Magnesium in PDB 5t64: X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah

The structure of X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah, PDB code: 5t64 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 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.340, 110.894, 143.251, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22

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

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah (pdb code 5t64). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah, PDB code: 5t64:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah


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 C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:18.3 occ:1.00 O A:HOH644 2.0 16.6 1.0 O A:HOH952 2.1 16.3 1.0 O A:HOH772 2.2 18.6 1.0 O A:HOH983 2.3 16.4 1.0 O A:HOH973 3.9 25.7 1.0 OE1 A:GLU396 4.2 19.3 1.0 O A:LYS393 4.3 13.7 1.0 O A:HOH738 4.3 18.5 1.0 O A:HOH646 4.4 24.0 1.0 OE2 A:GLU396 4.4 24.8 1.0 O A:HOH695 4.4 14.9 1.0 CD A:GLU396 4.8 22.4 1.0

Magnesium binding site 2 out of 3 in the X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah


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 C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:53.5 occ:1.00 O A:HOH943 1.9 54.4 1.0 O A:HOH628 2.1 28.1 1.0 O A:HOH996 2.2 42.0 1.0 O A:HOH629 2.2 38.0 1.0 O A:HOH935 2.3 44.5 1.0 O A:HOH817 2.4 43.9 1.0 OE2 A:GLU244 4.0 19.6 1.0 OE1 A:GLU244 4.3 18.5 1.0 CA A:GLY266 4.3 21.3 1.0 O A:HOH887 4.4 40.3 1.0 O A:ARG268 4.4 18.5 1.0 CD A:GLU244 4.6 18.6 1.0 O A:GLY266 4.7 20.8 1.0 N A:GLY266 4.9 22.4 1.0 C A:GLY266 4.9 21.3 1.0 CD A:PRO270 5.0 20.4 1.0

Magnesium binding site 3 out of 3 in the X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of the C3-Methyltransferase KIJD1 From Actinomadura Kijaniata in Complex with Tdp and Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:46.0 occ:1.00 O A:HOH768 2.0 24.7 1.0 O A:HOH845 2.1 34.1 1.0 OD2 A:ASP25 2.1 23.1 1.0 CG A:ASP25 3.1 17.9 1.0 OD1 A:ASP25 3.4 18.4 1.0 NE A:ARG48 3.9 21.2 1.0 NH2 A:ARG48 4.1 20.7 1.0 CB A:ASP25 4.5 17.0 1.0 CZ A:ARG48 4.5 20.4 1.0 O A:HOH879 4.9 26.5 1.0 CD A:ARG48 4.9 21.1 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