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Iron in PDB 3lw5: Improved Model of Plant Photosystem I

Protein crystallography data

The structure of Improved Model of Plant Photosystem I, PDB code: 3lw5 was solved by N.Nelson, H.Toporik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 120.655, 189.086, 129.388, 90.00, 91.24, 90.00
R / Rfree (%) 34.9 / 38.3

Other elements in 3lw5:

The structure of Improved Model of Plant Photosystem I also contains other interesting chemical elements:

Magnesium (Mg) 174 atoms

Iron Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iron atom in the Improved Model of Plant Photosystem I (pdb code 3lw5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the Improved Model of Plant Photosystem I, PDB code: 3lw5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 3lw5

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Iron binding site 1 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe8001

b:18.0
occ:1.00
 FE1 A:SF48001 0.0 18.0 1.0
S4 A:SF48001 2.1 17.2 1.0
S3 A:SF48001 2.1 19.7 1.0
S2 A:SF48001 2.1 21.2 1.0
FE3 A:SF48001 2.5 18.1 1.0
FE4 A:SF48001 2.5 16.4 1.0
FE2 A:SF48001 2.5 15.8 1.0
SG A:CYS581 2.6 18.0 1.0
SG A:CYS590 3.2 16.7 1.0
SG B:CYS559 3.2 17.2 1.0
S1 A:SF48001 3.6 12.6 1.0
N A:PRO584 3.9 17.0 1.0
CD A:PRO584 4.0 17.0 1.0
CD1 B:ILE702 4.1 13.1 1.0
CB A:CYS581 4.2 17.7 1.0
O B:ASP560 4.2 17.7 1.0
CA A:GLY583 4.2 17.2 1.0
C A:GLY583 4.2 17.1 1.0
CA A:PRO584 4.4 16.9 1.0
N A:GLY583 4.5 17.4 1.0
CG A:PRO584 4.6 16.9 1.0
CB A:CYS590 4.6 16.1 1.0
O A:GLY588 4.6 16.2 1.0
O A:THR589 4.6 16.2 1.0
CA A:CYS590 4.7 16.2 1.0
CB B:CYS559 4.9 17.1 1.0
O A:CYS581 4.9 18.0 1.0

Iron binding site 2 out of 12 in 3lw5

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Iron binding site 2 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe8001

b:15.8
occ:1.00
 FE2 A:SF48001 0.0 15.8 1.0
S3 A:SF48001 2.1 19.7 1.0
S1 A:SF48001 2.1 12.6 1.0
S4 A:SF48001 2.1 17.2 1.0
FE3 A:SF48001 2.5 18.1 1.0
FE4 A:SF48001 2.5 16.4 1.0
FE1 A:SF48001 2.5 18.0 1.0
O B:ASP560 3.1 17.7 1.0
SG A:CYS581 3.3 18.0 1.0
S2 A:SF48001 3.6 21.2 1.0
O B:THR567 3.7 17.5 1.0
SG B:CYS559 3.8 17.2 1.0
SG B:CYS568 3.8 16.6 1.0
N B:PRO562 4.3 17.7 1.0
C B:ASP560 4.3 17.6 1.0
CD1 A:ILE727 4.4 13.8 1.0
C B:GLY561 4.4 17.6 1.0
CD B:PRO562 4.5 17.8 1.0
CA B:PRO562 4.6 17.7 1.0
SG A:CYS590 4.7 16.7 1.0
O B:GLY561 4.7 17.7 1.0
CB B:PRO562 4.8 17.8 1.0
CA B:GLY561 4.9 17.5 1.0
C B:THR567 4.9 17.2 1.0
N B:ASP560 4.9 17.4 1.0

Iron binding site 3 out of 12 in 3lw5

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Iron binding site 3 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe8001

b:18.1
occ:1.00
 FE3 A:SF48001 0.0 18.1 1.0
S4 A:SF48001 2.1 17.2 1.0
S2 A:SF48001 2.1 21.2 1.0
S1 A:SF48001 2.1 12.6 1.0
SG B:CYS559 2.5 17.2 1.0
FE2 A:SF48001 2.5 15.8 1.0
FE1 A:SF48001 2.5 18.0 1.0
FE4 A:SF48001 2.5 16.4 1.0
SG A:CYS590 3.5 16.7 1.0
CB B:CYS559 3.6 17.1 1.0
SG B:CYS568 3.6 16.6 1.0
S3 A:SF48001 3.6 19.7 1.0
CD1 B:ILE702 4.1 13.1 1.0
O B:ASP560 4.1 17.7 1.0
SG A:CYS581 4.2 18.0 1.0
CA B:CYS559 4.2 17.1 1.0
O B:THR567 4.5 17.5 1.0
N B:ASP560 4.5 17.4 1.0
CG1 B:ILE702 4.8 12.0 1.0
CB B:CYS568 4.9 17.0 1.0
C B:CYS559 5.0 17.2 1.0

