Magnesium in PDB 5t67: X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product

The structure of X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product, PDB code: 5t67 was solved by H.M.Holden, J.B.Thoden, G.T.Dow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.088, 108.893, 142.783, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.9

The structure of X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product (pdb code 5t67). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product, PDB code: 5t67:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:26.3 occ:1.00 O A:HOH812 1.9 24.8 1.0 O A:HOH692 2.0 24.1 1.0 O A:HOH1050 2.2 26.1 1.0 O A:HOH1008 2.2 20.9 1.0 OE2 A:GLU396 4.2 23.5 1.0 OE1 A:GLU396 4.2 23.9 1.0 O A:LYS393 4.3 21.5 1.0 O A:HOH797 4.3 28.3 1.0 O A:HOH756 4.4 16.1 1.0 O A:HOH660 4.5 21.2 1.0 CD A:GLU396 4.7 21.9 1.0

Magnesium binding site 2 out of 2 in the X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of the KIJD1 C3-Methyltransferase From Actinomadura Kijaniata in Complex with Sah and Dtdp-Sugar Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:34.2 occ:1.00 O A:HOH1014 2.0 32.6 1.0 O A:HOH912 2.1 45.6 1.0 O A:HOH693 2.2 27.1 1.0 O A:HOH626 2.2 25.1 1.0 O A:HOH991 2.3 37.0 1.0 OE2 A:GLU244 4.1 20.6 1.0 OE1 A:GLU244 4.1 18.1 1.0 CA A:GLY266 4.3 27.6 1.0 O A:ARG268 4.4 19.4 1.0 CD A:GLU244 4.5 22.7 1.0 O A:HOH908 4.6 30.7 1.0 O A:GLY266 4.7 29.1 1.0 N A:GLY266 4.8 23.8 1.0 C A:GLY266 4.8 24.0 1.0 CD A:PRO270 4.9 15.1 1.0

G.T.Dow, J.B.Thoden, H.M.Holden. Structural Studies on KIJD1, A Sugar C-3'-Methyltransferase. Protein Sci. V. 25 2282 2016.
ISSN: ESSN 1469-896X
PubMed: 27595766
DOI: 10.1002/PRO.3034