Iron in PDB 4l6v: Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803

All present enzymatic activity of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803:
1.97.1.12;

The structure of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803, PDB code: 4l6v was solved by Y.Mazor, D.Nataf, H.Toporik, N.Nelson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	214.619, 133.680, 219.846, 90.00, 111.14, 90.00
R / Rfree (%)	25.3 / 29.7

The structure of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 also contains other interesting chemical elements:

Magnesium

(Mg)

273 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 Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 (pdb code 4l6v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803, PDB code: 4l6v:
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 Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:85.6 occ:1.00 FE1 A:SF43001 0.0 85.6 1.0 SG B:CYS556 2.0 0.5 1.0 S3 A:SF43001 2.3 58.3 1.0 S2 A:SF43001 2.3 62.9 1.0 S4 A:SF43001 2.3 50.1 1.0 CB B:CYS556 3.6 0.1 1.0 N A:PRO577 3.7 91.7 1.0 FE4 A:SF43001 3.7 0.4 1.0 FE2 A:SF43001 3.7 84.0 1.0 FE3 A:SF43001 3.7 0.7 1.0 CD A:PRO577 3.8 93.1 1.0 CB A:PRO577 3.8 92.2 1.0 S1 A:SF43001 3.8 50.7 1.0 CA A:PRO577 3.9 91.2 1.0 C A:GLY576 4.1 0.7 1.0 CD1 B:ILE699 4.1 99.4 1.0 CG A:PRO577 4.2 93.4 1.0 SG A:CYS583 4.3 88.5 1.0 N B:GLY558 4.4 97.6 1.0 CA B:GLY558 4.5 97.1 1.0 CA A:GLY576 4.6 0.3 1.0 O A:GLY576 4.6 99.6 1.0 CA B:CYS556 4.8 0.1 1.0 SG B:CYS565 4.9 0.8 1.0 SG A:CYS574 4.9 0.5 1.0

Iron binding site 2 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:84.0 occ:1.00 FE2 A:SF43001 0.0 84.0 1.0 SG A:CYS583 1.8 88.5 1.0 S3 A:SF43001 2.3 58.3 1.0 S1 A:SF43001 2.3 50.7 1.0 S4 A:SF43001 2.3 50.1 1.0 CB A:CYS583 2.7 87.5 1.0 CA A:CYS583 3.6 87.1 1.0 FE4 A:SF43001 3.7 0.4 1.0 FE1 A:SF43001 3.7 85.6 1.0 FE3 A:SF43001 3.7 0.7 1.0 S2 A:SF43001 3.8 62.9 1.0 SG A:CYS574 4.0 0.5 1.0 N A:CYS583 4.2 86.9 1.0 CB A:CYS574 4.3 89.5 1.0 CE3 B:TRP664 4.3 90.5 1.0 SG B:CYS565 4.4 0.8 1.0 NH2 A:ARG724 4.5 89.6 1.0 CZ3 B:TRP664 4.8 91.2 1.0 C A:CYS583 4.9 86.3 1.0

Iron binding site 3 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:0.7 occ:1.00 FE3 A:SF43001 0.0 0.7 1.0 SG B:CYS565 1.6 0.8 1.0 CB B:CYS565 2.1 0.4 1.0 S1 A:SF43001 2.3 50.7 1.0 S4 A:SF43001 2.3 50.1 1.0 S2 A:SF43001 2.3 62.9 1.0 CA B:CYS565 2.7 0.6 1.0 N B:CYS565 3.3 1.0 1.0 FE4 A:SF43001 3.7 0.4 1.0 FE1 A:SF43001 3.7 85.6 1.0 FE2 A:SF43001 3.7 84.0 1.0 CB B:CYS556 3.8 0.1 1.0 S3 A:SF43001 3.9 58.3 1.0 SG B:CYS556 3.9 0.5 1.0 C B:CYS565 4.1 0.3 1.0 C B:THR564 4.1 0.7 1.0 O B:THR564 4.4 0.6 1.0 N B:ASP566 4.5 0.6 1.0 CD1 A:ILE720 4.8 94.7 1.0 NH1 B:ARG703 4.8 0.4 1.0 N B:THR564 4.9 0.2 1.0

Iron binding site 4 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe3001 b:0.4 occ:1.00 FE4 A:SF43001 0.0 0.4 1.0 SG A:CYS574 2.0 0.5 1.0 S3 A:SF43001 2.3 58.3 1.0 S2 A:SF43001 2.3 62.9 1.0 S1 A:SF43001 2.3 50.7 1.0 SG B:CYS565 3.6 0.8 1.0 FE1 A:SF43001 3.7 85.6 1.0 FE2 A:SF43001 3.7 84.0 1.0 FE3 A:SF43001 3.7 0.7 1.0 CB A:CYS574 3.7 89.5 1.0 N B:PRO559 3.8 95.4 1.0 S4 A:SF43001 3.8 50.1 1.0 CD1 A:ILE720 3.9 94.7 1.0 CA B:PRO559 4.0 95.8 1.0 CB B:PRO559 4.0 94.8 1.0 CD B:PRO559 4.0 94.4 1.0 C B:GLY558 4.1 97.5 1.0 CG B:PRO559 4.5 94.4 1.0 O B:GLY558 4.5 98.4 1.0 CA B:GLY558 4.7 97.1 1.0 CA A:CYS574 4.9 89.3 1.0 N A:GLY576 4.9 0.4 1.0 CB A:PRO573 5.0 91.5 1.0

