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Iron in PDB 5l8r: The Structure of Plant Photosystem I Super-Complex at 2.6 Angstrom Resolution.

Enzymatic activity of The Structure of Plant Photosystem I Super-Complex at 2.6 Angstrom Resolution.

All present enzymatic activity of The Structure of Plant Photosystem I Super-Complex at 2.6 Angstrom Resolution.:
1.97.1.12;

Protein crystallography data

The structure of The Structure of Plant Photosystem I Super-Complex at 2.6 Angstrom Resolution., PDB code: 5l8r was solved by Y.Mazor, A.Borovikova, I.Caspy, N.Nelson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.91 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 189.611, 200.994, 212.943, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 23.2

Other elements in 5l8r:

The structure of The Structure of Plant Photosystem I Super-Complex at 2.6 Angstrom Resolution. also contains other interesting chemical elements:

Magnesium (Mg) 156 atoms
Calcium (Ca) 2 atoms

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 2.6 Angstrom Resolution. (pdb code 5l8r). 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 2.6 Angstrom Resolution., PDB code: 5l8r:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 5l8r

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Iron binding site 1 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe843

b:0.2
occ:1.00
 FE1 A:SF4843 0.0 0.2 1.0
S4 A:SF4843 2.2 45.5 1.0
S3 A:SF4843 2.3 78.0 1.0
S2 A:SF4843 2.3 0.9 1.0
SG A:CYS581 2.6 65.5 1.0
FE2 A:SF4843 2.7 59.6 1.0
FE3 A:SF4843 2.7 60.0 1.0
FE4 A:SF4843 2.7 91.3 1.0
CB A:CYS581 2.9 46.7 1.0
S1 A:SF4843 3.8 85.1 1.0
N A:GLY583 4.4 48.1 1.0
CB A:CYS590 4.4 46.9 1.0
CA A:CYS581 4.4 47.1 1.0
CA A:GLY583 4.4 47.9 1.0
CA A:CYS590 4.5 47.3 1.0
C A:GLY583 4.6 58.8 1.0
O A:PRO580 4.8 47.9 1.0
SG A:CYS590 4.8 75.6 1.0
CD B:PRO562 4.8 55.0 1.0
N A:CYS590 4.9 48.0 1.0
O A:GLY583 4.9 48.5 1.0
CD1 A:ILE727 4.9 44.4 1.0
N A:CYS581 4.9 49.6 1.0
C A:PRO580 5.0 46.2 1.0
SG B:CYS559 5.0 46.4 1.0

Iron binding site 2 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 2 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe843

b:59.6
occ:1.00
 FE2 A:SF4843 0.0 59.6 1.0
S3 A:SF4843 2.2 78.0 1.0
S4 A:SF4843 2.2 45.5 1.0
S1 A:SF4843 2.3 85.1 1.0
SG B:CYS559 2.4 46.4 1.0
FE1 A:SF4843 2.7 0.2 1.0
FE4 A:SF4843 2.7 91.3 1.0
FE3 A:SF4843 2.7 60.0 1.0
CB B:CYS559 3.5 61.0 1.0
S2 A:SF4843 3.9 0.9 1.0
N A:PRO584 4.3 48.8 1.0
CD A:PRO584 4.4 48.0 1.0
C A:GLY583 4.5 58.8 1.0
CB A:PRO584 4.6 48.4 1.0
CD1 B:ILE702 4.6 51.1 1.0
CA A:PRO584 4.6 48.6 1.0
N B:GLY561 4.6 46.5 1.0
CA B:GLY561 4.6 46.5 1.0
CA A:GLY583 4.8 47.9 1.0
C B:GLY561 4.9 45.9 1.0
CA B:CYS559 4.9 46.3 1.0
SG A:CYS581 4.9 65.5 1.0
CG A:PRO584 5.0 50.9 1.0

Iron binding site 3 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 3 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe843

b:60.0
occ:1.00
 FE3 A:SF4843 0.0 60.0 1.0
S2 A:SF4843 2.3 0.9 1.0
S4 A:SF4843 2.3 45.5 1.0
S1 A:SF4843 2.3 85.1 1.0
SG B:CYS568 2.7 65.7 1.0
FE1 A:SF4843 2.7 0.2 1.0
FE4 A:SF4843 2.7 91.3 1.0
FE2 A:SF4843 2.7 59.6 1.0
CB B:CYS568 3.3 65.2 1.0
S3 A:SF4843 3.8 78.0 1.0
CA B:CYS568 4.0 44.4 1.0
CZ3 B:TRP667 4.0 45.0 1.0
CD1 A:ILE727 4.2 44.4 1.0
N B:CYS568 4.2 44.3 1.0
SG B:CYS559 4.6 46.4 1.0
CE3 B:TRP667 4.6 45.5 1.0
CG2 A:ILE727 4.7 44.3 1.0
CB B:CYS559 4.8 61.0 1.0
SG A:CYS581 4.9 65.5 1.0
CG1 A:ILE727 4.9 43.9 1.0

