Magnesium in PDB 7vmy: Crystal Structure of Limf Prenyltransferase Bound with Gspp

The structure of Crystal Structure of Limf Prenyltransferase Bound with Gspp, PDB code: 7vmy was solved by K.Hamada, S.Kobayashi, C.Okada, Y.Zhang, S.Inoue, Y.Goto, H.Suga, K.Ogata, T.Sengoku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.52 / 1.77
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.28, 47.52, 61.19, 100.12, 104.69, 96.68
R / Rfree (%)	17 / 21

The binding sites of Magnesium atom in the Crystal Structure of Limf Prenyltransferase Bound with Gspp (pdb code 7vmy). 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 Limf Prenyltransferase Bound with Gspp, PDB code: 7vmy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Limf Prenyltransferase Bound with Gspp


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 Limf Prenyltransferase Bound with Gspp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:20.4 occ:1.00 O3B A:GST402 2.0 21.6 1.0 O A:HOH529 2.1 19.2 1.0 OE1 A:GLU186 2.1 20.4 1.0 O A:HOH555 2.1 23.4 1.0 O1A A:GST402 2.1 24.4 1.0 O A:HOH509 2.3 19.6 1.0 CD A:GLU186 3.0 21.5 1.0 PB A:GST402 3.2 23.5 1.0 PA A:GST402 3.3 24.8 1.0 OE2 A:GLU186 3.4 20.3 1.0 O1B A:GST402 3.5 25.2 1.0 OH A:TYR188 3.7 20.1 1.0 O A:HOH547 3.9 27.9 1.0 OH A:TYR237 4.1 19.1 1.0 O A:HOH570 4.1 20.7 1.0 O A:HOH549 4.2 20.3 1.0 O2A A:GST402 4.3 31.7 1.0 C1 A:GST402 4.3 29.6 1.0 O3A A:GST402 4.4 25.0 1.0 OD1 A:ASN231 4.4 24.0 1.0 CG A:GLU186 4.4 18.7 1.0 O2B A:GST402 4.4 29.0 1.0 OD2 A:ASP176 4.5 23.8 1.0 CZ A:TYR188 4.6 21.5 1.0 S1 A:GST402 4.7 32.6 1.0 CB A:GLU186 4.7 16.7 1.0 CE2 A:TYR188 4.8 21.1 1.0 NZ A:LYS137 4.8 28.4 1.0 O A:HOH624 5.0 21.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Limf Prenyltransferase Bound with Gspp


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 Limf Prenyltransferase Bound with Gspp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:19.1 occ:1.00 O2B B:GST402 2.0 21.8 1.0 O2A B:GST402 2.1 21.0 1.0 O B:HOH554 2.1 19.8 1.0 OE1 B:GLU186 2.1 19.2 1.0 O B:HOH579 2.1 19.9 1.0 O B:HOH527 2.2 17.8 1.0 CD B:GLU186 3.1 21.9 1.0 PB B:GST402 3.2 25.2 1.0 PA B:GST402 3.3 24.5 1.0 OE2 B:GLU186 3.4 19.0 1.0 O1B B:GST402 3.4 26.3 1.0 OH B:TYR188 3.7 18.7 1.0 OH B:TYR237 4.0 21.2 1.0 O B:HOH559 4.0 30.9 1.0 O B:HOH560 4.2 21.5 1.0 O1A B:GST402 4.2 29.1 1.0 O3B B:GST402 4.3 28.7 1.0 O B:HOH591 4.3 20.5 1.0 O3A B:GST402 4.3 24.1 1.0 C1 B:GST402 4.3 26.7 1.0 OD1 B:ASN231 4.4 21.5 1.0 CG B:GLU186 4.5 16.2 1.0 OD2 B:ASP176 4.5 23.4 1.0 S1 B:GST402 4.6 33.4 1.0 NZ B:LYS137 4.6 28.2 1.0 CZ B:TYR188 4.6 19.4 1.0 CB B:GLU186 4.7 17.0 1.0 CE2 B:TYR188 4.8 18.4 1.0 O B:HOH589 4.9 36.7 1.0 NZ B:LYS135 5.0 26.8 1.0 O B:HOH644 5.0 19.0 1.0

Y.Zhang, K.Hamada, D.T.Nguyen, S.Inoue, M.Satake, S.Kobayashi, C.Okada, K.Ogata, M.Okada, T.Sengoku, Y.Goto, H.Suga. Limf Is A Versatile Prenyltransferase For Histidine-C-Geranylation on Diverse Non-Natural Substrates Nat Catal 2022.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00822-2