Magnesium in PDB 6lm1: The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075

The structure of The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075, PDB code: 6lm1 was solved by T.Hosaka, T.Kimura-Someya, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.48 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.920, 129.666, 127.626, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.4

The binding sites of Magnesium atom in the The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075 (pdb code 6lm1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075, PDB code: 6lm1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:46.7 occ:1.00 O A:HOH420 2.0 52.2 1.0 O A:THR118 2.1 31.5 1.0 OE2 A:GLU185 2.1 74.5 1.0 O A:HOH403 2.2 42.0 1.0 O A:HOH424 2.2 38.4 1.0 O A:HOH445 2.2 57.7 1.0 C A:THR118 3.2 27.8 1.0 CD A:GLU185 3.3 69.0 1.0 O A:GLU120 3.4 33.4 1.0 O A:HOH464 3.4 60.5 1.0 OE1 A:GLU185 3.9 75.3 1.0 CA A:THR118 3.9 25.1 1.0 O A:HOH466 4.0 61.7 1.0 N A:LEU119 4.3 22.1 1.0 O A:ALA117 4.3 25.5 1.0 C A:LEU119 4.4 32.9 1.0 O A:HOH406 4.4 33.2 1.0 CG A:GLU185 4.5 49.8 1.0 N A:GLU120 4.5 30.9 1.0 CA A:LEU119 4.5 24.7 1.0 CG2 A:THR118 4.5 31.7 1.0 C A:GLU120 4.5 36.3 1.0 CB A:GLU185 4.6 44.4 1.0 O A:LEU119 4.7 31.9 1.0 CA A:GLU185 4.8 43.5 1.0 CB A:THR118 4.9 33.0 1.0 N A:THR118 5.0 22.3 1.0

Magnesium binding site 2 out of 3 in the The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:52.3 occ:1.00 O B:HOH439 2.0 50.8 1.0 O B:HOH403 2.1 44.5 1.0 O B:HOH447 2.1 46.4 1.0 O B:THR118 2.2 29.4 1.0 O B:HOH421 2.4 34.3 1.0 O B:HOH448 3.1 66.0 1.0 C B:THR118 3.3 28.7 1.0 CA B:THR118 3.9 26.3 1.0 O B:GLU120 3.9 32.6 1.0 CA B:GLU185 4.1 44.3 1.0 CB B:GLU185 4.1 36.0 1.0 CG2 B:THR118 4.2 30.6 1.0 O B:GLU185 4.4 50.3 1.0 N B:LEU119 4.4 25.2 1.0 O B:ALA117 4.5 24.9 1.0 C B:GLU185 4.7 46.2 1.0 CB B:THR118 4.7 31.9 1.0 CA B:LEU119 4.8 28.9 1.0 C B:LEU119 4.8 35.5 1.0 N B:GLU120 5.0 33.2 1.0

Magnesium binding site 3 out of 3 in the The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Cyanorhodopsin (Cyr) N4075R From Cyanobacteria Tolypothrix Sp. Nies-4075 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:47.8 occ:1.00 OE2 C:GLU185 2.0 69.2 1.0 O C:HOH403 2.0 43.8 1.0 O C:HOH440 2.1 57.6 1.0 O C:THR118 2.1 26.5 1.0 O C:HOH412 2.3 42.3 1.0 O C:HOH413 2.3 33.3 1.0 CD C:GLU185 3.1 65.1 1.0 C C:THR118 3.2 27.2 1.0 O C:GLU120 3.4 30.1 1.0 OE1 C:GLU185 3.6 70.8 1.0 O C:HOH462 3.7 56.3 1.0 CA C:THR118 3.9 26.6 1.0 N C:LEU119 4.2 23.9 1.0 O C:ALA117 4.3 21.8 1.0 CG C:GLU185 4.3 47.8 1.0 C C:LEU119 4.4 31.0 1.0 O C:HOH407 4.4 30.4 1.0 CG2 C:THR118 4.4 30.3 1.0 CA C:LEU119 4.5 23.8 1.0 O C:HOH402 4.6 61.6 1.0 N C:GLU120 4.6 26.0 1.0 CB C:GLU185 4.6 39.6 1.0 C C:GLU120 4.6 31.9 1.0 O C:LEU119 4.7 29.4 1.0 CB C:THR118 4.8 25.5 1.0 CA C:GLU185 4.9 39.6 1.0 N C:THR118 5.0 21.3 1.0

M.Hasegawa, T.Hosaka, K.Kojima, Y.Nishimura, Y.Nakajima, T.Kimura-Someya, M.Shirouzu, Y.Sudo, S.Yoshizawa. A Unique Clade of Light-Driven Proton-Pumping Rhodopsins Evolved in the Cyanobacterial Lineage. Sci Rep V. 10 16752 2020.
ISSN: ESSN 2045-2322
PubMed: 33028840
DOI: 10.1038/S41598-020-73606-Y