Nickel in PDB 5fpz: The Structure of Kdgf From Yersinia Enterocolitica with Malonate Bound in the Active Site.

The structure of The Structure of Kdgf From Yersinia Enterocolitica with Malonate Bound in the Active Site., PDB code: 5fpz was solved by J.K.Hobbs, S.M.Lee, M.Robb, F.Hof, C.Barr, K.T.Abe, J.H.Hehemann, R.Mclean, D.W.Abbott, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.13 / 1.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.190, 60.190, 67.831, 90.00, 90.00, 120.00
R / Rfree (%)	16.975 / 20.488

The binding sites of Nickel atom in the The Structure of Kdgf From Yersinia Enterocolitica with Malonate Bound in the Active Site. (pdb code 5fpz). 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 The Structure of Kdgf From Yersinia Enterocolitica with Malonate Bound in the Active Site., PDB code: 5fpz:

Nickel binding site 1 out of 1 in the The Structure of Kdgf From Yersinia Enterocolitica with Malonate Bound in the Active Site.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Structure of Kdgf From Yersinia Enterocolitica with Malonate Bound in the Active Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1111 b:11.9 occ:0.88 O3A A:MLA1112 2.1 14.4 1.0 O1A A:MLA1112 2.1 15.0 1.0 NE2 A:HIS87 2.1 14.1 1.0 NE2 A:HIS48 2.1 14.0 1.0 OE1 A:GLN53 2.1 13.0 1.0 NE2 A:HIS46 2.2 13.6 1.0 C3 A:MLA1112 3.0 15.2 1.0 CE1 A:HIS48 3.0 13.8 1.0 C1 A:MLA1112 3.0 15.8 1.0 CE1 A:HIS46 3.1 14.4 1.0 CE1 A:HIS87 3.1 13.5 1.0 CD A:GLN53 3.1 13.3 1.0 CD2 A:HIS87 3.2 12.9 1.0 CD2 A:HIS48 3.2 14.0 1.0 CD2 A:HIS46 3.2 14.0 1.0 C2 A:MLA1112 3.3 16.1 1.0 NE2 A:GLN53 3.5 15.2 1.0 ND1 A:HIS48 4.2 14.2 1.0 O3B A:MLA1112 4.2 16.1 1.0 ND1 A:HIS87 4.2 13.6 1.0 O1B A:MLA1112 4.2 17.9 1.0 ND1 A:HIS46 4.2 14.4 1.0 CG A:HIS87 4.3 13.5 1.0 CG A:HIS48 4.3 14.3 1.0 CG A:HIS46 4.3 14.0 1.0 CE1 A:PHE102 4.4 11.8 1.0 CG A:GLN53 4.5 12.7 1.0 O A:HOH2186 4.5 27.9 1.0 NH1 A:ARG106 4.8 15.6 1.0 CZ A:PHE102 4.8 12.2 1.0 CB A:GLN53 4.9 12.6 1.0 O A:HOH2113 4.9 36.6 1.0

J.K.Hobbs, S.M.Lee, M.Robb, F.Hof, C.Barr, K.T.Abe, J.Hehemann, R.Mclean, D.W.Abbott, A.B.Boraston. Kdgf, the Missing Link in the Microbial Metabolism of Uronate Sugars From Pectin and Alginate. Proc.Natl.Acad.Sci.Usa V. 113 6188 2016.
ISSN: ISSN 0027-8424
PubMed: 27185956
DOI: 10.1073/PNAS.1524214113