Nickel in PDB 3pgu: PHE3GLU Mutant of Ecfadl

The structure of PHE3GLU Mutant of Ecfadl, PDB code: 3pgu was solved by B.W.Lepore, M.Indic, H.Pham, E.Hearn, D.Patel, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.51 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.200, 65.200, 280.280, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 18

The structure of PHE3GLU Mutant of Ecfadl also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Nickel atom in the PHE3GLU Mutant of Ecfadl (pdb code 3pgu). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the PHE3GLU Mutant of Ecfadl, PDB code: 3pgu:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the PHE3GLU Mutant of Ecfadl


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of PHE3GLU Mutant of Ecfadl within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni440 b:20.8 occ:1.00 NE2 A:HIS423 2.2 35.6 1.0 O A:HOH681 2.5 42.8 1.0 NE2 A:HIS425 2.6 86.5 1.0 O A:HOH682 2.8 55.6 1.0 CE1 A:HIS425 3.0 86.2 1.0 CE1 A:HIS423 3.2 38.1 1.0 CD2 A:HIS423 3.2 38.0 1.0 CD2 A:HIS425 3.6 85.2 1.0 ND1 A:HIS425 4.0 86.1 1.0 ND1 A:HIS423 4.3 35.5 1.0 CG A:HIS425 4.3 85.0 1.0 CG A:HIS423 4.4 36.0 1.0

Nickel binding site 2 out of 2 in the PHE3GLU Mutant of Ecfadl


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of PHE3GLU Mutant of Ecfadl within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni441 b:19.2 occ:1.00 OD2 A:ASP365 2.2 23.8 1.0 OD1 A:ASP349 2.7 43.2 1.0 O A:HOH683 2.7 49.5 1.0 OD1 A:ASP365 2.9 21.2 1.0 CG A:ASP365 2.9 19.6 1.0 CG A:ASP349 3.1 30.3 1.0 OD2 A:ASP349 3.2 30.5 1.0 O A:HOH684 4.0 44.1 1.0 CB A:ASP349 4.3 14.5 1.0 CB A:ASP365 4.3 17.6 1.0 O A:HOH585 4.5 30.9 1.0 CA A:ASP349 4.5 13.7 1.0 CZ A:PHE347 4.5 32.1 1.0 O A:HOH600 4.5 31.2 1.0 CE2 A:PHE347 4.6 29.6 1.0 O A:HOH577 4.6 32.8 1.0 N A:SER350 4.6 15.9 1.0 O A:HOH662 4.9 31.6 1.0 C A:ASP349 4.9 17.6 1.0

B.W.Lepore, M.Indic, H.Pham, E.M.Hearn, D.R.Patel, B.Van Den Berg. From the Cover: Ligand-Gated Diffusion Across the Bacterial Outer Membrane. Proc.Natl.Acad.Sci.Usa V. 108 10121 2011.
ISSN: ISSN 0027-8424
PubMed: 21593406
DOI: 10.1073/PNAS.1018532108