Magnesium in PDB 5m7k: Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL

The structure of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL, PDB code: 5m7k 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)	55.44 / 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 / 27.4

The structure of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL also contains other interesting chemical elements:

Iron

(Fe)

5 atoms

The binding sites of Magnesium atom in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL (pdb code 5m7k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL, PDB code: 5m7k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:48.1 occ:1.00 MG B:BCL301 0.0 48.1 1.0 ND B:BCL301 2.0 49.0 1.0 NB B:BCL301 2.1 50.1 1.0 NC B:BCL301 2.1 45.5 1.0 NA B:BCL301 2.2 51.1 1.0 NE2 C:HIS180 2.8 49.5 1.0 C4D B:BCL301 3.0 49.1 1.0 C4B B:BCL301 3.1 48.0 1.0 C1B B:BCL301 3.1 50.2 1.0 C1C B:BCL301 3.1 47.3 1.0 C1D B:BCL301 3.1 46.6 1.0 C4A B:BCL301 3.2 50.5 1.0 C4C B:BCL301 3.2 45.8 1.0 C1A B:BCL301 3.2 50.3 1.0 CHC B:BCL301 3.4 47.8 1.0 CHB B:BCL301 3.4 49.4 1.0 CHA B:BCL301 3.4 49.2 1.0 CHD B:BCL301 3.5 45.8 1.0 CD2 C:HIS180 3.5 50.1 1.0 CE1 C:HIS180 3.8 51.1 1.0 C3D B:BCL301 4.2 47.4 1.0 C2D B:BCL301 4.3 46.8 1.0 C2B B:BCL301 4.3 48.7 1.0 C3B B:BCL301 4.3 47.8 1.0 OBB C:BPB402 4.4 54.3 1.0 C2C B:BCL301 4.4 46.1 1.0 C3C B:BCL301 4.4 47.1 1.0 C3A B:BCL301 4.5 52.4 1.0 C2A B:BCL301 4.5 51.1 1.0 CG C:HIS180 4.7 51.5 1.0 C22 C:NS5405 4.8 49.4 1.0 ND1 C:HIS180 4.9 58.6 1.0 CE2 B:PHE181 4.9 48.0 1.0 CBD B:BCL301 4.9 48.3 1.0 CBA B:BCL301 4.9 50.4 1.0

Magnesium binding site 2 out of 4 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:51.2 occ:1.00 MG B:BCL302 0.0 51.2 1.0 ND B:BCL302 2.0 49.0 1.0 NB B:BCL302 2.1 45.1 1.0 NC B:BCL302 2.1 46.9 1.0 NA B:BCL302 2.2 52.6 1.0 CE1 B:HIS173 2.9 43.8 1.0 C4D B:BCL302 3.0 50.2 1.0 C1B B:BCL302 3.1 47.1 1.0 C4B B:BCL302 3.1 43.9 1.0 C1D B:BCL302 3.1 46.7 1.0 C1C B:BCL302 3.1 43.8 1.0 C4A B:BCL302 3.1 49.5 1.0 C4C B:BCL302 3.2 45.8 1.0 CBB C:BCL401 3.2 46.5 1.0 CAB C:BCL401 3.2 46.7 1.0 C1A B:BCL302 3.2 53.4 1.0 CHB B:BCL302 3.4 46.2 1.0 OBB C:BCL401 3.4 45.4 1.0 CHC B:BCL302 3.4 43.8 1.0 CHD B:BCL302 3.5 46.3 1.0 CHA B:BCL302 3.5 51.9 1.0 NE2 B:HIS173 3.6 45.5 1.0 C3B C:BCL401 3.9 44.0 1.0 ND1 B:HIS173 4.0 48.1 1.0 C3D B:BCL302 4.2 50.2 1.0 C2B B:BCL302 4.3 45.9 1.0 C2D B:BCL302 4.3 45.9 1.0 C3B B:BCL302 4.3 43.8 1.0 C2C B:BCL302 4.5 42.2 1.0 C3A B:BCL302 4.5 51.2 1.0 C3C B:BCL302 4.5 43.6 1.0 C2A B:BCL302 4.5 50.8 1.0 C4B C:BCL401 4.6 45.0 1.0 C2B C:BCL401 4.7 43.0 1.0 CD1 B:TRP167 4.8 45.9 1.0 NE1 B:TRP167 4.9 46.4 1.0 CD2 B:HIS173 4.9 45.5 1.0 CHC C:BCL401 4.9 45.7 1.0 CG1 B:VAL157 4.9 42.5 1.0 CBD B:BCL302 5.0 51.0 1.0

