Iron in PDB 5oy0: Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution

All present enzymatic activity of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution:
1.97.1.12;

The structure of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution, PDB code: 5oy0 was solved by N.Nelson, T.Malavath, I.Caspy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.48 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	212.170, 137.622, 225.095, 90.00, 116.74, 90.00
R / Rfree (%)	22.8 / 26.4

The structure of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	287 atoms
Calcium	(Ca)	6 atoms
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution (pdb code 5oy0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution, PDB code: 5oy0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:0.8 occ:1.00 FE1 A:SF43001 0.0 0.8 1.0 S2 A:SF43001 2.1 90.9 1.0 S3 A:SF43001 2.2 68.0 1.0 S4 A:SF43001 2.2 87.6 1.0 SG B:CYS565 2.4 44.2 1.0 FE3 A:SF43001 2.6 40.7 1.0 FE4 A:SF43001 2.6 0.6 1.0 FE2 A:SF43001 2.6 93.8 1.0 CB B:CYS565 3.6 38.7 1.0 S1 A:SF43001 3.7 86.5 1.0 CZ3 B:TRP664 3.9 33.4 1.0 CA B:CYS565 4.1 39.4 1.0 CD1 A:ILE720 4.1 35.6 1.0 N B:CYS565 4.4 40.0 1.0 CE3 B:TRP664 4.5 33.0 1.0 SG B:CYS556 4.6 44.1 1.0 SG A:CYS574 4.8 35.9 1.0 CB B:CYS556 4.8 36.2 1.0 CG2 A:ILE720 4.8 34.4 1.0 CG1 A:ILE720 4.9 35.8 1.0 SG A:CYS583 4.9 49.6 1.0 CH2 B:TRP664 4.9 36.5 1.0

Iron binding site 2 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:93.8 occ:1.00 FE2 A:SF43001 0.0 93.8 1.0 S1 A:SF43001 2.1 86.5 1.0 S3 A:SF43001 2.2 68.0 1.0 S4 A:SF43001 2.2 87.6 1.0 SG A:CYS583 2.4 49.6 1.0 FE4 A:SF43001 2.6 0.6 1.0 FE3 A:SF43001 2.6 40.7 1.0 FE1 A:SF43001 2.6 0.8 1.0 CB A:CYS583 3.2 36.0 1.0 S2 A:SF43001 3.7 90.9 1.0 CA A:CYS583 4.0 31.5 1.0 CE3 B:TRP664 4.0 33.0 1.0 CD1 B:ILE699 4.1 33.7 1.0 CZ3 B:TRP664 4.3 33.4 1.0 N A:CYS583 4.3 31.4 1.0 SG A:CYS574 4.5 35.9 1.0 CB A:CYS574 4.6 32.8 1.0 SG B:CYS565 4.8 44.2 1.0 SG B:CYS556 4.9 44.1 1.0 CG1 B:ILE699 4.9 44.9 1.0 NH2 A:ARG724 5.0 36.7 1.0

Iron binding site 3 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:40.7 occ:1.00 FE3 A:SF43001 0.0 40.7 1.0 S2 A:SF43001 2.1 90.9 1.0 S4 A:SF43001 2.1 87.6 1.0 S1 A:SF43001 2.2 86.5 1.0 SG A:CYS574 2.4 35.9 1.0 FE1 A:SF43001 2.6 0.8 1.0 FE4 A:SF43001 2.6 0.6 1.0 FE2 A:SF43001 2.6 93.8 1.0 CB A:CYS574 3.4 32.8 1.0 S3 A:SF43001 3.7 68.0 1.0 CD B:PRO559 4.4 36.0 1.0 N A:GLY576 4.6 33.8 1.0 N B:PRO559 4.6 41.1 1.0 CD1 A:ILE720 4.6 35.6 1.0 CA A:GLY576 4.6 34.2 1.0 SG A:CYS583 4.7 49.6 1.0 SG B:CYS565 4.7 44.2 1.0 CA A:CYS574 4.7 32.6 1.0 SG B:CYS556 4.8 44.1 1.0 CB B:PRO559 4.8 36.1 1.0 C A:GLY576 4.8 35.6 1.0 CB A:CYS583 4.9 36.0 1.0 C B:GLY558 4.9 42.5 1.0 CA A:CYS583 5.0 31.5 1.0 CA B:PRO559 5.0 39.5 1.0 N A:CYS574 5.0 35.7 1.0 CG B:PRO559 5.0 36.0 1.0

