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

The structure of Reaction of Phosphorylated Chey with Imidazole 3 of 3, PDB code: 5dkf 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)	81.30 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.580, 53.740, 162.610, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.8

The structure of Reaction of Phosphorylated Chey with Imidazole 3 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 3 of 3 (pdb code 5dkf). 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 3 of 3, PDB code: 5dkf:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Reaction of Phosphorylated Chey with Imidazole 3 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 3 of 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:12.9 occ:1.00 OD2 A:ASP57 2.1 12.1 1.0 OD1 A:ASP13 2.1 13.2 1.0 F1 A:BEF202 2.2 12.8 1.0 O A:LYS59 2.2 11.5 1.0 N1 A:IMD203 2.3 16.1 0.8 O A:HOH312 2.3 11.2 1.0 C5 A:IMD203 3.1 23.2 0.8 CG A:ASP13 3.1 14.0 1.0 CG A:ASP57 3.1 11.1 1.0 BE A:BEF202 3.4 16.4 1.0 C2 A:IMD203 3.4 22.8 0.8 C A:LYS59 3.4 13.0 1.0 OD2 A:ASP13 3.4 15.9 1.0 OD1 A:ASP57 3.5 12.2 1.0 OD1 A:ASP12 4.0 10.7 1.0 CB A:LYS59 4.1 15.7 1.0 CA A:LYS59 4.2 12.6 1.0 C4 A:IMD203 4.3 22.6 0.8 CG A:MET60 4.3 10.7 1.0 N A:LYS59 4.4 11.6 1.0 OE1 A:GLN14 4.4 20.4 1.0 F3 A:BEF202 4.4 12.6 1.0 CB A:ASP57 4.4 10.2 1.0 N3 A:IMD203 4.5 22.8 0.8 F2 A:BEF202 4.5 13.4 1.0 N A:ASP13 4.5 11.3 1.0 N A:MET60 4.5 11.5 1.0 CB A:ASP13 4.5 13.5 1.0 O A:HOH346 4.6 27.2 1.0 CG A:ASP12 4.6 10.8 1.0 NZ A:LYS109 4.7 12.1 1.0 CG A:GLN14 4.7 18.6 1.0 CA A:MET60 4.8 11.7 1.0 CG A:LYS59 4.8 20.8 1.0 CD A:GLN14 4.8 22.1 1.0 OD2 A:ASP12 4.8 12.5 1.0 N3 A:IMD204 4.9 22.1 0.8 CA A:ASP13 4.9 12.9 1.0

Manganese binding site 2 out of 2 in the Reaction of Phosphorylated Chey with Imidazole 3 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 3 of 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:14.4 occ:1.00 OD2 B:ASP57 2.1 12.4 1.0 OD1 B:ASP13 2.1 13.8 1.0 F1 B:BEF202 2.2 14.5 1.0 O B:LYS59 2.2 12.7 1.0 O B:HOH312 2.3 11.3 1.0 N1 B:IMD204 2.3 20.1 0.8 CG B:ASP13 3.1 15.9 1.0 CG B:ASP57 3.1 12.0 1.0 C5 B:IMD204 3.1 24.9 0.8 BE B:BEF202 3.3 13.7 1.0 C2 B:IMD204 3.4 27.7 0.8 C B:LYS59 3.4 14.8 1.0 OD2 B:ASP13 3.4 18.0 1.0 OD1 B:ASP57 3.5 12.1 1.0 OD1 B:ASP12 3.9 12.2 1.0 CB B:LYS59 4.2 18.4 1.0 CA B:LYS59 4.2 14.8 1.0 CG B:MET60 4.3 12.8 1.0 F3 B:BEF202 4.3 10.7 1.0 N B:LYS59 4.4 13.0 1.0 C4 B:IMD204 4.4 26.9 0.8 OE1 B:GLN14 4.4 22.7 1.0 CB B:ASP57 4.4 10.8 1.0 F2 B:BEF202 4.4 11.8 1.0 CB B:ASP13 4.5 15.3 1.0 N B:ASP13 4.5 12.9 1.0 N B:MET60 4.5 13.1 1.0 N3 B:IMD204 4.5 30.0 0.8 O B:HOH409 4.6 29.4 1.0 CG B:ASP12 4.6 11.7 1.0 O B:HOH357 4.6 29.5 1.0 CG B:GLN14 4.7 21.5 1.0 CA B:MET60 4.7 13.9 1.0 NZ B:LYS109 4.8 11.1 1.0 CD B:GLN14 4.8 24.2 1.0 CG B:LYS59 4.8 22.1 1.0 N3 B:IMD203 4.8 29.7 0.8 OD2 B:ASP12 4.9 12.4 1.0 CA B:ASP13 4.9 14.4 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