Magnesium in PDB 6pd1: Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola

The structure of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola, PDB code: 6pd1 was solved by M.D.L.Suits, J.Whiteside, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 2.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.053, 129.012, 135.797, 90.00, 92.99, 90.00
R / Rfree (%)	19.9 / 23.3

The structure of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Magnesium atom in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola (pdb code 6pd1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola, PDB code: 6pd1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:50.2 occ:1.00 OE2 A:GLU220 2.2 68.5 1.0 OD1 A:ASP106 2.4 56.1 1.0 OD2 A:ASP106 2.8 71.3 1.0 OE1 A:GLU104 2.8 71.8 1.0 CG A:ASP106 2.9 60.3 1.0 CD A:GLU220 3.0 69.2 1.0 O A:HOH849 3.0 53.3 1.0 CB A:GLU104 3.4 42.6 1.0 CD A:GLU104 3.5 55.9 1.0 CG A:GLU220 3.6 69.0 1.0 OE1 A:GLU220 3.9 65.7 1.0 CG A:GLU104 3.9 44.1 1.0 OE2 A:GLU104 4.3 62.6 1.0 CB A:ASP106 4.4 58.5 1.0 N A:ASP106 4.7 49.6 1.0 CA A:GLU104 4.8 45.1 1.0 N A:SER105 5.0 45.1 1.0

Magnesium binding site 2 out of 4 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:34.3 occ:1.00 OE2 B:GLU220 2.1 49.7 1.0 OE2 B:GLU104 2.3 59.9 1.0 OD2 B:ASP106 2.7 53.2 1.0 OD1 B:ASP106 2.8 53.1 1.0 CG B:ASP106 3.1 49.3 1.0 CD B:GLU220 3.3 60.9 1.0 CD B:GLU104 3.4 56.7 1.0 CB B:GLU104 3.8 43.7 1.0 O B:HOH828 3.8 38.9 1.0 CG B:GLU220 4.0 54.1 1.0 NZ B:LYS25 4.0 59.5 1.0 CG B:GLU104 4.0 49.9 1.0 OE1 B:GLU220 4.2 57.6 1.0 OE1 B:GLU104 4.3 52.7 1.0 CB B:ASP106 4.6 43.2 1.0 CE B:LYS25 5.0 48.7 1.0

Magnesium binding site 3 out of 4 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1102 b:61.2 occ:1.00 OD2 C:ASP106 2.8 80.3 1.0 O C:HOH1225 2.9 58.6 1.0 OE1 C:GLU104 3.2 70.5 1.0 CG C:ASP106 3.3 69.0 1.0 OD1 C:ASP106 3.3 64.9 1.0 OE2 C:GLU220 3.6 90.6 1.0 NZ C:LYS25 3.7 87.5 1.0 CD C:GLU104 4.1 67.1 1.0 CB C:GLU104 4.2 57.7 1.0 CE C:LYS25 4.5 82.5 1.0 CG C:GLU104 4.5 55.5 1.0 CB C:ASP106 4.6 62.5 1.0 CD C:GLU220 4.7 89.5 1.0

Magnesium binding site 4 out of 4 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:74.8 occ:1.00 OD2 D:ASP106 2.6 70.8 1.0 OE1 D:GLU104 2.7 76.1 1.0 OD1 D:ASP106 2.9 62.0 1.0 CG D:ASP106 3.1 64.8 1.0 OE1 D:GLU220 3.1 78.4 1.0 CD D:GLU104 3.7 66.5 1.0 CB D:GLU104 3.9 46.9 1.0 NZ D:LYS25 4.0 69.9 1.0 CG D:GLU104 4.2 54.4 1.0 CD D:GLU220 4.3 78.5 1.0 CB D:ASP106 4.5 61.8 1.0 OE2 D:GLU104 4.7 61.0 1.0 CE D:LYS25 4.8 60.3 1.0 CG D:GLU220 4.8 69.8 1.0 N D:ASP106 4.9 54.6 1.0

K.Rice, K.Batul, J.Whiteside, J.Kelso, M.Papinski, E.Schmidt, A.Pratasouskaya, D.Wang, R.Sullivan, C.Bartlett, J.T.Weadge, M.W.Van Der Kamp, G.Moreno-Hagelsieb, M.D.Suits, G.P.Horsman. The Predominance of Nucleotidyl Activation in Bacterial Phosphonate Biosynthesis. Nat Commun V. 10 3698 2019.
ISSN: ESSN 2041-1723
PubMed: 31420548
DOI: 10.1038/S41467-019-11627-6