Magnesium binding site 3 out of 4 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:39.8 occ:1.00 MG B:BCL303 0.0 39.8 1.0 ND B:BCL303 2.0 35.8 1.0 NB B:BCL303 2.1 37.7 1.0 NC B:BCL303 2.1 40.2 1.0 NA B:BCL303 2.2 36.4 1.0 NE2 B:HIS153 2.8 35.0 1.0 C4D B:BCL303 3.0 37.4 1.0 C1B B:BCL303 3.0 36.3 1.0 C4B B:BCL303 3.1 41.3 1.0 C1D B:BCL303 3.1 36.7 1.0 C4A B:BCL303 3.1 37.7 1.0 C1C B:BCL303 3.1 37.9 1.0 C4C B:BCL303 3.2 38.7 1.0 C1A B:BCL303 3.2 38.2 1.0 CHB B:BCL303 3.4 37.6 1.0 CHC B:BCL303 3.4 38.7 1.0 CHA B:BCL303 3.5 36.6 1.0 CHD B:BCL303 3.5 38.2 1.0 CD2 B:HIS153 3.6 36.7 1.0 CE1 B:HIS153 3.9 41.0 1.0 C3D B:BCL303 4.2 39.4 1.0 OBB B:BPB304 4.2 49.0 1.0 C2B B:BCL303 4.2 41.0 1.0 C2D B:BCL303 4.3 40.0 1.0 C3B B:BCL303 4.3 43.5 1.0 C2C B:BCL303 4.4 35.0 1.0 C3A B:BCL303 4.4 37.0 1.0 C3C B:BCL303 4.4 34.7 1.0 C2A B:BCL303 4.5 36.5 1.0 CE2 C:TYR208 4.6 38.6 1.0 CG B:HIS153 4.8 40.7 1.0 CBD B:BCL303 4.9 35.4 1.0 ND1 B:HIS153 5.0 45.2 1.0 CMA B:BCL303 5.0 36.9 1.0

Magnesium binding site 4 out of 4 in the Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Blastochloris Viridis Photosynthetic Reaction Center - RC_VIR_XFEL within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:42.5 occ:1.00 MG C:BCL401 0.0 42.5 1.0 ND C:BCL401 2.0 46.1 1.0 NB C:BCL401 2.1 41.6 1.0 NC C:BCL401 2.1 42.1 1.0 NA C:BCL401 2.2 44.1 1.0 CE1 C:HIS200 2.8 49.0 1.0 C4D C:BCL401 3.0 44.8 1.0 C4B C:BCL401 3.1 45.0 1.0 C1B C:BCL401 3.1 43.4 1.0 C1C C:BCL401 3.1 41.5 1.0 C1D C:BCL401 3.1 44.4 1.0 C4A C:BCL401 3.1 42.5 1.0 C4C C:BCL401 3.2 42.9 1.0 C1A C:BCL401 3.2 43.9 1.0 CHC C:BCL401 3.4 45.7 1.0 CHB C:BCL401 3.4 43.5 1.0 CHA C:BCL401 3.4 44.0 1.0 CBB B:BCL302 3.5 43.2 1.0 CHD C:BCL401 3.5 42.2 1.0 NE2 C:HIS200 3.7 45.8 1.0 CAB B:BCL302 3.8 42.1 1.0 ND1 C:HIS200 3.8 47.2 1.0 C3D C:BCL401 4.2 45.7 1.0 OBB B:BCL302 4.2 43.2 1.0 C2B C:BCL401 4.2 43.0 1.0 C3B C:BCL401 4.3 44.0 1.0 C2D C:BCL401 4.3 44.6 1.0 C2C C:BCL401 4.4 41.5 1.0 C3C C:BCL401 4.4 44.2 1.0 C3B B:BCL302 4.5 43.8 1.0 C3A C:BCL401 4.5 41.2 1.0 C2A C:BCL401 4.5 42.6 1.0 CBD C:BCL401 4.8 45.6 1.0 CD2 C:HIS200 4.9 45.8 1.0 CMC C:BCL401 4.9 41.5 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