Manganese in PDB 5d2c: Reaction of Phosphorylated Chey with Imidazole 1 of 3

The structure of Reaction of Phosphorylated Chey with Imidazole 1 of 3, PDB code: 5d2c was solved by S.Page, R.E.Silversmith, R.B.Bourret, E.J.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.20 / 2.06
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.620, 53.720, 162.450, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.5

The structure of Reaction of Phosphorylated Chey with Imidazole 1 of 3 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Manganese atom in the Reaction of Phosphorylated Chey with Imidazole 1 of 3 (pdb code 5d2c). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Reaction of Phosphorylated Chey with Imidazole 1 of 3, PDB code: 5d2c:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Reaction of Phosphorylated Chey with Imidazole 1 of 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Reaction of Phosphorylated Chey with Imidazole 1 of 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:29.4 occ:1.00 OD2 A:ASP57 2.1 28.8 1.0 OD1 A:ASP13 2.2 28.8 1.0 F1 A:BEF202 2.2 27.5 1.0 O A:LYS59 2.3 25.5 1.0 O A:HOH302 2.3 26.6 1.0 N1 A:IMD203 2.4 33.5 0.9 CG A:ASP13 3.1 28.1 1.0 CG A:ASP57 3.1 25.6 1.0 C5 A:IMD203 3.1 42.8 0.9 OD2 A:ASP13 3.4 33.2 1.0 C A:LYS59 3.4 30.3 1.0 BE A:BEF202 3.4 26.5 1.0 OD1 A:ASP57 3.5 28.8 1.0 C2 A:IMD203 3.6 44.0 0.9 OD1 A:ASP12 3.9 25.8 1.0 CB A:LYS59 4.1 32.0 1.0 CA A:LYS59 4.1 28.9 1.0 OE1 A:GLN14 4.3 35.1 1.0 N A:LYS59 4.3 27.6 1.0 CG A:MET60 4.3 27.4 1.0 F3 A:BEF202 4.4 24.2 1.0 CB A:ASP57 4.4 24.6 1.0 C4 A:IMD203 4.4 41.6 0.9 N A:MET60 4.5 26.5 1.0 F2 A:BEF202 4.5 27.1 1.0 N A:ASP13 4.5 25.5 1.0 CB A:ASP13 4.5 28.2 1.0 O A:HOH330 4.6 45.9 1.0 N3 A:IMD203 4.6 44.7 0.9 CG A:ASP12 4.6 27.2 1.0 NZ A:LYS109 4.7 28.2 1.0 CG A:GLN14 4.7 35.7 1.0 CA A:MET60 4.8 29.5 1.0 CG A:LYS59 4.8 37.2 1.0 CD A:GLN14 4.8 38.3 1.0 OD2 A:ASP12 4.8 28.2 1.0 N3 A:IMD204 4.9 37.1 0.8 CA A:ASP13 4.9 26.8 1.0

Manganese binding site 2 out of 2 in the Reaction of Phosphorylated Chey with Imidazole 1 of 3


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Reaction of Phosphorylated Chey with Imidazole 1 of 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:30.6 occ:1.00 OD2 B:ASP57 2.1 28.8 1.0 F1 B:BEF202 2.1 28.9 1.0 OD1 B:ASP13 2.2 31.3 1.0 O B:LYS59 2.2 29.9 1.0 O B:HOH306 2.3 26.9 1.0 N1 B:IMD203 2.4 44.0 1.0 C2 B:IMD203 3.1 50.2 1.0 CG B:ASP13 3.1 32.6 1.0 CG B:ASP57 3.1 28.6 1.0 OD2 B:ASP13 3.4 35.2 1.0 BE B:BEF202 3.4 27.0 1.0 C B:LYS59 3.4 30.7 1.0 OD1 B:ASP57 3.5 29.5 1.0 C5 B:IMD203 3.6 53.3 1.0 OD1 B:ASP12 3.9 28.8 1.0 CB B:LYS59 4.1 32.9 1.0 CA B:LYS59 4.1 30.1 1.0 N B:LYS59 4.3 27.8 1.0 CG B:MET60 4.3 27.8 1.0 N3 B:IMD203 4.3 52.6 1.0 F3 B:BEF202 4.4 30.3 1.0 F2 B:BEF202 4.4 24.9 1.0 CB B:ASP57 4.4 25.7 1.0 OE1 B:GLN14 4.4 38.2 1.0 N B:MET60 4.5 28.3 1.0 CB B:ASP13 4.5 31.8 1.0 N B:ASP13 4.5 30.1 1.0 O B:HOH343 4.5 43.7 1.0 O B:HOH386 4.6 46.8 1.0 CG B:ASP12 4.6 32.2 1.0 C4 B:IMD203 4.6 51.4 1.0 CG B:GLN14 4.7 39.2 1.0 CA B:MET60 4.8 29.6 1.0 NZ B:LYS109 4.8 28.7 1.0 CG B:LYS59 4.8 39.9 1.0 CD B:GLN14 4.8 41.3 1.0 OD2 B:ASP12 4.8 27.3 1.0 CA B:ASP13 4.9 28.8 1.0

S.C.Page, R.E.Silversmith, E.J.Collins, R.B.Bourret. Imidazole As A Small Molecule Analogue in Two-Component Signal Transduction. Biochemistry V. 54 7248 2015.
ISSN: ISSN 0006-2960
PubMed: 26569142
DOI: 10.1021/ACS.BIOCHEM.5B01082