 90.2 1.0
CB C:CYS48 4.9 87.2 1.0
N C:THR23 4.9 79.9 1.0
CA C:VAL25 5.0 78.8 1.0
CG C:PRO22 5.0 78.8 1.0

Iron binding site 6 out of 12 in 4y28

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Iron binding site 6 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:0.1
occ:1.00
 FE2 C:SF43002 0.0 0.1 1.0
S1 C:SF43002 2.1 0.1 1.0
S4 C:SF43002 2.1 97.1 1.0
S3 C:SF43002 2.1 77.7 1.0
SG C:CYS54 2.8 76.3 1.0
FE1 C:SF43002 3.0 0.1 1.0
FE3 C:SF43002 3.0 0.4 1.0
FE4 C:SF43002 3.1 0.5 1.0
CB C:CYS54 3.1 65.5 1.0
S2 C:SF43002 3.8 73.9 1.0
CG2 C:VAL67 3.9 60.4 1.0
N C:CYS54 4.0 78.1 1.0
CA C:CYS54 4.2 72.1 1.0
CA C:LYS52 4.5 63.7 1.0
CD2 C:LEU26 4.5 86.2 1.0
N C:LYS52 4.6 69.4 1.0
N C:ARG53 4.6 61.1 1.0
C C:LYS52 4.7 65.9 1.0

Iron binding site 7 out of 12 in 4y28

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Iron binding site 7 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:0.4
occ:1.00
 FE3 C:SF43002 0.0 0.4 1.0
S2 C:SF43002 2.1 73.9 1.0
S4 C:SF43002 2.1 97.1 1.0
S1 C:SF43002 2.1 0.1 1.0
FE1 C:SF43002 2.8 0.1 1.0
SG C:CYS51 2.9 81.7 1.0
FE2 C:SF43002 3.0 0.1 1.0
FE4 C:SF43002 3.1 0.5 1.0
N C:CYS51 3.5 77.9 1.0
N C:LYS52 3.6 69.4 1.0
S3 C:SF43002 3.7 77.7 1.0
CD C:PRO22 3.9 77.7 1.0
CG2 C:VAL49 4.1 67.6 1.0
CB C:CYS51 4.1 87.8 1.0
CA C:CYS51 4.1 78.5 1.0
N C:GLY50 4.1 69.7 1.0
N C:ARG53 4.2 61.1 1.0
C C:CYS51 4.2 75.8 1.0
CG C:PRO22 4.4 78.8 1.0
C C:GLY50 4.4 78.1 1.0
CA C:LYS52 4.5 63.7 1.0
CA C:GLY50 4.5 65.4 1.0
C C:LYS52 4.8 65.9 1.0
N C:VAL49 4.9 81.2 1.0
CB C:ARG53 4.9 61.3 1.0
N C:CYS54 5.0 78.1 1.0

Iron binding site 8 out of 12 in 4y28

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Iron binding site 8 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3002

b:0.5
occ:1.00
 FE4 C:SF43002 0.0 0.5 1.0
S2 C:SF43002 2.1 73.9 1.0
S1 C:SF43002 2.1 0.1 1.0
S3 C:SF43002 2.1 77.7 1.0
SG C:CYS48 2.7 91.8 1.0
FE1 C:SF43002 2.9 0.1 1.0
CB C:CYS48 2.9 87.2 1.0
FE3 C:SF43002 3.1 0.4 1.0
FE2 C:SF43002 3.1 0.1 1.0
S4 C:SF43002 3.7 97.1 1.0
CA C:CYS48 3.8 90.0 1.0
N C:GLY50 3.9 69.7 1.0
N C:VAL49 3.9 81.2 1.0
CG2 C:VAL25 4.1 73.0 1.0
C C:CYS48 4.3 86.8 1.0
CA C:GLY50 4.4 65.4 1.0
CG2 C:VAL5 4.4 71.2 1.0
CB C:VAL25 4.6 80.3 1.0
CG2 C:VAL67 4.8 60.4 1.0
CG1 C:VAL25 4.8 90.2 1.0
CG1 C:VAL67 4.9 65.4 1.0
C C:VAL49 4.9 74.1 1.0
CA C:VAL49 5.0 78.6 1.0

Iron binding site 9 out of 12 in 4y28

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Iron binding site 9 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3003

b:0.6
occ:1.00
 FE1 C:SF43003 0.0 0.6 1.0
S4 C:SF43003 2.1 0.9 1.0
S3 C:SF43003 2.1 0.5 1.0
S2 C:SF43003 2.1 89.7 1.0
SG C:CYS14 2.6 83.7 1.0
FE3 C:SF43003 2.7 0.1 1.0
FE2 C:SF43003 2.9 0.7 1.0
FE4 C:SF43003 2.9 0.0 1.0
CB C:CYS14 3.5 95.5 1.0
N C:THR15 3.6 74.7 1.0
S1 C:SF43003 3.6 92.6 1.0
N C:CYS14 3.7 92.8 1.0
CA C:CYS14 4.0 90.1 1.0
N C:GLN16 4.0 87.6 1.0
CD C:PRO59 4.0 58.0 1.0
C C:CYS14 4.2 79.7 1.0
CA C:THR15 4.4 84.8 1.0
SG C:CYS17 4.5 78.8 1.0
C C:THR15 4.6 85.4 1.0
C C:GLY13 4.7 92.5 1.0
N C:GLY13 4.8 88.6 1.0
CG1 C:ILE12 4.8 73.5 1.0
N C:CYS17 4.8 73.7 1.0
CB C:GLN16 4.8 73.1 1.0
SG C:CYS58 4.9 88.5 1.0
CA C:GLN16 4.9 82.5 1.0
CG C:PRO59 4.9 65.1 1.0

Iron binding site 10 out of 12 in 4y28

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Iron binding site 10 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe3003

b:0.7
occ:1.00
 FE2 C:SF43003 0.0 0.7 1.0
S3 C:SF43003 2.1 0.5 1.0
S4 C:SF43003 2.1 0.9 1.0
S1 C:SF43003 2.1 92.6 1.0
SG C:CYS11 2.6 80.2 1.0
FE3 C:SF43003 2.8 0.1 1.0
FE1 C:SF43003 2.9 0.6 1.0
FE4 C:SF43003 2.9 0.0 1.0
CB C:CYS11 3.2 85.6 1.0
CA C:CYS11 3.5 89.4 1.0
S2 C:SF43003 3.7 89.7 1.0
N C:ILE12 3.7 85.7 1.0
C C:CYS11 4.0 84.9 1.0
N C:GLY13 4.1 88.6 1.0
CB C:SER64 4.3 68.0 1.0
OG C:SER64 4.7 71.9 1.0
N C:CYS11 4.8 89.1 1.0
CA C:GLY13 4.8 94.1 1.0
CB C:ALA40 4.8 62.2 1.0
CA C:ILE12 4.8 84.7 1.0
N C:CYS14 4.8 92.8 1.0
C C:ILE12 4.9 89.9 1.0
SG C:CYS58 5.0 88.5 1.0

Reference:

Y.Mazor, A.Borovikova, N.Nelson. The Structure of Plant Photosystem I Super-Complex at 2.8 Angstrom Resolution. Elife V. 4 07433 2015.
ISSN: ESSN 2050-084X
PubMed: 26076232
DOI: 10.7554/ELIFE.07433
Page generated: Mon Aug 5 16:05:26 2024

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