Iron binding site 5 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 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 SG C:CYS51 2.0 0.1 1.0 S3 C:SF43002 2.3 60.3 1.0 S4 C:SF43002 2.3 61.3 1.0 S2 C:SF43002 2.3 89.7 1.0 N C:CYS51 3.3 0.0 1.0 CB C:CYS51 3.4 0.8 1.0 N C:LYS52 3.5 0.1 1.0 FE2 C:SF43002 3.7 0.7 1.0 FE3 C:SF43002 3.7 94.8 1.0 FE4 C:SF43002 3.7 88.6 1.0 CA C:CYS51 3.7 0.6 1.0 S1 C:SF43002 3.8 60.6 1.0 C C:CYS51 3.9 0.3 1.0 SG C:CYS21 4.0 0.0 1.0 SG C:CYS48 4.1 0.3 1.0 N C:ARG53 4.1 0.0 1.0 CD C:PRO22 4.2 0.8 1.0 C C:GLY50 4.2 0.8 1.0 SG C:CYS54 4.3 0.5 1.0 N C:GLY50 4.3 0.8 1.0 CA C:LYS52 4.4 0.0 1.0 CG2 C:VAL49 4.5 0.8 1.0 CA C:GLY50 4.5 0.4 1.0 CB C:ARG53 4.8 0.1 1.0 C C:LYS52 4.8 0.8 1.0 CG C:PRO22 4.8 99.9 1.0 O C:CYS51 5.0 0.2 1.0 CA C:ARG53 5.0 1.0 1.0 N C:CYS54 5.0 0.6 1.0

Iron binding site 6 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:0.7 occ:1.00 FE2 C:SF43002 0.0 0.7 1.0 SG C:CYS21 0.6 0.0 1.0 S4 C:SF43002 2.3 61.3 1.0 S1 C:SF43002 2.3 60.6 1.0 S3 C:SF43002 2.3 60.3 1.0 CB C:CYS21 2.3 0.1 1.0 CA C:CYS21 3.2 0.2 1.0 FE1 C:SF43002 3.7 0.7 1.0 FE4 C:SF43002 3.7 88.6 1.0 FE3 C:SF43002 3.7 94.8 1.0 CB C:VAL25 3.8 0.8 1.0 CG2 C:VAL25 3.8 0.7 1.0 S2 C:SF43002 3.8 89.7 1.0 SG C:CYS48 3.9 0.3 1.0 C C:CYS21 4.0 0.5 1.0 CD C:PRO22 4.2 0.8 1.0 N C:PRO22 4.3 0.1 1.0 N C:VAL25 4.4 0.4 1.0 N C:CYS21 4.4 0.7 1.0 N C:LEU23 4.6 0.3 1.0 CG C:LEU26 4.6 0.6 1.0 CA C:VAL25 4.7 0.3 1.0 SG C:CYS54 4.7 0.5 1.0 O C:CYS21 4.7 0.8 1.0 CG1 C:VAL25 4.8 1.0 1.0 CD1 C:LEU26 4.9 0.6 1.0

Iron binding site 7 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:94.8 occ:1.00 FE3 C:SF43002 0.0 94.8 1.0 SG C:CYS54 1.2 0.5 1.0 S4 C:SF43002 2.3 61.3 1.0 S1 C:SF43002 2.3 60.6 1.0 S2 C:SF43002 2.3 89.7 1.0 CB C:CYS54 2.6 0.1 1.0 FE2 C:SF43002 3.7 0.7 1.0 FE1 C:SF43002 3.7 0.7 1.0 N C:CYS54 3.7 0.6 1.0 FE4 C:SF43002 3.7 88.6 1.0 CA C:CYS54 3.7 0.8 1.0 SG C:CYS21 3.8 0.0 1.0 CG2 C:VAL67 3.8 0.3 1.0 S3 C:SF43002 3.8 60.3 1.0 SG C:CYS48 4.4 0.3 1.0 CD1 C:LEU26 4.6 0.6 1.0 CA C:LYS52 4.7 0.0 1.0 N C:ARG53 4.7 0.0 1.0 C C:CYS54 4.8 0.9 1.0 N C:GLU55 4.8 0.1 1.0 N C:LYS52 4.8 0.1 1.0 CD1 C:ILE65 4.9 1.0 1.0 CB C:CYS21 4.9 0.1 1.0 C C:ARG53 5.0 0.1 1.0