Iron binding site 4 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 4 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe843

b:91.3
occ:1.00
 FE4 A:SF4843 0.0 91.3 1.0
S1 A:SF4843 2.3 85.1 1.0
S3 A:SF4843 2.3 78.0 1.0
S2 A:SF4843 2.3 0.9 1.0
FE2 A:SF4843 2.7 59.6 1.0
SG A:CYS590 2.7 75.6 1.0
FE3 A:SF4843 2.7 60.0 1.0
FE1 A:SF4843 2.7 0.2 1.0
CB A:CYS590 3.1 46.9 1.0
S4 A:SF4843 3.8 45.5 1.0
CE3 B:TRP667 4.0 45.5 1.0
CA A:CYS590 4.0 47.3 1.0
CZ3 B:TRP667 4.2 45.0 1.0
CD1 B:ILE702 4.2 51.1 1.0
N A:CYS590 4.3 48.0 1.0
CG2 B:ILE702 4.8 58.6 1.0
CB A:CYS581 4.8 46.7 1.0
SG B:CYS559 4.8 46.4 1.0
CG1 B:ILE702 4.9 48.3 1.0
O B:HOH959 4.9 45.9 1.0

Iron binding site 5 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 5 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:53.7
occ:1.00
 FE1 C:SF4101 0.0 53.7 1.0
S4 C:SF4101 2.3 61.9 1.0
S2 C:SF4101 2.3 57.5 1.0
S3 C:SF4101 2.3 74.5 1.0
SG C:CYS21 2.7 58.0 1.0
FE2 C:SF4101 2.7 58.6 1.0
FE4 C:SF4101 2.7 54.2 1.0
FE3 C:SF4101 2.7 63.2 1.0
CB C:CYS21 3.3 54.6 1.0
CA C:CYS21 3.8 70.4 1.0
S1 C:SF4101 3.9 74.5 1.0
CD C:PRO22 3.9 59.4 1.0
CG2 C:VAL25 4.2 56.8 1.0
CB C:VAL25 4.2 56.9 1.0
OG1 C:THR23 4.3 76.2 1.0
N C:PRO22 4.5 65.2 1.0
C C:CYS21 4.6 71.9 1.0
CD1 C:LEU26 4.7 57.7 1.0
SG C:CYS54 4.9 51.5 1.0
SG C:CYS51 5.0 68.5 1.0
N C:CYS21 5.0 65.3 1.0

Iron binding site 6 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 6 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:58.6
occ:1.00
 FE2 C:SF4101 0.0 58.6 1.0
S3 C:SF4101 2.3 74.5 1.0
S4 C:SF4101 2.3 61.9 1.0
S1 C:SF4101 2.3 74.5 1.0
SG C:CYS54 2.5 51.5 1.0
FE1 C:SF4101 2.7 53.7 1.0
FE4 C:SF4101 2.7 54.2 1.0
FE3 C:SF4101 2.8 63.2 1.0
CB C:CYS54 3.5 60.2 1.0
CG2 C:VAL67 3.8 63.9 1.0
S2 C:SF4101 3.9 57.5 1.0
N C:CYS54 4.1 57.9 1.0
N C:LYS52 4.4 53.3 1.0
CA C:LYS52 4.4 52.2 1.0
CA C:CYS54 4.5 51.0 1.0
N C:ARG53 4.6 49.7 1.0
CD1 C:LEU26 4.7 57.7 1.0
C C:LYS52 4.8 57.6 1.0

Iron binding site 7 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 7 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:63.2
occ:1.00
 FE3 C:SF4101 0.0 63.2 1.0
S2 C:SF4101 2.3 57.5 1.0
S4 C:SF4101 2.3 61.9 1.0
S1 C:SF4101 2.3 74.5 1.0
SG C:CYS51 2.6 68.5 1.0
FE1 C:SF4101 2.7 53.7 1.0
FE4 C:SF4101 2.8 54.2 1.0
FE2 C:SF4101 2.8 58.6 1.0
N C:CYS51 3.5 71.2 1.0
N C:LYS52 3.6 53.3 1.0
S3 C:SF4101 3.9 74.5 1.0
CD C:PRO22 3.9 59.4 1.0
CB C:CYS51 3.9 69.2 1.0
CA C:CYS51 4.0 65.7 1.0
C C:CYS51 4.2 61.3 1.0
N C:ARG53 4.2 49.7 1.0
N C:GLY50 4.2 57.4 1.0
C C:GLY50 4.4 63.0 1.0
CG2 C:VAL49 4.4 53.3 1.0
CA C:LYS52 4.4 52.2 1.0
CG C:PRO22 4.5 65.6 1.0
CA C:GLY50 4.6 51.8 1.0
C C:LYS52 4.8 57.6 1.0
SG C:CYS54 4.9 51.5 1.0
N C:VAL49 5.0 64.7 1.0
SG C:CYS21 5.0 58.0 1.0
CB C:ARG53 5.0 50.3 1.0

