Nickel in PDB 4zxi: Crystal Structure of Holo-AB3403 A Four Domain Nonribosomal Peptide Synthetase Bound to Amp and Glycine

The structure of Crystal Structure of Holo-AB3403 A Four Domain Nonribosomal Peptide Synthetase Bound to Amp and Glycine, PDB code: 4zxi was solved by E.J.Drake, B.R.Miller, C.L.Allen, A.M.Gulick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.03 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.100, 116.100, 342.020, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.5

The structure of Crystal Structure of Holo-AB3403 A Four Domain Nonribosomal Peptide Synthetase Bound to Amp and Glycine also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Holo-AB3403 A Four Domain Nonribosomal Peptide Synthetase Bound to Amp and Glycine (pdb code 4zxi). 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 Crystal Structure of Holo-AB3403 A Four Domain Nonribosomal Peptide Synthetase Bound to Amp and Glycine, PDB code: 4zxi:

Nickel binding site 1 out of 1 in the Crystal Structure of Holo-AB3403 A Four Domain Nonribosomal Peptide Synthetase Bound to Amp and Glycine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Holo-AB3403 A Four Domain Nonribosomal Peptide Synthetase Bound to Amp and Glycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1405 b:67.4 occ:1.00 N A:HIS0 1.9 79.8 1.0 ND1 A:HIS0 2.0 56.5 1.0 C A:GLY-1 2.8 83.4 1.0 CA A:GLY-1 2.8 85.4 1.0 CG A:HIS0 2.9 59.7 1.0 CA A:HIS0 3.0 67.7 1.0 CE1 A:HIS0 3.1 52.8 1.0 CB A:HIS0 3.1 63.0 1.0 O A:GLY-1 4.0 81.4 1.0 N A:MET1 4.0 97.2 1.0 N A:GLY-1 4.0 84.2 1.0 C A:HIS0 4.0 62.6 1.0 CD2 A:HIS0 4.0 54.2 1.0 NE2 A:HIS0 4.1 51.6 1.0 CD2 A:PHE94 4.7 67.4 1.0

E.J.Drake, B.R.Miller, C.Shi, J.T.Tarrasch, J.A.Sundlov, C.L.Allen, G.Skiniotis, C.C.Aldrich, A.M.Gulick. Structures of Two Distinct Conformations of Holo-Non-Ribosomal Peptide Synthetases. Nature V. 529 235 2016.
ISSN: ESSN 1476-4687
PubMed: 26762461
DOI: 10.1038/NATURE16163