Nickel in PDB 5fpx: The Structure of Kdgf From Yersinia Enterocolitica.

The structure of The Structure of Kdgf From Yersinia Enterocolitica., PDB code: 5fpx 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)	55.33 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.920, 73.760, 83.680, 90.00, 90.00, 90.00
R / Rfree (%)	17.118 / 19.928

The binding sites of Nickel atom in the The Structure of Kdgf From Yersinia Enterocolitica. (pdb code 5fpx). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Structure of Kdgf From Yersinia Enterocolitica., PDB code: 5fpx:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The Structure of Kdgf From Yersinia Enterocolitica.


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. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1105 b:19.5 occ:1.00 O E:GLY1 2.1 17.7 1.0 OE1 A:GLN53 2.1 22.0 1.0 NE2 A:HIS87 2.1 18.5 1.0 NE2 A:HIS46 2.2 19.0 1.0 NE2 A:HIS48 2.2 18.9 1.0 N E:GLY1 2.2 24.8 1.0 C E:GLY1 2.8 19.3 1.0 CA E:GLY1 2.9 22.9 1.0 CE1 A:HIS48 3.0 21.0 1.0 CE1 A:HIS87 3.0 16.1 1.0 CE1 A:HIS46 3.1 19.7 1.0 CD2 A:HIS87 3.2 17.4 1.0 CD2 A:HIS46 3.2 20.6 1.0 CD A:GLN53 3.2 25.7 1.0 CD2 A:HIS48 3.3 19.3 1.0 NE2 A:GLN53 3.7 29.9 1.0 O A:HOH2093 3.9 31.8 1.0 O A:HOH2086 4.0 45.7 1.0 N E:SER2 4.1 20.6 1.0 ND1 A:HIS87 4.2 15.7 1.0 ND1 A:HIS46 4.2 20.0 1.0 ND1 A:HIS48 4.2 23.4 1.0 CG A:HIS46 4.3 18.3 1.0 CG A:HIS87 4.3 15.0 1.0 CG A:HIS48 4.3 21.4 1.0 O E:SER3 4.3 29.2 1.0 CG A:GLN53 4.5 22.7 1.0 O E:HOH2001 4.9 56.6 1.0 CA E:SER2 4.9 20.9 1.0 CB A:GLN53 4.9 19.6 1.0

Nickel binding site 2 out of 2 in the The Structure of Kdgf From Yersinia Enterocolitica.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Structure of Kdgf From Yersinia Enterocolitica. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1105 b:20.1 occ:1.00 O F:GLY1 2.1 19.0 1.0 NE2 B:HIS48 2.1 19.9 1.0 NE2 B:HIS87 2.1 17.8 1.0 OE1 B:GLN53 2.2 23.1 1.0 NE2 B:HIS46 2.2 17.6 1.0 N F:GLY1 2.3 24.0 1.0 C F:GLY1 2.8 20.8 1.0 CA F:GLY1 2.9 22.8 1.0 CE1 B:HIS48 3.0 21.6 1.0 CE1 B:HIS87 3.1 17.7 1.0 CD2 B:HIS46 3.1 20.2 1.0 CE1 B:HIS46 3.1 20.5 1.0 CD2 B:HIS48 3.2 21.0 1.0 CD B:GLN53 3.2 24.2 1.0 CD2 B:HIS87 3.2 17.7 1.0 NE2 B:GLN53 3.5 24.6 1.0 O B:HOH2066 4.0 39.5 1.0 O B:HOH2072 4.1 37.6 1.0 N F:SER2 4.1 20.0 1.0 ND1 B:HIS48 4.1 21.5 1.0 ND1 B:HIS87 4.2 17.5 1.0 ND1 B:HIS46 4.2 19.4 1.0 CG B:HIS46 4.2 19.3 1.0 CG B:HIS48 4.3 20.1 1.0 CG B:HIS87 4.3 16.1 1.0 O F:SER3 4.4 27.2 1.0 CG B:GLN53 4.5 22.4 1.0 O F:HOH2001 4.7 45.7 1.0 CA F:SER2 4.9 20.5 1.0 CB B:GLN53 4.9 19.1 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