Magnesium in PDB 7vmw: Crystal Structure of Limf Prenyltransferase Bound with A Peptide Substrate and Gspp

The structure of Crystal Structure of Limf Prenyltransferase Bound with A Peptide Substrate and Gspp, PDB code: 7vmw 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)	40.24 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.66, 48.43, 91.04, 90, 117.87, 90
R / Rfree (%)	18.2 / 23.2

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

Magnesium binding site 1 out of 2 in the Crystal Structure of Limf Prenyltransferase Bound with A Peptide Substrate and 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 A Peptide Substrate and Gspp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:26.0 occ:1.00 O3A A:GST402 2.1 27.1 1.0 O2B A:GST402 2.1 29.8 1.0 OE1 A:GLU186 2.1 20.9 1.0 O A:HOH586 2.1 26.2 1.0 O A:HOH530 2.1 21.5 1.0 O A:HOH544 2.2 25.5 1.0 CD A:GLU186 3.1 24.1 1.0 PB A:GST402 3.2 32.0 1.0 PA A:GST402 3.3 32.0 1.0 OE2 A:GLU186 3.4 22.6 1.0 O1B A:GST402 3.6 32.1 1.0 O A:HOH549 3.7 41.4 1.0 OH A:TYR188 3.8 25.5 1.0 O1A A:GST402 4.1 38.8 1.0 OH A:TYR237 4.2 28.1 1.0 O A:HOH596 4.2 25.9 1.0 O3B A:GST402 4.2 35.3 1.0 O A:HOH593 4.2 23.2 1.0 OD1 A:ASN231 4.3 25.5 1.0 O2A A:GST402 4.3 39.5 1.0 CG A:GLU186 4.5 23.1 1.0 OD2 A:ASP176 4.6 29.8 1.0 NZ A:LYS137 4.7 32.4 1.0 CB A:GLU186 4.8 22.7 1.0 S1 A:GST402 4.8 43.0 1.0 CZ A:TYR188 4.8 24.8 1.0 CE2 A:TYR188 4.9 21.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Limf Prenyltransferase Bound with A Peptide Substrate and 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 A Peptide Substrate and Gspp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:67.7 occ:1.00 O B:HOH513 2.1 55.3 1.0 O22 B:PPV402 2.3 65.7 1.0 O11 B:PPV402 2.3 59.5 1.0 O B:HOH628 2.7 58.3 1.0 O B:HOH520 2.9 55.5 1.0 OPP B:PPV402 3.0 59.4 1.0 P2 B:PPV402 3.1 62.9 1.0 P1 B:PPV402 3.2 81.8 1.0 OH B:TYR188 3.6 52.0 1.0 O12 B:PPV402 4.0 55.5 1.0 O31 B:PPV402 4.1 67.5 1.0 O32 B:PPV402 4.3 63.5 1.0 OH B:TYR237 4.3 64.3 1.0 O21 B:PPV402 4.3 66.5 1.0 CZ B:TYR188 4.6 57.2 1.0 CE2 B:TYR188 4.7 57.2 1.0 NZ B:LYS137 4.9 53.8 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