Iron in PDB 5m7j: Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach

The structure of Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach, PDB code: 5m7j was solved by A.S.Sharma, L.Johansson, E.Dunevall, W.Y.Wahlgren, R.Neutze, G.Katona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.76 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.900, 84.800, 384.300, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 27.3

The structure of Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Iron atom in the Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach (pdb code 5m7j). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach, PDB code: 5m7j:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:41.8 occ:1.00 FE A:HEC401 0.0 41.8 1.0 NA A:HEC401 2.1 40.5 1.0 NB A:HEC401 2.1 45.4 1.0 NC A:HEC401 2.1 43.9 1.0 ND A:HEC401 2.1 45.5 1.0 NE2 A:HIS91 2.5 38.6 1.0 SD A:MET74 2.9 50.8 1.0 C1B A:HEC401 3.0 47.3 1.0 C1C A:HEC401 3.0 46.7 1.0 C4B A:HEC401 3.0 46.4 1.0 C4C A:HEC401 3.1 46.9 1.0 C4A A:HEC401 3.1 44.4 1.0 C1D A:HEC401 3.1 49.4 1.0 C1A A:HEC401 3.1 44.8 1.0 C4D A:HEC401 3.1 41.8 1.0 CD2 A:HIS91 3.2 42.0 1.0 CHB A:HEC401 3.4 44.5 1.0 CHC A:HEC401 3.4 50.8 1.0 CHD A:HEC401 3.4 56.6 1.0 CHA A:HEC401 3.5 41.8 1.0 CE1 A:HIS91 3.6 41.1 1.0 CG A:MET74 3.6 45.3 1.0 CE A:MET74 3.9 39.7 1.0 C2B A:HEC401 4.2 49.6 1.0 C3B A:HEC401 4.2 46.0 1.0 C2C A:HEC401 4.2 48.2 1.0 C3C A:HEC401 4.2 48.6 1.0 C3A A:HEC401 4.3 54.8 1.0 C2D A:HEC401 4.3 36.2 1.0 C2A A:HEC401 4.3 47.7 1.0 C3D A:HEC401 4.3 35.2 1.0 CG A:HIS91 4.4 41.9 1.0 CB A:MET74 4.5 44.4 1.0 ND1 A:HIS91 4.6 41.1 1.0

Iron binding site 2 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:14.3 occ:1.00 FE A:HEC402 0.0 14.3 1.0 ND A:HEC402 2.1 25.4 1.0 NA A:HEC402 2.1 35.3 1.0 NC A:HEC402 2.1 33.4 1.0 NB A:HEC402 2.1 23.7 1.0 NE2 A:HIS136 2.5 31.6 1.0 SD A:MET110 2.9 31.8 1.0 C1B A:HEC402 3.0 26.5 1.0 C4B A:HEC402 3.0 33.1 1.0 C4C A:HEC402 3.0 31.8 1.0 C1C A:HEC402 3.1 31.3 1.0 C1D A:HEC402 3.1 23.5 1.0 C4A A:HEC402 3.1 35.3 1.0 C4D A:HEC402 3.1 36.0 1.0 C1A A:HEC402 3.1 31.3 1.0 CHD A:HEC402 3.4 31.0 1.0 CG A:MET110 3.4 24.1 1.0 CHB A:HEC402 3.4 28.4 1.0 CE A:MET110 3.4 32.1 1.0 CHC A:HEC402 3.4 30.8 1.0 CE1 A:HIS136 3.4 29.8 1.0 CHA A:HEC402 3.4 33.0 1.0 CD2 A:HIS136 3.5 29.4 1.0 CB A:MET110 4.2 22.7 1.0 C2B A:HEC402 4.2 33.5 1.0 C3B A:HEC402 4.2 38.8 1.0 C3C A:HEC402 4.2 30.4 1.0 C2C A:HEC402 4.2 28.6 1.0 C2D A:HEC402 4.3 35.6 1.0 C3A A:HEC402 4.3 31.4 1.0 C3D A:HEC402 4.3 49.3 1.0 C2A A:HEC402 4.3 28.1 1.0 ND1 A:HIS136 4.6 30.9 1.0 CG A:HIS136 4.6 29.4 1.0

