Magnesium in PDB 6pd2: Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep

The structure of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep, PDB code: 6pd2 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)	47.98 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.450, 154.050, 134.580, 90.00, 90.90, 90.00
R / Rfree (%)	22 / 25.4

The binding sites of Magnesium atom in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep (pdb code 6pd2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep, PDB code: 6pd2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep


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 in Complex with Cytidine Monophosphate-Aep within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:31.8 occ:1.00 O3B A:0RC705 1.9 37.1 1.0 O A:HOH814 2.1 29.4 1.0 O1A A:0RC705 2.1 29.2 1.0 OD2 A:ASP222 2.2 30.1 1.0 OE1 A:GLU220 2.2 28.3 1.0 OD2 A:ASP106 2.3 33.3 1.0 PB A:0RC705 2.5 32.0 1.0 MG A:MG703 2.9 27.2 1.0 O3A A:0RC705 3.0 28.4 1.0 CG A:ASP222 3.1 28.3 1.0 C1B A:0RC705 3.2 36.5 1.0 PA A:0RC705 3.2 29.3 1.0 CG A:ASP106 3.2 29.9 1.0 OD1 A:ASP222 3.2 28.8 1.0 OD1 A:ASP106 3.3 28.9 1.0 CD A:GLU220 3.4 28.3 1.0 NZ A:LYS25 3.8 28.3 1.0 C14 A:0RC705 3.9 27.6 1.0 O2B A:0RC705 4.0 32.4 1.0 OE2 A:GLU220 4.0 26.0 1.0 O2A A:0RC705 4.1 29.4 1.0 CB A:GLU220 4.3 26.1 1.0 C5' A:0RC705 4.4 27.2 1.0 O5' A:0RC705 4.4 30.0 1.0 CG A:GLU220 4.5 27.9 1.0 CB A:ASP222 4.5 32.0 1.0 O A:HOH879 4.6 27.6 1.0 OE1 A:GLU104 4.6 21.9 1.0 CB A:ASP106 4.7 28.8 1.0 CE A:LYS25 4.7 32.3 1.0 N15 A:0RC705 4.9 25.6 1.0 CA A:ASP222 4.9 29.8 1.0 OD2 A:ASP136 4.9 28.9 1.0 O A:HOH807 5.0 28.9 1.0

Magnesium binding site 2 out of 8 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep


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 in Complex with Cytidine Monophosphate-Aep within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:27.2 occ:1.00 O3B A:0RC705 1.9 37.1 1.0 OD1 A:ASP222 2.1 28.8 1.0 C1B A:0RC705 2.1 36.5 1.0 O A:HOH879 2.1 27.6 1.0 OE2 A:GLU220 2.3 26.0 1.0 OD2 A:ASP136 2.3 28.9 1.0 PB A:0RC705 2.3 32.0 1.0 OE1 A:GLU220 2.5 28.3 1.0 CD A:GLU220 2.7 28.3 1.0 MG A:MG702 2.9 31.8 1.0 O2B A:0RC705 3.0 32.4 1.0 CG A:ASP222 3.0 28.3 1.0 OD2 A:ASP222 3.3 30.1 1.0 CG A:ASP136 3.4 31.5 1.0 C14 A:0RC705 3.7 27.6 1.0 NH1 A:ARG15 3.9 27.6 1.0 O3A A:0RC705 3.9 28.4 1.0 CB A:ASP136 4.0 26.3 1.0 O A:ASP136 4.1 29.0 1.0 CG A:GLU220 4.2 27.9 1.0 O A:HOH814 4.4 29.4 1.0 CB A:ASP222 4.4 32.0 1.0 O2 A:EDO717 4.4 27.2 1.0 C2 A:EDO717 4.4 30.2 1.0 NZ A:LYS153 4.4 25.7 1.0 OD1 A:ASP136 4.4 34.3 1.0 O1A A:0RC705 4.6 29.2 1.0 N15 A:0RC705 4.7 25.6 1.0 OD2 A:ASP106 4.9 33.3 1.0 CE A:LYS153 4.9 29.7 1.0 PA A:0RC705 4.9 29.3 1.0 C A:ASP136 4.9 28.3 1.0 CE1 A:HIS226 5.0 30.4 1.0