Iron binding site 4 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:0.6 occ:1.00 FE4 A:SF43001 0.0 0.6 1.0 S3 A:SF43001 2.1 68.0 1.0 S1 A:SF43001 2.2 86.5 1.0 S2 A:SF43001 2.2 90.9 1.0 SG B:CYS556 2.4 44.1 1.0 FE2 A:SF43001 2.6 93.8 1.0 FE3 A:SF43001 2.6 40.7 1.0 FE1 A:SF43001 2.6 0.8 1.0 CB B:CYS556 3.5 36.2 1.0 S4 A:SF43001 3.7 87.6 1.0 CD1 B:ILE699 4.3 33.7 1.0 CD A:PRO577 4.5 35.0 1.0 N A:PRO577 4.5 36.4 1.0 N B:GLY558 4.6 36.9 1.0 CA B:GLY558 4.6 36.5 1.0 SG B:CYS565 4.7 44.2 1.0 CB A:PRO577 4.7 34.7 1.0 SG A:CYS583 4.7 49.6 1.0 CA A:PRO577 4.8 38.1 1.0 SG A:CYS574 4.8 35.9 1.0 C A:GLY576 4.8 35.6 1.0 CA B:CYS556 4.9 42.4 1.0

Iron binding site 5 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:0.7 occ:1.00 FE1 C:SF43002 0.0 0.7 1.0 S4 C:SF43002 2.3 80.0 1.0 S2 C:SF43002 2.3 58.7 1.0 S3 C:SF43002 2.3 65.8 1.0 SG C:CYS51 2.7 42.7 1.0 FE3 C:SF43002 2.7 43.2 1.0 FE2 C:SF43002 2.7 0.5 1.0 FE4 C:SF43002 2.7 55.9 1.0 N C:CYS51 3.5 35.1 1.0 N C:LYS52 3.7 36.3 1.0 S1 C:SF43002 3.9 72.0 1.0 CB C:CYS51 3.9 36.8 1.0 CA C:CYS51 4.1 34.8 1.0 N C:GLY50 4.2 35.3 1.0 N C:ARG53 4.2 37.0 1.0 CD C:PRO22 4.3 36.0 1.0 C C:CYS51 4.3 35.5 1.0 C C:GLY50 4.3 35.3 1.0 CA C:GLY50 4.5 35.6 1.0 CA C:LYS52 4.6 37.1 1.0 CG2 C:VAL49 4.7 34.0 1.0 C C:LYS52 4.9 50.5 1.0 CG C:PRO22 4.9 37.6 1.0 CB C:ARG53 4.9 36.8 1.0 SG C:CYS48 5.0 40.2 1.0

Iron binding site 6 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:0.5 occ:1.00 FE2 C:SF43002 0.0 0.5 1.0 S1 C:SF43002 2.3 72.0 1.0 S4 C:SF43002 2.3 80.0 1.0 S3 C:SF43002 2.3 65.8 1.0 SG C:CYS21 2.7 66.5 1.0 FE3 C:SF43002 2.7 43.2 1.0 FE1 C:SF43002 2.7 0.7 1.0 FE4 C:SF43002 2.7 55.9 1.0 CB C:CYS21 3.3 55.4 1.0 CA C:CYS21 3.8 45.2 1.0 S2 C:SF43002 3.9 58.7 1.0 CG2 C:VAL25 4.0 38.9 1.0 CB C:VAL25 4.2 39.8 1.0 CD C:PRO22 4.2 36.0 1.0 C C:CYS21 4.6 38.3 1.0 CD1 C:LEU26 4.6 40.6 1.0 N C:PRO22 4.6 36.5 1.0 CG C:LEU26 4.8 43.3 1.0 N C:VAL25 4.9 41.6 1.0 N C:CYS21 4.9 43.8 1.0 N C:LEU23 4.9 39.8 1.0 SG C:CYS51 5.0 42.7 1.0

Iron binding site 7 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:43.2 occ:1.00 FE3 C:SF43002 0.0 43.2 1.0 S1 C:SF43002 2.3 72.0 1.0 S4 C:SF43002 2.3 80.0 1.0 S2 C:SF43002 2.3 58.7 1.0 SG C:CYS54 2.7 49.5 1.0 FE2 C:SF43002 2.7 0.5 1.0 FE1 C:SF43002 2.7 0.7 1.0 FE4 C:SF43002 2.7 55.9 1.0 CB C:CYS54 3.5 39.9 1.0 CG2 C:VAL67 3.9 47.7 1.0 S3 C:SF43002 3.9 65.8 1.0 N C:CYS54 4.0 47.7 1.0 CA C:CYS54 4.4 41.2 1.0 N C:ARG53 4.5 37.0 1.0 CD1 C:LEU26 4.6 40.6 1.0 N C:LYS52 4.6 36.3 1.0 CA C:LYS52 4.7 37.1 1.0 C C:LYS52 4.9 50.5 1.0 SG C:CYS51 5.0 42.7 1.0

