Magnesium in PDB 7qgk: The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State

The structure of The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State, PDB code: 7qgk was solved by K.M.Boyko, A.Y.Nikolaeva, F.A.Gaivoronskii, A.V.Vlaskina, O.M.Subach, V.O.Popov, F.V.Subach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.62 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.338, 66.253, 96.496, 90, 90, 90
R / Rfree (%)	17.4 / 19.5

The binding sites of Magnesium atom in the The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State (pdb code 7qgk). 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 Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State, PDB code: 7qgk:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:25.0 occ:1.00 O A:HOH554 2.6 37.0 1.0 O A:HOH548 2.8 30.1 1.0 O A:HOH442 3.1 19.9 1.0 N A:ASP83 3.1 13.2 1.0 CB A:ASP83 3.7 12.8 1.0 CA A:PRO82 3.8 14.0 1.0 CA A:ASP83 3.9 12.8 1.0 NE2 A:GLN87 4.0 15.1 1.0 C A:PRO82 4.0 13.4 1.0 CG A:GLN87 4.1 14.0 1.0 CD A:GLN87 4.2 15.0 1.0 O A:ASP83 4.3 12.9 1.0 O A:HOH556 4.5 28.6 1.0 C A:ASP83 4.5 12.9 1.0 O A:HOH401 4.6 20.0 0.5 CB A:PRO82 4.6 14.3 1.0 O A:ILE81 4.7 14.1 1.0 O A:HOH482 4.8 20.8 1.0 O A:HOH424 4.9 19.0 1.0 N A:PRO82 4.9 13.7 1.0 OE1 A:GLN87 4.9 16.8 1.0

Magnesium binding site 2 out of 3 in the The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:27.6 occ:1.00 O A:HOH448 2.9 24.0 1.0 O A:HOH515 3.1 34.8 1.0 CD2 A:LEU175 3.6 32.3 1.0 CD A:PRO136 3.7 26.2 1.0 CD A:PRO132 3.8 26.8 1.0 CG2 A:VAL137 3.8 23.4 1.0 N A:VAL137 3.9 23.5 1.0 CA A:GLY135 3.9 27.2 1.0 N A:PRO136 4.0 25.0 1.0 CB A:VAL137 4.0 22.7 1.0 C A:GLY135 4.1 25.8 1.0 CD1 A:PHE131 4.3 22.4 1.0 CG A:PRO136 4.3 26.4 1.0 CG A:PRO132 4.4 28.3 1.0 O A:GLY104 4.5 26.9 0.5 CA A:VAL137 4.6 22.9 1.0 N A:PRO132 4.6 26.7 1.0 CD1 A:LEU175 4.6 32.7 1.0 CG A:LEU175 4.7 32.2 1.0 O A:GLU102 4.7 27.4 1.0 CB A:PRO132 4.8 27.6 1.0 C A:PRO136 4.8 23.3 1.0 O A:PRO132 4.8 27.5 1.0 CA A:PRO136 4.8 24.5 1.0 O A:GLY135 4.9 25.5 1.0 N A:GLY135 5.0 28.4 1.0

Magnesium binding site 3 out of 3 in the The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer in Its Red State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:21.2 occ:1.00 OG A:SER210 3.0 18.3 1.0 O A:HOH422 3.1 37.1 1.0 N A:ASN212 3.3 22.8 1.0 CB A:SER210 3.5 18.8 1.0 CB A:ASN212 3.6 26.2 1.0 CG A:MET214 3.6 22.3 0.5 CB A:MET214 3.7 20.5 1.0 CG A:MET214 3.7 20.3 0.5 CA A:ASN212 3.8 23.8 1.0 N A:MET214 3.9 19.1 1.0 N A:ASP211 3.9 19.6 1.0 C A:ASN212 4.0 22.6 1.0 ND2 A:ASN212 4.1 32.7 1.0 N A:GLU213 4.1 20.9 1.0 C A:SER210 4.2 18.9 1.0 CG A:ASN212 4.3 30.5 1.0 C A:ASP211 4.4 22.2 1.0 CA A:MET214 4.4 18.9 1.0 CA A:SER210 4.4 18.2 1.0 CA A:ASP211 4.6 21.2 1.0 O A:ASN212 4.6 23.6 1.0 SD A:MET214 4.7 24.8 0.5 O A:SER210 4.8 19.3 1.0 CB A:ASP211 4.9 21.8 1.0 C A:GLU213 4.9 20.2 1.0

O.M.Subach, A.Tashkeev, A.V.Vlaskina, D.E.Petrenko, F.A.Gaivoronskii, A.Y.Nikolaeva, O.I.Ivashkina, K.V.Anokhin, V.O.Popov, K.M.Boyko, F.V.Subach. The Mrubyft Protein, Genetically Encoded Blue-to-Red Fluorescent Timer. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 35328628
DOI: 10.3390/IJMS23063208