Iron binding site 3 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:17.5 occ:1.00 FE A:HEC403 0.0 17.5 1.0 NC A:HEC403 2.0 23.2 1.0 NA A:HEC403 2.0 25.1 1.0 NB A:HEC403 2.0 24.2 1.0 ND A:HEC403 2.1 27.9 1.0 NE2 A:HIS248 2.5 23.1 1.0 SD A:MET233 2.8 31.4 1.0 C1B A:HEC403 3.0 25.6 1.0 C4B A:HEC403 3.0 31.0 1.0 C4A A:HEC403 3.0 32.9 1.0 C1C A:HEC403 3.0 20.0 1.0 C4C A:HEC403 3.0 29.4 1.0 CD2 A:HIS248 3.1 25.7 1.0 C1A A:HEC403 3.1 24.5 1.0 C1D A:HEC403 3.1 29.4 1.0 C4D A:HEC403 3.1 28.4 1.0 CG A:MET233 3.3 24.9 1.0 CHB A:HEC403 3.4 35.1 1.0 CHC A:HEC403 3.4 27.2 1.0 CHD A:HEC403 3.4 29.4 1.0 CHA A:HEC403 3.5 30.2 1.0 CE1 A:HIS248 3.6 28.4 1.0 CE A:MET233 3.8 27.0 1.0 CB A:MET233 4.1 21.2 1.0 C2B A:HEC403 4.2 26.1 1.0 C3B A:HEC403 4.2 31.4 1.0 C2C A:HEC403 4.2 23.2 1.0 C3C A:HEC403 4.3 31.3 1.0 C3A A:HEC403 4.3 24.4 1.0 C2A A:HEC403 4.3 19.4 1.0 C2D A:HEC403 4.3 27.7 1.0 C3D A:HEC403 4.3 24.6 1.0 CG A:HIS248 4.3 29.5 1.0 ND1 A:HIS248 4.6 32.3 1.0 CA A:MET233 5.0 27.5 1.0

Iron binding site 4 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:30.4 occ:1.00 FE A:HEC404 0.0 30.4 1.0 ND A:HEC404 2.0 32.2 1.0 NA A:HEC404 2.0 37.9 1.0 NC A:HEC404 2.1 39.3 1.0 NB A:HEC404 2.1 28.1 1.0 NE2 A:HIS309 2.3 37.6 1.0 NE2 A:HIS124 2.4 34.9 1.0 C4D A:HEC404 3.0 35.3 1.0 C1D A:HEC404 3.0 40.2 1.0 C1A A:HEC404 3.0 38.3 1.0 C4B A:HEC404 3.1 33.6 1.0 C1B A:HEC404 3.1 27.4 1.0 C4C A:HEC404 3.1 41.8 1.0 C1C A:HEC404 3.1 37.7 1.0 C4A A:HEC404 3.1 30.7 1.0 CE1 A:HIS309 3.1 39.0 1.0 CE1 A:HIS124 3.2 32.2 1.0 CHA A:HEC404 3.4 36.3 1.0 CD2 A:HIS124 3.4 28.0 1.0 CHD A:HEC404 3.4 39.6 1.0 CHC A:HEC404 3.4 36.6 1.0 CD2 A:HIS309 3.5 40.1 1.0 CHB A:HEC404 3.5 27.7 1.0 C3B A:HEC404 4.2 33.4 1.0 C2B A:HEC404 4.2 34.0 1.0 C3D A:HEC404 4.2 41.9 1.0 C2D A:HEC404 4.2 46.0 1.0 C2A A:HEC404 4.3 33.0 1.0 C2C A:HEC404 4.3 39.4 1.0 C3C A:HEC404 4.3 46.8 1.0 C3A A:HEC404 4.3 29.5 1.0 ND1 A:HIS309 4.3 51.2 1.0 ND1 A:HIS124 4.4 30.8 1.0 CG A:HIS124 4.5 32.9 1.0 CG A:HIS309 4.5 42.5 1.0 CD A:PRO315 4.9 36.5 1.0 CG A:PRO315 4.9 38.3 1.0

Iron binding site 5 out of 5 in the Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Blastochloris Viridis Photosynthetic Reaction Center Structure Using Best Crystal Approach within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe307 b:54.4 occ:1.00 NE2 C:HIS217 2.5 56.7 1.0 NE2 C:HIS264 2.5 62.3 1.0 NE2 B:HIS190 2.5 66.5 1.0 OE2 C:GLU232 2.5 62.8 1.0 OE1 C:GLU232 2.6 65.1 1.0 NE2 B:HIS230 2.6 52.5 1.0 CD C:GLU232 2.9 63.7 1.0 CE1 C:HIS264 3.2 67.7 1.0 CE1 C:HIS217 3.3 57.0 1.0 CE1 B:HIS190 3.4 71.1 1.0 CE1 B:HIS230 3.4 56.2 1.0 CD2 B:HIS190 3.4 64.4 1.0 CD2 C:HIS264 3.5 61.5 1.0 CD2 C:HIS217 3.5 57.0 1.0 CD2 B:HIS230 3.7 58.4 1.0 ND1 C:HIS264 4.3 65.8 1.0 CG C:GLU232 4.4 62.4 1.0 ND1 C:HIS217 4.5 53.6 1.0 CG1 B:ILE194 4.5 51.3 1.0 CG C:HIS264 4.5 67.9 1.0 ND1 B:HIS190 4.5 69.7 1.0 CG B:HIS190 4.6 68.5 1.0 ND1 B:HIS230 4.6 63.1 1.0 CG C:HIS217 4.6 58.3 1.0 CG B:HIS230 4.7 60.5 1.0 CG1 C:ILE221 4.8 46.8 1.0

A.Sharma, L.Johansson, E.Dunevall, W.Y.Wahlgren, R.Neutze, G.Katona. Asymmetry in Serial Femtosecond Crystallography Data. Acta Crystallogr A Found Adv V. 73 93 2017.
ISSN: ESSN 2053-2733
PubMed: 28248658
DOI: 10.1107/S2053273316018696