Magnesium in PDB 8rpr: Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion

The structure of Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion, PDB code: 8rpr was solved by R.Saleem-Batcha, Z.Zou, J.Breiltgens, M.Mueller, J.N.Andexer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.40 / 2.14
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.031, 67.031, 182.745, 90, 90, 90
R / Rfree (%)	19.5 / 23.2

The structure of Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion (pdb code 8rpr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion, PDB code: 8rpr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:65.0 occ:1.00 O A:ALA12 2.9 47.0 1.0 O A:HOH606 3.0 54.2 1.0 C A:ALA12 3.7 49.3 1.0 N A:ALA16 3.8 41.5 1.0 CG2 A:ILE15 3.9 45.1 1.0 CA A:ALA12 3.9 55.5 1.0 CB A:ALA16 4.0 44.2 1.0 CB A:ILE15 4.0 49.0 1.0 CB A:ALA12 4.1 57.1 1.0 CA A:ALA16 4.3 46.5 1.0 C A:ILE15 4.6 43.8 1.0 CA A:ILE15 4.8 45.8 1.0 N A:ASP13 4.9 52.5 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:45.8 occ:1.00 OD2 A:ASP23 2.8 47.1 1.0 CG A:ASP23 4.0 45.6 1.0 CB A:PRO22 4.2 37.4 1.0 N A:ASP23 4.3 36.6 1.0 CA A:ASP23 4.5 38.3 1.0 C A:PRO22 4.5 37.5 1.0 O A:HOH570 4.6 38.6 1.0 O A:PRO22 4.8 36.0 1.0 OD1 A:ASP23 4.8 51.0 1.0 CB A:ASP23 4.9 37.1 1.0 CA A:PRO22 5.0 35.6 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:69.8 occ:1.00 O A:HIS10 3.0 52.8 1.0 O A:HOH581 3.4 64.5 1.0 CB A:HIS10 3.6 63.9 1.0 C A:HIS10 3.7 58.8 1.0 CA A:HIS10 3.8 62.9 1.0 CA A:GLY14 4.2 38.8 1.0 N A:GLY14 4.2 46.0 1.0 CG A:HIS10 4.3 70.5 1.0 ND1 A:HIS10 4.7 76.6 1.0 N A:LEU11 4.8 62.8 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:53.5 occ:1.00 O A:ALA64 2.7 46.2 1.0 CB A:ARG67 3.4 47.2 1.0 N A:TYR68 3.5 48.1 1.0 C A:ALA64 3.6 48.4 1.0 CA A:ALA64 3.9 50.2 1.0 NE A:ARG67 3.9 50.5 1.0 C A:ARG67 3.9 49.7 1.0 NH2 A:ARG67 4.0 52.1 1.0 CA A:TYR68 4.1 48.2 1.0 CB A:TYR68 4.1 42.3 1.0 CA A:ARG67 4.2 46.1 1.0 CZ A:ARG67 4.3 55.6 1.0 CB A:ALA64 4.3 47.9 1.0 CG A:ARG67 4.6 47.1 1.0 N A:ARG67 4.6 46.7 1.0 O A:ARG67 4.7 46.0 1.0 CD A:ARG67 4.8 50.7 1.0 N A:LEU65 4.9 49.6 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Sgvm Methyltransferase in Complex with Alpha- Ketoleucine and ZN2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:51.0 occ:1.00 O A:HOH604 2.5 61.8 1.0 O A:GLY19 2.7 43.8 1.0 O A:ILE15 2.9 41.7 1.0 N A:GLY19 3.4 40.5 1.0 C A:GLY19 3.5 41.3 1.0 CA A:GLY19 3.5 41.8 1.0 C A:ILE15 3.8 43.8 1.0 CG2 A:ILE15 3.8 45.1 1.0 CA A:ILE15 4.0 45.8 1.0 C A:SER18 4.1 40.5 1.0 CB A:SER18 4.2 41.1 1.0 CB A:ILE15 4.5 49.0 1.0 O A:HOH570 4.5 38.6 1.0 CA A:SER18 4.7 40.0 1.0 N A:PRO20 4.7 39.5 1.0 O A:SER18 4.9 39.2 1.0 CG1 A:ILE15 5.0 45.4 1.0 N A:ALA16 5.0 41.5 1.0

C.Sommer-Kamann, J.Breiltgens, Z.Zou, S.Gerhardt, R.Saleem-Batcha, F.Kemper, O.Einsle, J.N.Andexer, M.Muller. Structures and Protein Engineering of the Alpha-Keto Acid C-Methyltransferases Sgvm and Mrsa For Rational Substrate Transfer. Chembiochem 00258 2024.
ISSN: ESSN 1439-7633
PubMed: 38887142
DOI: 10.1002/CBIC.202400258