Magnesium in PDB 5z43: Crystal Structure of Prenyltransferase AMBP1 Apo Structure

The structure of Crystal Structure of Prenyltransferase AMBP1 Apo Structure, PDB code: 5z43 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)	41.11 / 2.36
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	116.263, 116.263, 48.723, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 24

The binding sites of Magnesium atom in the Crystal Structure of Prenyltransferase AMBP1 Apo Structure (pdb code 5z43). 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 Prenyltransferase AMBP1 Apo Structure, PDB code: 5z43:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Prenyltransferase AMBP1 Apo Structure


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 Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:74.8 occ:1.00 OD2 A:ASP65 1.8 0.0 1.0 OD1 A:ASN41 1.9 0.1 1.0 OE1 A:GLU63 1.9 0.4 1.0 CD A:GLU63 2.7 96.4 1.0 CG A:ASP65 2.7 0.8 1.0 CG A:ASN41 2.8 70.8 1.0 OE2 A:GLU63 2.9 98.7 1.0 ND2 A:ASN41 3.2 63.6 1.0 OD1 A:ASP65 3.3 0.7 1.0 CB A:ASP65 3.7 0.3 1.0 CG A:GLU63 4.1 83.4 1.0 CB A:ASN41 4.1 70.5 1.0 N A:ASP65 4.1 89.8 1.0 O A:ASP40 4.2 78.9 1.0 N A:GLU64 4.4 81.6 1.0 CA A:GLU63 4.5 71.2 1.0 CA A:ASP65 4.6 91.5 1.0 CA A:ASN41 4.6 73.1 1.0 CB A:GLU63 4.7 67.4 1.0 C A:ASP40 4.9 76.4 1.0 C A:GLU63 5.0 81.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Prenyltransferase AMBP1 Apo Structure


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 Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:83.7 occ:1.00 OD1 B:ASP65 1.5 0.1 1.0 OD1 B:ASN41 1.7 1.0 1.0 OE1 B:GLU63 2.3 95.6 1.0 CG B:ASP65 2.6 0.2 1.0 CG B:ASN41 2.9 92.0 1.0 CD B:GLU63 3.1 93.9 1.0 OE2 B:GLU63 3.3 92.2 1.0 OD2 B:ASP65 3.4 1.0 1.0 ND2 B:ASN41 3.6 87.3 1.0 CB B:ASP65 3.7 86.7 1.0 N B:ASP65 3.9 91.6 1.0 CB B:ASN41 4.1 84.7 1.0 O B:ASP40 4.2 97.8 1.0 CA B:ASN41 4.4 86.6 1.0 N B:GLU64 4.4 83.3 1.0 CA B:ASP65 4.4 0.2 1.0 CG B:GLU63 4.6 91.7 1.0 CA B:GLU63 4.8 89.7 1.0 C B:ASP40 4.8 96.8 1.0 N B:ASN41 4.9 91.0 1.0 OD2 B:ASP40 4.9 0.0 1.0 C B:GLU64 4.9 89.7 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