Magnesium binding site 3 out of 8 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep


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 in Complex with Cytidine Monophosphate-Aep within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:34.8 occ:1.00 O3B B:0RC705 1.8 41.2 1.0 O B:HOH819 2.1 29.9 1.0 O1A B:0RC705 2.1 33.6 1.0 OE1 B:GLU220 2.2 34.9 1.0 OD1 B:ASP222 2.4 34.2 1.0 OD2 B:ASP106 2.4 33.1 1.0 PB B:0RC705 2.5 35.4 1.0 MG B:MG703 2.9 33.7 1.0 C1B B:0RC705 3.1 41.5 1.0 CG B:ASP222 3.2 35.9 1.0 CG B:ASP106 3.2 34.9 1.0 CD B:GLU220 3.3 35.2 1.0 O3A B:0RC705 3.3 33.6 1.0 OD2 B:ASP222 3.3 37.5 1.0 PA B:0RC705 3.3 34.8 1.0 OD1 B:ASP106 3.3 31.3 1.0 NZ B:LYS25 3.7 37.4 1.0 OE2 B:GLU220 3.8 36.8 1.0 O2B B:0RC705 3.9 34.4 1.0 C14 B:0RC705 4.0 36.8 1.0 C5' B:0RC705 4.2 33.1 1.0 CB B:GLU220 4.3 32.9 1.0 O2A B:0RC705 4.3 43.6 1.0 CG B:GLU220 4.4 32.9 1.0 O5' B:0RC705 4.4 38.7 1.0 OE1 B:GLU104 4.5 28.4 1.0 CE B:LYS25 4.6 35.1 1.0 CB B:ASP222 4.6 39.8 1.0 CB B:ASP106 4.7 29.8 1.0 O B:HOH823 4.7 34.7 1.0 OD2 B:ASP136 4.9 37.1 1.0 O B:HOH854 5.0 25.9 1.0

Magnesium binding site 4 out of 8 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep


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 in Complex with Cytidine Monophosphate-Aep within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:33.7 occ:1.00 O3B B:0RC705 2.0 41.2 1.0 O B:HOH823 2.1 34.7 1.0 C1B B:0RC705 2.1 41.5 1.0 PB B:0RC705 2.3 35.4 1.0 OE2 B:GLU220 2.3 36.8 1.0 OD2 B:ASP222 2.3 37.5 1.0 OD2 B:ASP136 2.4 37.1 1.0 OE1 B:GLU220 2.5 34.9 1.0 O2B B:0RC705 2.7 34.4 1.0 CD B:GLU220 2.7 35.2 1.0 MG B:MG702 2.9 34.8 1.0 CG B:ASP222 3.3 35.9 1.0 CG B:ASP136 3.5 38.6 1.0 OD1 B:ASP222 3.6 34.2 1.0 C14 B:0RC705 3.7 36.8 1.0 O3A B:0RC705 3.9 33.6 1.0 O B:ASP136 3.9 37.9 1.0 O B:HOH1092 4.0 28.9 1.0 CB B:ASP136 4.1 31.8 1.0 NH2 B:ARG15 4.2 40.8 1.0 CG B:GLU220 4.3 32.9 1.0 O B:HOH819 4.3 29.9 1.0 OD1 B:ASP136 4.4 40.5 1.0 O1A B:0RC705 4.5 33.6 1.0 NZ B:LYS153 4.5 32.0 1.0 N15 B:0RC705 4.5 34.0 1.0 CB B:ASP222 4.7 39.8 1.0 CE B:LYS153 4.8 36.4 1.0 C B:ASP136 4.9 36.7 1.0 OD2 B:ASP106 4.9 33.1 1.0 PA B:0RC705 4.9 34.8 1.0 NH1 B:ARG15 5.0 45.0 1.0