Iron binding site 4 out of 12 in 3lw5

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Iron binding site 4 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe8001

b:16.4
occ:1.00
 FE4 A:SF48001 0.0 16.4 1.0
S2 A:SF48001 2.1 21.2 1.0
S1 A:SF48001 2.1 12.6 1.0
S3 A:SF48001 2.1 19.7 1.0
SG A:CYS581 2.3 18.0 1.0
SG A:CYS590 2.5 16.7 1.0
FE1 A:SF48001 2.5 18.0 1.0
FE3 A:SF48001 2.5 18.1 1.0
FE2 A:SF48001 2.5 15.8 1.0
S4 A:SF48001 3.6 17.2 1.0
CB A:CYS581 3.6 17.7 1.0
CB A:CYS590 4.1 16.1 1.0
SG B:CYS568 4.2 16.6 1.0
CA A:CYS590 4.5 16.2 1.0
CD1 B:TRP667 4.6 14.5 1.0
SG B:CYS559 4.7 17.2 1.0
CA A:CYS581 4.8 17.8 1.0
NE1 B:TRP667 4.9 14.9 1.0
N A:CYS581 4.9 17.8 1.0

Iron binding site 5 out of 12 in 3lw5

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Iron binding site 5 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe8002

b:17.9
occ:1.00
 FE1 C:SF48002 0.0 17.9 1.0
S2 C:SF48002 2.1 28.6 1.0
S4 C:SF48002 2.1 16.3 1.0
S3 C:SF48002 2.1 16.1 1.0
FE4 C:SF48002 2.5 17.5 1.0
FE3 C:SF48002 2.5 24.6 1.0
FE2 C:SF48002 2.5 14.7 1.0
O C:VAL49 3.1 18.3 1.0
OD2 C:ASP24 3.1 21.7 1.0
SG C:CYS21 3.3 24.7 1.0
S1 C:SF48002 3.6 15.3 1.0
C C:VAL49 3.7 18.3 1.0
N C:CYS51 3.7 19.4 1.0
SG C:CYS51 3.8 21.3 1.0
CG C:ASP24 4.0 21.6 1.0
CB C:CYS51 4.1 19.7 1.0
N C:GLY50 4.2 18.5 1.0
CA C:GLY50 4.2 18.9 1.0
CB C:ASP24 4.2 21.3 1.0
C C:GLY50 4.5 19.1 1.0
CA C:CYS51 4.5 19.6 1.0
CG1 C:VAL49 4.6 17.9 1.0
N C:VAL49 4.6 18.1 1.0
CA C:VAL49 4.7 18.2 1.0
O C:CYS48 4.7 17.8 1.0
C C:CYS48 4.8 17.9 1.0
CB C:CYS48 4.9 17.9 1.0

Iron binding site 6 out of 12 in 3lw5

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Iron binding site 6 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe8002

b:14.7
occ:1.00
 FE2 C:SF48002 0.0 14.7 1.0
S1 C:SF48002 2.1 15.3 1.0
S4 C:SF48002 2.1 16.3 1.0
S3 C:SF48002 2.1 16.1 1.0
FE3 C:SF48002 2.5 24.6 1.0
FE4 C:SF48002 2.5 17.5 1.0
FE1 C:SF48002 2.5 17.9 1.0
SG C:CYS51 2.8 21.3 1.0
N C:CYS51 3.3 19.4 1.0
S2 C:SF48002 3.6 28.6 1.0
CB C:CYS54 3.7 19.7 1.0
CB C:CYS51 3.8 19.7 1.0
N C:LYS52 3.9 19.1 1.0
CA C:CYS51 3.9 19.6 1.0
SG C:CYS21 4.0 24.7 1.0
SG C:CYS54 4.2 20.4 1.0
C C:GLY50 4.3 19.1 1.0
C C:CYS51 4.5 19.3 1.0
CA C:GLY50 4.5 18.9 1.0
O C:VAL49 4.5 18.3 1.0
CA C:CYS54 4.7 19.8 1.0
N C:CYS54 4.7 19.5 1.0
CA C:LYS52 4.9 18.9 1.0
OD2 C:ASP24 4.9 21.7 1.0

Iron binding site 7 out of 12 in 3lw5

Go back to Iron Binding Sites List in 3lw5
Iron binding site 7 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe8002

b:24.6
occ:1.00
 FE3 C:SF48002 0.0 24.6 1.0
SG C:CYS21 1.6 24.7 1.0
S4 C:SF48002 2.1 16.3 1.0
S1 C:SF48002 2.1 15.3 1.0
S2 C:SF48002 2.1 28.6 1.0
FE2 C:SF48002 2.5 14.7 1.0
FE1 C:SF48002 2.5 17.9 1.0
FE4 C:SF48002 2.5 17.5 1.0
SG C:CYS51 2.5 21.3 1.0
CB C:CYS21 3.0 23.0 1.0
S3 C:SF48002 3.6 16.1 1.0
CB C:CYS51 3.8 19.7 1.0
CA C:CYS21 3.9 22.9 1.0
CB C:CYS54 4.0 19.7 1.0
SG C:CYS54 4.4 20.4 1.0
CA C:CYS54 4.4 19.8 1.0
N C:CYS54 4.4 19.5 1.0
C C:CYS21 4.6 22.6 1.0
CB C:ASP24 4.6 21.3 1.0
N C:CYS51 4.7 19.4 1.0
O C:ALA20 4.7 22.7 1.0
CD C:PRO22 4.7 22.2 1.0
OD2 C:ASP24 4.8 21.7 1.0
N C:PRO22 4.8 22.2 1.0
CA C:CYS51 4.8 19.6 1.0

