Nickel 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:

Magnesium

(Mg)

4 atoms

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was determined in the Pntc-Aept: Fusion Protein of Phosphonate-Specific Cytidylyltransferase and 2-Aminoethylphosphonate (Aep) Transaminase From Treponema Denticola, PDB code: 6pd1:

Nickel binding site 1 out of 1 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 Nickel with other atoms in the Ni 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 C:Ni1106 b:55.2 occ:1.00 CD2 C:HIS622 2.2 60.0 1.0 ND1 C:HIS620 2.3 51.9 1.0 NE2 C:HIS622 2.9 54.9 1.0 CE1 C:HIS620 3.1 57.1 1.0 O C:HOH1226 3.3 31.3 1.0 CG C:HIS622 3.4 50.8 1.0 CG C:HIS620 3.4 50.0 1.0 CB C:HIS620 3.8 42.4 1.0 CB C:HIS622 4.1 49.1 1.0 CE1 C:HIS622 4.2 43.8 1.0 NE2 C:HIS620 4.3 47.0 1.0 ND1 C:HIS622 4.4 47.9 1.0 CD2 C:HIS620 4.5 51.0 1.0 CA C:HIS620 4.6 46.5 1.0 N C:HIS622 4.6 53.9 1.0 N C:HIS621 4.9 56.2 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