Nickel in PDB 4q29: Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens

The structure of Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens, PDB code: 4q29 was solved by F.Wang, K.Michalska, H.Li, R.Jedrzejczak, G.Babnigg, C.A.Bingman, R.Yennamalli, S.Weerth, M.D.Miller, M.G.Thomas, A.Joachimiak, G.N.Phillips Jr., Enzyme Discovery For Natural Product Biosynthesis(Natpro), Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.90 / 1.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	55.738, 147.687, 83.843, 90.00, 90.00, 90.00
R / Rfree (%)	12.6 / 15.5

The structure of Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens also contains other interesting chemical elements:

Sodium

(Na)

20 atoms

The binding sites of Nickel atom in the Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens (pdb code 4q29). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens, PDB code: 4q29:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:16.2 occ:0.03 O A:HOH334 2.0 15.1 0.1 NE2 A:HIS52 2.2 17.6 0.1 NE2 A:HIS50 2.2 16.9 0.1 OE2 A:GLU56 2.3 15.9 0.1 HE1 A:HIS90 2.4 16.1 0.1 NE2 A:HIS90 2.5 16.1 0.1 CE1 A:HIS90 2.6 16.2 0.1 CD A:GLU56 3.0 15.3 0.1 CE1 A:HIS50 3.1 16.7 0.1 CE1 A:HIS52 3.1 17.8 0.1 OE1 A:GLU56 3.2 15.0 0.1 CD2 A:HIS52 3.2 18.5 0.1 CD2 A:HIS50 3.2 17.9 0.1 HE1 A:HIS50 3.2 16.1 0.1 HE1 A:HIS52 3.3 17.4 0.1 HD2 A:HIS52 3.3 18.6 0.1 HD2 A:HIS50 3.4 18.4 0.1 CD2 A:HIS90 3.6 16.3 0.1 ND1 A:HIS90 3.6 16.5 0.1 HD2 A:HIS90 4.1 16.3 0.1 CG A:HIS90 4.1 16.6 0.1 ND1 A:HIS50 4.2 17.4 0.1 O A:HOH385 4.3 14.7 0.1 ND1 A:HIS52 4.3 18.8 0.1 CG A:HIS50 4.3 18.3 0.1 CG A:HIS52 4.3 19.3 0.1 HG21 A:ILE84 4.4 16.5 0.1 HG13 A:ILE84 4.5 14.9 0.1 CG A:GLU56 4.5 14.9 0.1 HE1 A:PHE58 4.6 13.7 0.1 HB2 A:GLU56 4.6 16.2 0.1 HB3 A:GLU56 4.8 15.8 0.1 HG2 A:GLU56 4.9 14.7 0.1 CB A:GLU56 4.9 15.7 0.1 HZ A:PHE58 4.9 14.0 0.1

Nickel binding site 2 out of 2 in the Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ensemble Refinement of PLU4264 Protein From Photorhabdus Luminescens within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:16.8 occ:0.04 HE1 B:HIS50 1.7 17.2 0.1 NE2 B:HIS52 2.2 18.2 0.0 NE2 B:HIS90 2.2 17.2 0.0 OE2 B:GLU56 2.3 16.2 0.1 CE1 B:HIS50 2.4 17.5 0.0 HE1 B:HIS90 2.5 16.8 0.1 CD2 B:HIS90 3.1 16.8 0.0 CD B:GLU56 3.1 15.5 0.1 NE2 B:HIS50 3.1 17.0 0.0 NE2 B:HIS52 3.1 18.2 0.0 CD2 B:HIS52 3.1 19.1 0.0 CE1 B:HIS52 3.2 18.6 0.0 CE1 B:HIS90 3.2 18.3 0.0 HD2 B:HIS90 3.2 16.1 0.1 CE1 B:HIS90 3.2 16.6 0.0 HD2 B:HIS52 3.3 19.2 0.1 HD2 B:HIS52 3.3 19.2 0.1 HE1 B:HIS52 3.3 18.1 0.1 HE1 B:HIS90 3.4 18.8 0.1 ND1 B:HIS50 3.4 18.5 0.0 NE2 B:HIS90 3.5 15.9 0.0 OE1 B:GLU56 3.5 14.9 0.1 CD2 B:HIS52 3.5 19.2 0.0 HG3 B:ARG49 3.9 16.7 0.1 HB3 B:ARG49 4.1 18.4 0.1 HB2 B:ARG49 4.2 17.7 0.1 CG B:HIS90 4.3 17.5 0.0 ND1 B:HIS52 4.3 19.7 0.0 CG B:HIS52 4.3 20.1 0.0 ND1 B:HIS90 4.3 18.4 0.0 CG B:GLU56 4.3 15.4 0.1 CD2 B:HIS50 4.3 17.7 0.0 CE1 B:HIS52 4.3 18.6 0.0 HG2 B:GLU56 4.4 15.1 0.1 CG B:HIS50 4.5 18.7 0.0 HB2 B:GLU56 4.5 16.7 0.1 ND1 B:HIS90 4.5 17.2 0.0 CB B:ARG49 4.5 17.9 0.0 HE1 B:PHE58 4.6 14.2 0.1 CG B:ARG49 4.6 17.0 0.0 HB3 B:GLU56 4.6 16.6 0.1 HE1 B:HIS52 4.7 18.2 0.1 CB B:GLU56 4.7 16.4 0.1 HD2 B:ARG49 4.8 17.8 0.1 HZ B:PHE58 4.8 14.5 0.1 HG13 B:ILE84 4.8 15.8 0.1 CD2 B:HIS90 4.8 16.1 0.0 CG B:HIS52 4.8 20.2 0.0

R.S.Weerth, K.Michalska, C.A.Bingman, R.M.Yennamalli, H.Li, R.Jedrzejczak, F.Wang, G.Babnigg, A.Joachimiak, M.G.Thomas, G.N.Phillips. Structure of A Cupin Protein PLU4264 From Photorhabdus Luminescens Subsp. Laumondii TTO1 at 1.35 Angstrom Resolution. Proteins 2014.
ISSN: ESSN 1097-0134
PubMed: 25354690
DOI: 10.1002/PROT.24705