Magnesium in PDB 5z46: Crystal Structure of Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile

The structure of Crystal Structure of Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile, PDB code: 5z46 was solved by T.Awakawa, Y.Nakashima, T.Mori, I.Abe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.75 / 2.00
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	117.267, 117.267, 49.324, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.5

The binding sites of Magnesium atom in the Crystal Structure of Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile (pdb code 5z46). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile, PDB code: 5z46:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile


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 Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:88.9 occ:1.00 O A:HOH538 2.3 58.4 1.0 O A:GLY208 2.3 62.7 1.0 O A:HOH510 2.4 86.3 1.0 OD1 A:ASN207 2.6 70.2 1.0 OE2 A:GLU209 2.8 78.3 1.0 OG1 A:THR173 2.8 52.2 1.0 C A:GLY208 3.3 62.7 1.0 CG A:ASN207 3.8 69.6 1.0 CD A:GLU209 4.0 67.3 1.0 CB A:THR173 4.0 36.6 1.0 CG2 A:THR173 4.1 36.0 1.0 N A:GLU209 4.2 44.5 1.0 CA A:GLY208 4.2 55.4 1.0 N A:GLY208 4.3 69.5 1.0 N A:THR173 4.3 33.8 1.0 CA A:GLU209 4.4 47.2 1.0 ND2 A:ASN207 4.5 68.8 1.0 C A:ASN207 4.7 63.8 1.0 OD1 A:ASP172 4.8 64.6 1.0 CG A:GLU209 4.8 48.0 1.0 CA A:THR173 4.8 36.2 1.0 OE1 A:GLU209 4.8 82.0 1.0 CB A:ASN207 4.8 64.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile


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 Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:43.5 occ:1.00 OD1 A:ASP65 2.0 70.5 1.0 OD1 A:ASN41 2.0 46.0 1.0 O A:HOH514 2.0 39.1 1.0 O A:HOH524 2.1 46.1 1.0 O A:HOH528 2.2 38.0 1.0 OE2 A:GLU63 2.2 56.2 1.0 CD A:GLU63 3.0 54.5 1.0 CG A:ASN41 3.1 42.9 1.0 OE1 A:GLU63 3.1 46.9 1.0 CG A:ASP65 3.1 62.6 1.0 ND2 A:ASN41 3.7 42.7 1.0 CB A:ASP65 3.8 54.9 1.0 O A:HOH507 4.1 40.2 1.0 OD2 A:ASP65 4.1 66.3 1.0 N A:ASP65 4.2 48.5 1.0 O A:ASP40 4.3 49.3 1.0 CB A:ASN41 4.3 40.7 1.0 CG A:GLU63 4.3 53.5 1.0 N A:GLU64 4.5 51.1 1.0 CA A:ASP65 4.6 55.0 1.0 CA A:GLU63 4.6 49.6 1.0 CA A:ASN41 4.7 47.1 1.0 CB A:GLU63 4.8 42.0 1.0 C A:ASP40 4.9 47.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile


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 Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:45.2 occ:1.00 OD1 B:ASN41 2.0 55.4 1.0 OD2 B:ASP65 2.0 70.1 1.0 O B:HOH504 2.1 43.8 1.0 O B:HOH535 2.1 44.8 1.0 O B:HOH518 2.3 42.9 1.0 OE1 B:GLU63 2.3 54.5 1.0 CG B:ASN41 3.1 46.3 1.0 CD B:GLU63 3.2 47.1 1.0 CG B:ASP65 3.2 61.6 1.0 OE2 B:GLU63 3.4 51.3 1.0 ND2 B:ASN41 3.8 44.4 1.0 CB B:ASP65 3.9 56.9 1.0 N B:ASP65 4.0 55.2 1.0 O B:ASP40 4.1 56.4 1.0 O B:HOH530 4.1 38.5 1.0 N B:GLU64 4.2 47.5 1.0 OD1 B:ASP65 4.2 71.2 1.0 CB B:ASN41 4.3 36.2 1.0 CG B:GLU63 4.5 44.3 1.0 CA B:ASN41 4.6 48.7 1.0 CA B:ASP65 4.6 53.5 1.0 CA B:GLU63 4.6 48.6 1.0 C B:ASP40 4.8 67.8 1.0 C B:GLU63 4.9 53.1 1.0 C B:GLU64 5.0 56.2 1.0 CB B:GLU63 5.0 44.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile


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 Prenyltransferase AMBP1 PH8 Complexed with Gspp and Cis-Indolyl Vinyl Isonitrile within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:69.1 occ:1.00 O B:HOH510 2.1 63.4 1.0 OE2 B:GLU209 2.6 84.1 1.0 O B:GLY208 2.8 78.2 1.0 OD1 B:ASP172 3.2 73.3 1.0 OE1 B:GLU209 3.3 84.0 1.0 CD B:GLU209 3.3 76.6 1.0 OG1 B:THR173 3.3 52.2 1.0 C B:GLY208 3.9 70.7 1.0 N B:THR173 3.9 26.0 1.0 CG B:ASP172 4.4 64.9 1.0 CB B:THR173 4.4 44.0 1.0 N B:GLY208 4.4 76.4 1.0 CA B:ASP172 4.5 38.2 1.0 CG2 B:THR173 4.6 40.9 1.0 N B:GLU209 4.7 62.3 1.0 C B:ASP172 4.7 36.3 1.0 CA B:GLY208 4.7 65.0 1.0 CA B:THR173 4.7 34.4 1.0 CG B:GLU209 4.8 66.2 1.0 CA B:GLU209 4.9 59.1 1.0 CB B:ASP172 5.0 39.7 1.0

T.Awakawa, T.Mori, Y.Nakashima, R.Zhai, C.P.Wong, M.L.Hillwig, X.Liu, I.Abe. Molecular Insight Into the MG2+-Dependent Allosteric Control of Indole Prenylation By Aromatic Prenyltransferase AMBP1 Angew. Chem. Int. Ed. Engl. V. 57 6810 2018.
ISSN: ESSN 1521-3773
PubMed: 29677386
DOI: 10.1002/ANIE.201800855