Magnesium binding site 5 out of 8 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2203 b:29.0 occ:1.00 O3B C:0RC2205 1.7 27.1 1.0 O C:HOH2345 2.0 24.1 1.0 OD2 C:ASP136 2.1 34.8 1.0 OD2 C:ASP222 2.1 29.1 1.0 OE2 C:GLU220 2.3 25.5 1.0 OE1 C:GLU220 2.4 33.6 1.0 PB C:0RC2205 2.5 29.3 1.0 CD C:GLU220 2.7 31.2 1.0 MG C:MG2211 2.9 26.5 1.0 CG C:ASP222 3.1 30.8 1.0 O2B C:0RC2205 3.1 34.9 1.0 C1B C:0RC2205 3.2 29.3 1.0 CG C:ASP136 3.3 35.6 1.0 OD1 C:ASP222 3.4 30.0 1.0 O C:ASP136 3.9 32.4 1.0 CB C:ASP136 3.9 35.3 1.0 O3A C:0RC2205 4.0 26.8 1.0 O C:HOH2326 4.1 30.4 1.0 CG C:GLU220 4.2 27.6 1.0 C14 C:0RC2205 4.2 28.8 1.0 O1A C:0RC2205 4.3 27.5 1.0 NH1 C:ARG15 4.3 32.6 1.0 OD1 C:ASP136 4.3 32.5 1.0 CB C:ASP222 4.4 30.2 1.0 O C:HOH2529 4.5 24.2 1.0 NZ C:LYS153 4.5 29.1 1.0 NH2 C:ARG15 4.5 34.8 1.0 CE1 C:HIS226 4.8 33.2 1.0 PA C:0RC2205 4.8 28.3 1.0 C C:ASP136 4.9 31.4 1.0 CZ C:ARG15 4.9 32.0 1.0 CE C:LYS153 4.9 30.9 1.0 N15 C:0RC2205 5.0 25.7 1.0 CB C:GLU220 5.0 26.3 1.0 OD2 C:ASP106 5.0 27.9 1.0

Magnesium binding site 6 out of 8 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2211 b:26.5 occ:1.00 O3B C:0RC2205 1.8 27.1 1.0 O C:HOH2326 2.0 30.4 1.0 O1A C:0RC2205 2.0 27.5 1.0 OD1 C:ASP222 2.1 30.0 1.0 OE2 C:GLU220 2.1 25.5 1.0 OD2 C:ASP106 2.2 27.9 1.0 CG C:ASP222 2.9 30.8 1.0 MG C:MG2203 2.9 29.0 1.0 OD2 C:ASP222 3.1 29.1 1.0 PB C:0RC2205 3.2 29.3 1.0 CG C:ASP106 3.3 26.7 1.0 CD C:GLU220 3.3 31.2 1.0 PA C:0RC2205 3.3 28.3 1.0 O3A C:0RC2205 3.5 26.8 1.0 OD1 C:ASP106 3.7 22.0 1.0 NZ C:LYS25 3.8 29.3 1.0 CB C:GLU220 4.0 26.3 1.0 OE1 C:GLU220 4.1 33.6 1.0 CG C:GLU220 4.2 27.6 1.0 O2A C:0RC2205 4.3 31.2 1.0 C1B C:0RC2205 4.3 29.3 1.0 CB C:ASP222 4.3 30.2 1.0 O2B C:0RC2205 4.4 34.9 1.0 C14 C:0RC2205 4.4 28.8 1.0 O5' C:0RC2205 4.5 28.5 1.0 O C:HOH2345 4.5 24.1 1.0 CE C:LYS25 4.6 28.7 1.0 OE1 C:GLU104 4.6 24.4 1.0 CB C:ASP106 4.6 24.1 1.0 C5' C:0RC2205 4.6 24.4 1.0 N C:ASP222 4.7 30.6 1.0 CA C:ASP222 4.8 30.9 1.0 OD2 C:ASP136 4.8 34.8 1.0 O C:ILE221 4.8 28.6 1.0 C C:ILE221 4.9 28.0 1.0 NH2 C:ARG15 4.9 34.8 1.0 N C:ILE221 5.0 23.8 1.0

