Magnesium in PDB 6vkz: Crystal Structure of the N-Prenyltransferase Daba in Complex with Gspp and MG2+

The structure of Crystal Structure of the N-Prenyltransferase Daba in Complex with Gspp and MG2+, PDB code: 6vkz was solved by J.R.Chekan, J.P.Noel, B.S.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.10 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	124.286, 124.286, 114.483, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.8

The binding sites of Magnesium atom in the Crystal Structure of the N-Prenyltransferase Daba in Complex with Gspp and MG2+ (pdb code 6vkz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the N-Prenyltransferase Daba in Complex with Gspp and MG2+, PDB code: 6vkz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the N-Prenyltransferase Daba in Complex with Gspp and MG2+


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 the N-Prenyltransferase Daba in Complex with Gspp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.2 occ:1.00 O3B A:GST503 2.2 24.4 0.5 O3B A:GST503 2.3 17.9 0.5 OD1 A:ASN351 2.4 25.1 1.0 O A:HOH610 2.5 22.6 1.0 O3A A:GST503 2.5 29.0 0.5 OE2 A:GLU359 2.5 32.2 1.0 OG1 A:THR355 2.7 24.2 1.0 MG A:MG502 3.3 33.9 1.0 CD A:GLU359 3.4 32.5 1.0 CB A:THR355 3.5 26.2 1.0 PA A:GST503 3.5 35.4 0.5 CG A:ASN351 3.5 24.8 1.0 PB A:GST503 3.6 34.0 0.5 CG2 A:THR355 3.6 21.6 1.0 PB A:GST503 3.6 27.8 0.5 O1B A:GST503 3.7 29.5 0.5 O A:HOH796 3.7 24.8 1.0 OE1 A:GLU359 3.8 30.0 1.0 C1 A:GST503 3.9 30.1 0.5 O2A A:GST503 3.9 32.3 0.5 O2A A:GST503 3.9 32.4 0.5 O1A A:GST503 3.9 29.8 0.5 ND2 A:ASN351 4.1 21.0 1.0 C1 A:GST503 4.2 35.3 0.5 O1B A:GST503 4.3 33.8 0.5 PA A:GST503 4.3 32.8 0.5 O A:ASN351 4.3 21.1 1.0 O A:HOH656 4.5 27.1 1.0 CG A:GLU359 4.5 32.0 1.0 S1 A:GST503 4.5 32.1 0.5 OD1 A:ASP352 4.5 22.7 1.0 O A:HOH644 4.6 28.7 1.0 S1 A:GST503 4.6 35.6 0.5 C A:ASN351 4.7 21.8 1.0 CB A:ASN351 4.7 15.8 1.0 O2B A:GST503 4.8 22.8 0.5 O2B A:GST503 4.8 29.5 0.5 O1A A:GST503 4.9 32.7 0.5 NH2 A:ARG358 4.9 25.9 1.0 CA A:THR355 4.9 27.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the N-Prenyltransferase Daba in Complex with Gspp and MG2+


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 the N-Prenyltransferase Daba in Complex with Gspp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:33.9 occ:1.00 O A:HOH644 2.3 28.7 1.0 O A:HOH656 2.4 27.1 1.0 O A:PHE366 2.4 29.0 1.0 O A:HOH610 2.5 22.6 1.0 O3B A:GST503 2.5 17.9 0.5 OE2 A:GLU359 2.7 32.2 1.0 MG A:MG501 3.3 30.2 1.0 CD A:GLU359 3.4 32.5 1.0 OE1 A:GLU359 3.4 30.0 1.0 C A:PHE366 3.6 29.9 1.0 O A:HOH757 3.6 42.0 1.0 PB A:GST503 3.6 34.0 0.5 O2B A:GST503 3.9 29.5 0.5 CB A:PHE366 3.9 31.7 1.0 O1A A:GST503 4.0 29.8 0.5 O A:HOH796 4.0 24.8 1.0 OD1 A:ASP352 4.2 22.7 1.0 OD2 A:ASP364 4.2 35.2 1.0 O2A A:GST503 4.3 32.3 0.5 OH A:TYR302 4.3 27.5 1.0 CA A:PHE366 4.4 27.8 1.0 N A:ASN367 4.6 23.4 1.0 CA A:ASN367 4.7 26.6 1.0 O1B A:GST503 4.7 29.5 0.5 O2A A:GST503 4.7 32.4 0.5 CB A:ASN367 4.7 22.5 1.0 CG A:GLU359 4.8 32.0 1.0 O3A A:GST503 4.8 29.0 0.5 PA A:GST503 4.9 35.4 0.5 CG A:ASP364 4.9 32.0 1.0 OD1 A:ASN351 4.9 25.1 1.0 O3B A:GST503 5.0 24.4 0.5 PA A:GST503 5.0 32.8 0.5

J.R.Chekan, S.M.K.Mckinnie, J.P.Noel, B.S.Moore. Algal Neurotoxin Biosynthesis Repurposes the Terpene Cyclase Structural Fold Into An N-Prenyltransferase To Be Published.