Iron in PDB 3prc: Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)

The structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted), PDB code: 3prc was solved by C.R.D.Lancaster, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	223.500, 223.500, 113.600, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.5

The structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Iron atom in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) (pdb code 3prc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted), PDB code: 3prc:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe337 b:28.0 occ:1.00 FE C:HEM337 0.0 28.0 1.0 NE2 C:HIS91 1.9 25.2 1.0 NC C:HEM337 2.0 25.8 1.0 ND C:HEM337 2.0 27.9 1.0 NA C:HEM337 2.0 29.6 1.0 NB C:HEM337 2.1 28.8 1.0 SD C:MET74 2.2 28.7 1.0 CE1 C:HIS91 2.9 25.9 1.0 CD2 C:HIS91 2.9 26.3 1.0 C4C C:HEM337 3.0 26.0 1.0 C1D C:HEM337 3.0 28.6 1.0 C1C C:HEM337 3.0 26.8 1.0 C4D C:HEM337 3.1 28.1 1.0 C1A C:HEM337 3.1 31.5 1.0 C4A C:HEM337 3.1 31.5 1.0 C1B C:HEM337 3.1 29.3 1.0 C4B C:HEM337 3.1 27.8 1.0 CHD C:HEM337 3.3 25.9 1.0 CHA C:HEM337 3.5 30.4 1.0 CHB C:HEM337 3.5 28.9 1.0 CHC C:HEM337 3.5 26.4 1.0 CE C:MET74 3.5 25.1 1.0 CG C:MET74 3.6 27.2 1.0 ND1 C:HIS91 4.0 27.1 1.0 CG C:HIS91 4.0 26.2 1.0 C3C C:HEM337 4.2 25.9 1.0 C2C C:HEM337 4.2 24.2 1.0 C2D C:HEM337 4.3 28.0 1.0 C3D C:HEM337 4.3 27.3 1.0 C2A C:HEM337 4.3 33.7 1.0 C3A C:HEM337 4.3 33.7 1.0 C2B C:HEM337 4.3 29.0 1.0 C3B C:HEM337 4.3 28.1 1.0 CB C:MET74 4.4 27.5 1.0

Iron binding site 2 out of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe338 b:23.0 occ:1.00 FE C:HEM338 0.0 23.0 1.0 NE2 C:HIS136 1.9 20.4 1.0 ND C:HEM338 2.0 26.3 1.0 NA C:HEM338 2.0 25.6 1.0 NB C:HEM338 2.0 23.4 1.0 NC C:HEM338 2.1 24.8 1.0 SD C:MET110 2.2 26.4 1.0 CE1 C:HIS136 2.9 20.3 1.0 CD2 C:HIS136 3.0 19.2 1.0 C4D C:HEM338 3.0 28.9 1.0 C1A C:HEM338 3.0 27.2 1.0 C4A C:HEM338 3.1 26.5 1.0 C1D C:HEM338 3.1 27.3 1.0 C1B C:HEM338 3.1 24.3 1.0 C4B C:HEM338 3.1 25.3 1.0 C4C C:HEM338 3.1 22.9 1.0 C1C C:HEM338 3.1 23.2 1.0 CHA C:HEM338 3.4 29.6 1.0 CHB C:HEM338 3.4 25.0 1.0 CHD C:HEM338 3.5 25.6 1.0 CHC C:HEM338 3.5 24.4 1.0 CG C:MET110 3.5 24.8 1.0 CE C:MET110 3.5 23.7 1.0 ND1 C:HIS136 4.1 20.7 1.0 CG C:HIS136 4.1 19.4 1.0 CB C:MET110 4.2 24.5 1.0 C3D C:HEM338 4.2 28.8 1.0 C3A C:HEM338 4.3 27.9 1.0 C2A C:HEM338 4.3 28.2 1.0 C2D C:HEM338 4.3 28.4 1.0 C2B C:HEM338 4.3 25.7 1.0 C3B C:HEM338 4.3 25.1 1.0 C3C C:HEM338 4.3 21.2 1.0 C2C C:HEM338 4.3 21.5 1.0 CE C:MET113 5.0 21.0 1.0

Iron binding site 3 out of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe339 b:15.3 occ:1.00 FE C:HEM339 0.0 15.3 1.0 NE2 C:HIS248 1.9 14.1 1.0 NC C:HEM339 1.9 14.7 1.0 ND C:HEM339 2.0 14.3 1.0 NB C:HEM339 2.0 14.2 1.0 NA C:HEM339 2.1 13.5 1.0 SD C:MET233 2.1 15.6 1.0 CD2 C:HIS248 2.9 13.3 1.0 CE1 C:HIS248 2.9 14.0 1.0 C1C C:HEM339 3.0 13.1 1.0 C4C C:HEM339 3.0 16.6 1.0 C1D C:HEM339 3.0 17.1 1.0 C4D C:HEM339 3.0 16.2 1.0 C4B C:HEM339 3.0 14.3 1.0 C1A C:HEM339 3.1 14.8 1.0 C1B C:HEM339 3.1 14.5 1.0 C4A C:HEM339 3.1 13.2 1.0 CHC C:HEM339 3.4 14.4 1.0 CHD C:HEM339 3.4 17.7 1.0 CE C:MET233 3.4 10.5 1.0 CHA C:HEM339 3.4 15.6 1.0 CG C:MET233 3.5 15.9 1.0 CHB C:HEM339 3.5 14.5 1.0 ND1 C:HIS248 4.1 13.0 1.0 CG C:HIS248 4.1 12.7 1.0 C3C C:HEM339 4.2 13.8 1.0 C2C C:HEM339 4.2 12.1 1.0 C2D C:HEM339 4.2 17.0 1.0 C3D C:HEM339 4.2 16.6 1.0 CB C:MET233 4.3 15.4 1.0 C3B C:HEM339 4.3 12.0 1.0 C2B C:HEM339 4.3 10.8 1.0 C2A C:HEM339 4.3 14.0 1.0 C3A C:HEM339 4.3 12.5 1.0