Iron binding site 8 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 8 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe101

b:54.2
occ:1.00
 FE4 C:SF4101 0.0 54.2 1.0
S3 C:SF4101 2.3 74.5 1.0
S1 C:SF4101 2.3 74.5 1.0
S2 C:SF4101 2.3 57.5 1.0
SG C:CYS48 2.6 55.3 1.0
FE1 C:SF4101 2.7 53.7 1.0
FE2 C:SF4101 2.7 58.6 1.0
FE3 C:SF4101 2.8 63.2 1.0
CB C:CYS48 3.5 68.7 1.0
N C:GLY50 3.8 57.4 1.0
S4 C:SF4101 3.9 61.9 1.0
CA C:CYS48 3.9 71.8 1.0
N C:VAL49 4.1 64.7 1.0
C C:CYS48 4.3 57.7 1.0
CA C:GLY50 4.3 51.8 1.0
CG2 C:VAL5 4.5 54.6 1.0
CG2 C:VAL25 4.5 56.8 1.0
CG1 C:VAL67 4.7 51.8 1.0
CG2 C:VAL67 4.7 63.9 1.0
N C:CYS51 4.8 71.2 1.0
CB C:VAL25 4.8 56.9 1.0
C C:VAL49 4.9 65.7 1.0
C C:GLY50 5.0 63.0 1.0

Iron binding site 9 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 9 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:0.9
occ:1.00
 FE1 C:SF4102 0.0 0.9 1.0
S4 C:SF4102 2.3 67.8 1.0
S3 C:SF4102 2.3 0.6 1.0
S2 C:SF4102 2.3 1.0 1.0
SG C:CYS14 2.6 65.5 1.0
FE2 C:SF4102 2.7 72.7 1.0
FE3 C:SF4102 2.7 0.3 1.0
FE4 C:SF4102 2.7 0.3 1.0
N C:CYS14 3.6 60.3 1.0
CB C:CYS14 3.8 68.6 1.0
S1 C:SF4102 3.9 82.8 1.0
CD C:PRO59 4.0 51.7 1.0
N C:THR15 4.1 56.2 1.0
CA C:CYS14 4.1 63.4 1.0
N C:GLN16 4.3 61.8 1.0
C C:CYS14 4.4 66.6 1.0
N C:GLY13 4.6 69.6 1.0
SG C:CYS17 4.6 65.1 1.0
CG C:PRO59 4.7 52.1 1.0
C C:GLY13 4.7 65.1 1.0
CG1 C:ILE12 4.8 55.4 1.0
N C:CYS17 4.8 62.3 1.0
CA C:GLY13 4.8 57.9 1.0
CB C:GLN16 4.9 52.9 1.0
CA C:THR15 5.0 72.3 1.0

Iron binding site 10 out of 12 in 5l8r

Go back to Iron Binding Sites List in 5l8r
Iron binding site 10 out of 12 in the The Structure of Plant Photosystem I Super-Complex at 2.6 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 2.6 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe102

b:72.7
occ:1.00
 FE2 C:SF4102 0.0 72.7 1.0
S4 C:SF4102 2.3 67.8 1.0
S3 C:SF4102 2.3 0.6 1.0
S1 C:SF4102 2.3 82.8 1.0
SG C:CYS11 2.6 73.1 1.0
FE1 C:SF4102 2.7 0.9 1.0
FE3 C:SF4102 2.7 0.3 1.0
FE4 C:SF4102 2.7 0.3 1.0
CB C:CYS11 3.3 59.8 1.0
N C:GLY13 3.8 69.6 1.0
CA C:CYS11 3.8 56.1 1.0
S2 C:SF4102 3.9 1.0 1.0
N C:ILE12 4.0 63.4 1.0
C C:CYS11 4.3 62.5 1.0
CA C:GLY13 4.3 57.9 1.0
CB C:ALA40 4.4 56.9 1.0
SG C:CYS17 4.5 65.1 1.0
N C:CYS14 4.6 60.3 1.0
CB C:SER64 4.7 65.2 1.0
N C:ALA40 4.8 58.5 1.0
C C:ILE12 4.8 73.0 1.0
CA C:ILE12 5.0 62.8 1.0
C C:GLY13 5.0 65.1 1.0

Reference:

Y.Mazor, A.Borovikova, I.Caspy, N.Nelson. Structure of the Plant Photosystem I Supercomplex at 2.6 Angstrom Resolution. Nat Plants V. 3 17014 2017.
ISSN: ESSN 2055-0278
PubMed: 28248295
DOI: 10.1038/NPLANTS.2017.14
Page generated: Sun Dec 13 16:06:48 2020

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