Nickel in PDB 6d3v: Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa

The structure of Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa, PDB code: 6d3v was solved by A.Hofmann, M.Cross, S.-Y.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.30 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.265, 66.820, 75.165, 90.00, 119.60, 90.00
R / Rfree (%)	18.8 / 21.8

The binding sites of Nickel atom in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa (pdb code 6d3v). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa, PDB code: 6d3v:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:34.5 occ:1.00 O B:HOH422 2.1 32.5 1.0 O A:HOH483 2.1 32.6 1.0 NE2 A:HIS0 2.2 28.9 1.0 NE2 B:HIS49 2.3 64.7 1.0 CE1 B:HIS49 3.0 44.3 1.0 CE1 A:HIS0 3.1 34.5 1.0 CD2 A:HIS0 3.3 47.4 1.0 CD2 B:HIS49 3.5 51.9 1.0 ND1 A:HIS0 4.3 32.0 1.0 ND1 B:HIS49 4.3 55.5 1.0 OG B:SER50 4.3 40.6 1.0 O B:HOH489 4.4 49.4 1.0 O B:HOH493 4.4 40.7 1.0 CG A:HIS0 4.4 29.1 1.0 O B:HOH467 4.5 37.2 1.0 CG B:HIS49 4.5 43.7 1.0 O B:HOH503 4.7 40.1 1.0

Nickel binding site 2 out of 3 in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:31.5 occ:1.00 OD2 A:ASP11 2.1 27.9 1.0 O A:HOH410 2.2 28.9 1.0 OD1 A:ASP220 2.2 25.9 1.0 O A:ASP13 2.3 27.2 1.0 O A:HOH418 2.3 26.3 1.0 O A:ACY301 2.4 37.7 1.0 CG A:ASP11 3.0 39.9 1.0 CG A:ASP220 3.2 30.0 1.0 OD1 A:ASP11 3.3 34.9 1.0 C A:ACY301 3.4 39.0 1.0 C A:ASP13 3.4 29.5 1.0 OD2 A:ASP220 3.5 30.6 1.0 O A:HOH402 3.9 59.4 1.0 OXT A:ACY301 4.1 37.3 1.0 OG A:SER221 4.1 27.4 1.0 OD2 A:ASP224 4.1 27.8 1.0 N A:ASP13 4.2 23.8 1.0 OG1 A:THR15 4.2 30.3 1.0 CH3 A:ACY301 4.2 37.8 1.0 CA A:ASP13 4.2 24.4 1.0 CB A:ASP11 4.3 29.7 1.0 OD2 A:ASP14 4.3 37.8 1.0 O A:HOH420 4.4 33.5 1.0 CB A:ASP14 4.4 29.7 1.0 CB A:ASP13 4.5 27.9 1.0 N A:ASP14 4.5 26.3 1.0 CB A:ASP220 4.5 24.6 1.0 C A:LEU12 4.7 23.0 1.0 N A:THR15 4.7 24.8 1.0 C A:ASP14 4.7 24.4 1.0 CA A:ASP14 4.8 23.1 1.0 N A:LEU12 4.8 23.3 1.0 N A:ASP220 4.9 25.8 1.0 CG A:ASP14 4.9 47.7 1.0 N A:SER221 4.9 21.3 1.0

Nickel binding site 3 out of 3 in the Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Chromosomal Trehalose-6-Phosphate Phosphatase From P. Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:31.4 occ:1.00 OD2 B:ASP11 2.0 28.9 1.0 O B:HOH408 2.1 26.6 1.0 OD1 B:ASP220 2.2 28.0 1.0 O B:ASP13 2.2 26.2 1.0 O B:HOH423 2.2 26.9 1.0 O B:ACY302 2.3 38.9 1.0 CG B:ASP11 3.0 37.0 1.0 CG B:ASP220 3.2 25.4 1.0 OD1 B:ASP11 3.3 31.4 1.0 C B:ACY302 3.3 39.1 1.0 C B:ASP13 3.4 30.7 1.0 OD2 B:ASP220 3.5 28.0 1.0 O B:HOH402 4.0 51.1 1.0 OXT B:ACY302 4.1 37.9 1.0 OG B:SER221 4.1 26.6 1.0 N B:ASP13 4.1 24.1 1.0 OD2 B:ASP224 4.1 27.5 1.0 OG1 B:THR15 4.2 28.7 1.0 CA B:ASP13 4.2 24.8 1.0 CH3 B:ACY302 4.2 35.7 1.0 O B:HOH409 4.3 37.1 1.0 OD2 B:ASP14 4.3 37.4 1.0 CB B:ASP11 4.3 27.4 1.0 CB B:ASP14 4.4 30.1 1.0 CB B:ASP13 4.4 27.9 1.0 N B:ASP14 4.4 26.0 1.0 CB B:ASP220 4.5 25.7 1.0 C B:LEU12 4.7 24.6 1.0 N B:THR15 4.7 24.0 1.0 C B:ASP14 4.7 25.1 1.0 CA B:ASP14 4.7 23.9 1.0 N B:LEU12 4.8 24.3 1.0 CG B:ASP14 4.9 44.1 1.0 N B:ASP220 4.9 24.5 1.0 N B:SER221 5.0 22.2 1.0

M.Cross, S.Biberacher, S.Y.Park, S.Rajan, P.Korhonen, R.B.Gasser, J.S.Kim, M.J.Coster, A.Hofmann. Trehalose 6-Phosphate Phosphatases of Pseudomonas Aeruginosa. Faseb J. V. 32 5470 2018.
ISSN: ESSN 1530-6860
PubMed: 29688811
DOI: 10.1096/FJ.201800500R