Iron binding site 8 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:55.9 occ:1.00 FE4 C:SF43002 0.0 55.9 1.0 S3 C:SF43002 2.3 65.8 1.0 S1 C:SF43002 2.3 72.0 1.0 S2 C:SF43002 2.3 58.7 1.0 SG C:CYS48 2.7 40.2 1.0 FE2 C:SF43002 2.7 0.5 1.0 FE3 C:SF43002 2.7 43.2 1.0 FE1 C:SF43002 2.7 0.7 1.0 CB C:CYS48 3.6 41.4 1.0 S4 C:SF43002 3.9 80.0 1.0 N C:GLY50 4.0 35.3 1.0 CA C:CYS48 4.1 36.4 1.0 CG2 C:VAL25 4.2 38.9 1.0 N C:VAL49 4.3 35.2 1.0 CA C:GLY50 4.4 35.6 1.0 CG2 C:VAL67 4.5 47.7 1.0 CB C:VAL25 4.6 39.8 1.0 CG2 C:VAL5 4.6 39.9 1.0 C C:CYS48 4.6 38.4 1.0 CG1 C:VAL67 4.8 43.5 1.0 CG1 C:VAL25 4.8 40.4 1.0 N C:CYS51 4.9 35.1 1.0

Iron binding site 9 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3003 b:53.4 occ:1.00 FE1 C:SF43003 0.0 53.4 1.0 S3 C:SF43003 2.3 78.5 1.0 S4 C:SF43003 2.3 84.1 1.0 S2 C:SF43003 2.3 65.0 1.0 FE2 C:SF43003 2.7 78.1 1.0 SG C:CYS58 2.7 46.0 1.0 FE4 C:SF43003 2.7 78.4 1.0 FE3 C:SF43003 2.7 69.2 1.0 SG C:CYS17 3.6 66.0 1.0 CB C:CYS58 3.8 44.2 1.0 S1 C:SF43003 3.9 74.8 1.0 CB C:SER64 3.9 47.6 1.0 CA C:CYS58 4.2 44.1 1.0 CD C:PRO59 4.3 46.1 1.0 CG2 C:ILE65 4.4 51.9 1.0 OG C:SER64 4.4 50.7 1.0 N C:ILE65 4.6 44.9 1.0 N C:SER64 4.6 49.8 1.0 CA C:SER64 4.7 46.9 1.0 C C:SER64 4.8 46.0 1.0 CB C:ILE65 4.9 53.5 1.0 CG2 C:THR60 4.9 49.6 1.0 SG C:CYS11 4.9 57.8 1.0 CB C:CYS17 5.0 42.7 1.0 N C:PRO59 5.0 45.7 1.0

Iron binding site 10 out of 36 in the Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Synechocystis Photosystem I Trimer at 2.5A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3003 b:78.1 occ:1.00 FE2 C:SF43003 0.0 78.1 1.0 SG C:CYS17 1.9 66.0 1.0 S4 C:SF43003 2.2 84.1 1.0 S3 C:SF43003 2.3 78.5 1.0 S1 C:SF43003 2.3 74.8 1.0 N C:CYS17 2.7 47.2 1.0 FE1 C:SF43003 2.7 53.4 1.0 FE4 C:SF43003 2.7 78.4 1.0 FE3 C:SF43003 2.7 69.2 1.0 CB C:CYS17 2.7 42.7 1.0 CA C:CYS17 3.0 42.0 1.0 C C:GLN16 3.8 51.9 1.0 S2 C:SF43003 3.9 65.0 1.0 N C:GLN16 4.0 52.1 1.0 SG C:CYS14 4.3 49.6 1.0 CA C:GLN16 4.3 43.9 1.0 C C:CYS17 4.5 41.3 1.0 CB C:GLN16 4.6 48.1 1.0 C C:THR15 4.6 54.7 1.0 O C:GLN16 4.8 51.8 1.0 N C:THR15 4.9 46.4 1.0 CG2 C:ILE65 4.9 51.9 1.0 SG C:CYS58 4.9 46.0 1.0 N C:VAL18 4.9 43.0 1.0 CA C:CYS58 5.0 44.1 1.0

T.Malavath, I.Caspy, S.Y.Netzer-El, D.Klaiman, N.Nelson. Structure and Function of Wild-Type and Subunit-Depleted Photosystem I in Synechocystis. Biochim. Biophys. Acta V.1859 645 2018.
ISSN: ISSN 0006-3002
PubMed: 29414678
DOI: 10.1016/J.BBABIO.2018.02.002