Iron binding site 4 out of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe340 b:17.6 occ:1.00 FE C:HEM340 0.0 17.6 1.0 NE2 C:HIS309 2.0 16.1 1.0 NE2 C:HIS124 2.0 18.5 1.0 ND C:HEM340 2.0 20.2 1.0 NC C:HEM340 2.0 18.5 1.0 NB C:HEM340 2.0 17.5 1.0 NA C:HEM340 2.0 20.3 1.0 CE1 C:HIS124 2.8 17.4 1.0 CE1 C:HIS309 2.8 16.2 1.0 C1D C:HEM340 3.0 20.5 1.0 C4C C:HEM340 3.0 19.7 1.0 C4D C:HEM340 3.0 21.8 1.0 C1C C:HEM340 3.1 20.2 1.0 C1B C:HEM340 3.1 17.0 1.0 C4B C:HEM340 3.1 17.2 1.0 CD2 C:HIS309 3.1 16.0 1.0 C4A C:HEM340 3.1 19.7 1.0 C1A C:HEM340 3.1 21.4 1.0 CD2 C:HIS124 3.1 18.9 1.0 CHD C:HEM340 3.4 19.9 1.0 CHC C:HEM340 3.4 20.0 1.0 CHB C:HEM340 3.4 16.6 1.0 CHA C:HEM340 3.4 22.2 1.0 ND1 C:HIS124 4.0 18.0 1.0 ND1 C:HIS309 4.0 16.0 1.0 CG C:HIS309 4.2 15.1 1.0 CG C:HIS124 4.2 18.7 1.0 C2D C:HEM340 4.2 22.7 1.0 C3D C:HEM340 4.2 24.1 1.0 C3C C:HEM340 4.2 19.2 1.0 C2C C:HEM340 4.3 17.8 1.0 C2B C:HEM340 4.3 16.7 1.0 C3B C:HEM340 4.3 15.6 1.0 C2A C:HEM340 4.3 18.5 1.0 C3A C:HEM340 4.3 17.8 1.0

Iron binding site 5 out of 5 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Qb- Depleted) within 5.0Å range: probe atom residue distance (Å) B Occ M:Fe500 b:14.4 occ:1.00 NE2 L:HIS190 1.9 12.8 1.0 OE2 M:GLU232 2.0 16.0 1.0 NE2 M:HIS217 2.1 11.6 1.0 NE2 M:HIS264 2.2 12.3 1.0 OE1 M:GLU232 2.2 20.5 1.0 NE2 L:HIS230 2.2 19.0 1.0 CD M:GLU232 2.4 17.8 1.0 CE1 L:HIS190 2.8 13.9 1.0 CE1 M:HIS217 2.9 12.9 1.0 CD2 L:HIS190 3.1 14.9 1.0 CE1 M:HIS264 3.1 10.3 1.0 CE1 L:HIS230 3.2 19.1 1.0 CD2 M:HIS264 3.3 10.3 1.0 CD2 M:HIS217 3.3 12.2 1.0 CD2 L:HIS230 3.3 19.5 1.0 CG M:GLU232 4.0 17.3 1.0 ND1 L:HIS190 4.0 13.1 1.0 CG L:HIS190 4.1 14.7 1.0 ND1 M:HIS217 4.2 10.8 1.0 ND1 M:HIS264 4.3 11.9 1.0 ND1 L:HIS230 4.3 16.5 1.0 CG M:HIS217 4.3 12.3 1.0 CG M:HIS264 4.4 9.3 1.0 CG L:HIS230 4.4 17.5 1.0 CG1 L:ILE194 4.5 15.4 1.0 CG1 M:ILE221 4.7 15.8 1.0 O M:HOH832 4.7 14.6 1.0 CD1 L:ILE194 4.9 16.6 1.0 CB M:GLU232 4.9 17.8 1.0

C.R.Lancaster, H.Michel. The Coupling of Light-Induced Electron Transfer and Proton Uptake As Derived From Crystal Structures of Reaction Centres From Rhodopseudomonas Viridis Modified at the Binding Site of the Secondary Quinone, Qb. Structure V. 5 1339 1997.
ISSN: ISSN 0969-2126
PubMed: 9351808
DOI: 10.1016/S0969-2126(97)00285-2