Iron binding site 8 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3002 b:88.6 occ:1.00 FE4 C:SF43002 0.0 88.6 1.0 SG C:CYS48 0.7 0.3 1.0 S3 C:SF43002 2.3 60.3 1.0 S1 C:SF43002 2.3 60.6 1.0 S2 C:SF43002 2.3 89.7 1.0 CB C:CYS48 2.5 0.8 1.0 CA C:CYS48 3.5 0.9 1.0 FE2 C:SF43002 3.7 0.7 1.0 FE1 C:SF43002 3.7 0.7 1.0 FE3 C:SF43002 3.7 94.8 1.0 S4 C:SF43002 3.8 61.3 1.0 C C:CYS48 4.1 0.6 1.0 N C:GLY50 4.2 0.8 1.0 CG2 C:VAL5 4.2 0.5 1.0 CG2 C:VAL25 4.2 0.7 1.0 N C:VAL49 4.2 0.6 1.0 SG C:CYS21 4.2 0.0 1.0 CG1 C:VAL25 4.5 1.0 1.0 CB C:VAL25 4.5 0.8 1.0 CA C:GLY50 4.5 0.4 1.0 CG1 C:VAL67 4.6 1.0 1.0 N C:CYS48 4.8 0.5 1.0 CG2 C:VAL67 4.8 0.3 1.0 SG C:CYS54 4.8 0.5 1.0 O C:CYS48 4.8 0.2 1.0

Iron binding site 9 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 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 SG C:CYS58 1.1 0.3 1.0 S3 C:SF43003 2.3 60.1 1.0 S2 C:SF43003 2.3 61.1 1.0 S4 C:SF43003 2.3 61.2 1.0 CB C:CYS58 2.5 0.7 1.0 CA C:CYS58 3.5 0.3 1.0 SG C:CYS11 3.6 0.8 1.0 FE2 C:SF43003 3.7 81.3 1.0 FE4 C:SF43003 3.7 0.8 1.0 FE3 C:SF43003 3.7 96.1 1.0 CB C:SER64 3.8 0.8 1.0 S1 C:SF43003 3.8 67.6 1.0 CD C:PRO59 4.0 0.7 1.0 OG C:SER64 4.1 0.3 1.0 N C:SER64 4.2 0.3 1.0 C C:CYS58 4.3 0.5 1.0 OG1 C:THR60 4.3 0.6 1.0 SG C:CYS14 4.4 0.8 1.0 N C:PRO59 4.4 0.2 1.0 CG2 C:ILE65 4.5 0.2 1.0 CA C:SER64 4.5 0.2 1.0 N C:ILE65 4.5 0.9 1.0 N C:CYS58 4.6 0.5 1.0 CG2 C:THR60 4.7 0.8 1.0 C C:SER64 4.8 0.8 1.0 CB C:CYS11 5.0 0.5 1.0

Iron binding site 10 out of 36 in the Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of A Virus Like Photosystem I From the Cyanobacterium Synechocystis Pcc 6803 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe3003 b:81.3 occ:1.00 FE2 C:SF43003 0.0 81.3 1.0 SG C:CYS14 1.3 0.8 1.0 S3 C:SF43003 2.3 60.1 1.0 S4 C:SF43003 2.3 61.2 1.0 S1 C:SF43003 2.3 67.6 1.0 CB C:CYS14 2.8 0.2 1.0 N C:CYS14 3.0 0.5 1.0 CA C:CYS14 3.3 0.6 1.0 N C:THR15 3.4 0.6 1.0 C C:CYS14 3.5 0.7 1.0 FE1 C:SF43003 3.7 0.6 1.0 FE4 C:SF43003 3.7 0.8 1.0 FE3 C:SF43003 3.7 96.1 1.0 S2 C:SF43003 3.8 61.1 1.0 SG C:CYS58 3.9 0.3 1.0 N C:GLN16 4.0 0.2 1.0 CD C:PRO59 4.1 0.7 1.0 C C:GLY13 4.2 0.4 1.0 SG C:CYS11 4.3 0.8 1.0 CA C:THR15 4.4 0.1 1.0 O C:CYS14 4.5 0.0 1.0 N C:GLY13 4.5 0.2 1.0 CG1 C:ILE12 4.7 0.1 1.0 CA C:GLY13 4.7 0.3 1.0 C C:THR15 4.7 0.3 1.0 CB C:GLN16 4.8 0.2 1.0 CG C:PRO59 4.9 0.2 1.0 CA C:GLN16 5.0 0.8 1.0

Y.Mazor, D.Nataf, H.Toporik, N.Nelson. Crystal Structures of Virus-Like Photosystem I Complexes From the Mesophilic Cyanobacterium Synechocystis Pcc 6803. Elife V. 3 01496 2014.
ISSN: ESSN 2050-084X
PubMed: 24473073
DOI: 10.7554/ELIFE.01496