Iron binding site 8 out of 12 in 3lw5

Go back to Iron Binding Sites List in 3lw5
Iron binding site 8 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe8002

b:17.5
occ:1.00
 FE4 C:SF48002 0.0 17.5 1.0
S3 C:SF48002 2.1 16.1 1.0
S1 C:SF48002 2.1 15.3 1.0
S2 C:SF48002 2.1 28.6 1.0
FE1 C:SF48002 2.5 17.9 1.0
FE2 C:SF48002 2.5 14.7 1.0
FE3 C:SF48002 2.5 24.6 1.0
SG C:CYS21 3.1 24.7 1.0
CB C:ASP24 3.2 21.3 1.0
OD2 C:ASP24 3.2 21.7 1.0
CG C:ASP24 3.4 21.6 1.0
S4 C:SF48002 3.6 16.3 1.0
SG C:CYS54 4.3 20.4 1.0
OD1 C:ASP24 4.4 21.9 1.0
CG1 C:VAL25 4.5 20.9 1.0
SG C:CYS51 4.5 21.3 1.0
O C:VAL49 4.7 18.3 1.0
CA C:ASP24 4.7 21.2 1.0
CB C:CYS21 4.7 23.0 1.0
CB C:CYS54 4.7 19.7 1.0

Iron binding site 9 out of 12 in 3lw5

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Iron binding site 9 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe8003

b:21.3
occ:1.00
 FE1 C:SF48003 0.0 21.3 1.0
S2 C:SF48003 2.1 14.4 1.0
S4 C:SF48003 2.1 15.1 1.0
S3 C:SF48003 2.1 20.6 1.0
SG C:CYS58 2.3 21.9 1.0
FE3 C:SF48003 2.5 19.8 1.0
FE2 C:SF48003 2.5 22.6 1.0
FE4 C:SF48003 2.5 18.6 1.0
CB C:CYS58 2.9 20.7 1.0
O C:GLY13 3.4 22.4 1.0
S1 C:SF48003 3.6 19.7 1.0
O C:CYS58 3.8 20.4 1.0
CG1 C:VAL18 4.0 22.0 1.0
C C:CYS58 4.0 20.5 1.0
CA C:CYS58 4.0 20.7 1.0
SG C:CYS17 4.3 21.8 1.0
CA C:ILE12 4.5 23.4 1.0
SG C:CYS11 4.5 24.9 1.0
O C:PRO59 4.5 20.1 1.0
C C:GLY13 4.5 22.6 1.0
CB C:CYS17 4.6 22.1 1.0
C C:ILE12 4.7 23.2 1.0
CB C:VAL18 4.7 21.7 1.0
N C:PRO59 4.8 20.5 1.0
N C:VAL18 4.8 21.8 1.0
N C:GLY13 5.0 23.0 1.0
N C:ILE12 5.0 23.4 1.0

Iron binding site 10 out of 12 in 3lw5

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Iron binding site 10 out of 12 in the Improved Model of Plant Photosystem I


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Improved Model of Plant Photosystem I within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe8003

b:22.6
occ:1.00
 FE2 C:SF48003 0.0 22.6 1.0
S3 C:SF48003 2.1 20.6 1.0
S4 C:SF48003 2.1 15.1 1.0
S1 C:SF48003 2.1 19.7 1.0
CA C:ILE12 2.3 23.4 1.0
FE1 C:SF48003 2.5 21.3 1.0
FE4 C:SF48003 2.5 18.6 1.0
FE3 C:SF48003 2.5 19.8 1.0
N C:ILE12 2.9 23.4 1.0
CB C:ILE12 3.1 23.4 1.0
C C:ILE12 3.1 23.2 1.0
CG1 C:ILE12 3.2 23.5 1.0
CG2 C:ILE12 3.4 23.5 1.0
S2 C:SF48003 3.6 14.4 1.0
O C:ILE12 3.7 23.2 1.0
SG C:CYS11 3.8 24.9 1.0
N C:GLY13 3.8 23.0 1.0
O C:GLY13 3.9 22.4 1.0
C C:CYS11 4.2 23.6 1.0
CD1 C:ILE12 4.3 24.0 1.0
SG C:CYS58 4.4 21.9 1.0
C C:GLY13 4.6 22.6 1.0
CB C:ASP9 4.7 22.6 1.0
O C:PRO59 4.9 20.1 1.0
CA C:GLY13 4.9 22.8 1.0
O C:CYS11 4.9 23.7 1.0

Reference:

A.Amunts, H.Toporik, A.Borovikova, N.Nelson. Structure Determination and Improved Model of Plant Photosystem I J.Biol.Chem. V. 285 3478 2010.
ISSN: ISSN 0021-9258
PubMed: 19923216
DOI: 10.1074/JBC.M109.072645
Page generated: Sun Aug 4 14:33:16 2024

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