Magnesium binding site 7 out of 8 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:41.0 occ:1.00 OE2 D:GLU220 1.9 37.2 1.0 O3B D:0RC705 2.0 35.2 1.0 O D:HOH841 2.1 31.0 1.0 OD2 D:ASP222 2.1 38.9 1.0 OD2 D:ASP136 2.2 39.9 1.0 OE1 D:GLU220 2.3 42.6 1.0 CD D:GLU220 2.3 39.0 1.0 MG D:MG703 2.9 46.3 1.0 CG D:ASP222 3.0 35.0 1.0 PB D:0RC705 3.1 37.2 1.0 OD1 D:ASP222 3.3 35.5 1.0 CG D:ASP136 3.3 39.8 1.0 O2B D:0RC705 3.6 39.0 1.0 C1B D:0RC705 3.8 35.4 1.0 CG D:GLU220 3.8 35.5 1.0 O D:ASP136 3.9 35.9 1.0 CB D:ASP136 3.9 36.1 1.0 O D:HOH803 4.2 32.5 1.0 O1A D:0RC705 4.3 35.7 1.0 O D:HOH978 4.3 31.5 1.0 C14 D:0RC705 4.3 35.7 1.0 OD1 D:ASP136 4.3 40.7 1.0 CB D:ASP222 4.4 38.0 1.0 O D:HOH1086 4.4 45.9 1.0 O3A D:0RC705 4.6 35.5 1.0 O D:HOH1001 4.6 35.7 1.0 NZ D:LYS153 4.6 38.9 1.0 CE1 D:HIS226 4.6 42.4 1.0 C D:ASP136 4.8 38.9 1.0 OD2 D:ASP106 4.8 40.0 1.0 CB D:GLU220 4.9 39.1 1.0 CA D:ASP136 5.0 38.4 1.0

Magnesium binding site 8 out of 8 in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola in Complex with Cytidine Monophosphate-Aep within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg703 b:46.3 occ:1.00 OE1 D:GLU220 1.1 42.6 1.0 O D:HOH803 2.1 32.5 1.0 CD D:GLU220 2.1 39.0 1.0 OD2 D:ASP106 2.2 40.0 1.0 OD1 D:ASP222 2.5 35.5 1.0 O3B D:0RC705 2.7 35.2 1.0 O1A D:0RC705 2.9 35.7 1.0 MG D:MG701 2.9 41.0 1.0 CG D:ASP106 3.0 36.6 1.0 CG D:GLU220 3.0 35.5 1.0 CB D:GLU220 3.1 39.1 1.0 OD1 D:ASP106 3.1 29.0 1.0 OE2 D:GLU220 3.1 37.2 1.0 CG D:ASP222 3.3 35.0 1.0 OD2 D:ASP222 3.4 38.9 1.0 PB D:0RC705 4.1 37.2 1.0 OE1 D:GLU104 4.3 28.7 1.0 O D:HOH912 4.3 30.9 1.0 PA D:0RC705 4.3 34.5 1.0 CA D:GLU220 4.3 33.3 1.0 CB D:ASP106 4.4 36.5 1.0 O D:HOH841 4.4 31.0 1.0 N D:ILE221 4.4 39.3 1.0 C D:GLU220 4.5 37.6 1.0 C14 D:0RC705 4.6 35.7 1.0 CB D:ASP222 4.6 38.0 1.0 NZ D:LYS25 4.6 41.0 1.0 N D:ASP222 4.6 38.5 1.0 O3A D:0RC705 4.6 35.5 1.0 C D:ILE221 4.8 42.2 1.0 C1B D:0RC705 4.9 35.4 1.0 CA D:ASP222 4.9 39.6 1.0 O D:ILE221 4.9 41.2 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