Nickel in PDB 5fq0: The Structure of Kdgf From Halomonas Sp.

The structure of The Structure of Kdgf From Halomonas Sp., PDB code: 5fq0 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)	62.36 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.934, 78.680, 68.002, 90.00, 113.91, 90.00
R / Rfree (%)	18.481 / 22.448

The binding sites of Nickel atom in the The Structure of Kdgf From Halomonas Sp. (pdb code 5fq0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the The Structure of Kdgf From Halomonas Sp., PDB code: 5fq0:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the The Structure of Kdgf From Halomonas Sp.


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 Halomonas Sp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1113 b:23.5 occ:1.00 NE2 A:HIS50 2.1 20.1 1.0 OG1 A:FLC1114 2.1 28.1 1.0 NE2 A:HIS89 2.1 22.4 1.0 OE1 A:GLN55 2.1 21.7 1.0 NE2 A:HIS48 2.2 23.0 1.0 OG2 A:FLC1114 2.2 31.7 1.0 CGC A:FLC1114 2.4 36.6 1.0 CE1 A:HIS50 2.9 21.7 1.0 CE1 A:HIS89 3.0 23.7 1.0 CE1 A:HIS48 3.0 24.6 1.0 CD2 A:HIS50 3.1 19.8 1.0 CD2 A:HIS89 3.2 21.2 1.0 CD A:GLN55 3.2 22.1 1.0 CD2 A:HIS48 3.2 24.6 1.0 NE2 A:GLN55 3.6 19.0 1.0 CG A:FLC1114 3.9 39.2 1.0 ND1 A:HIS50 4.1 21.9 1.0 ND1 A:HIS48 4.2 25.0 1.0 ND1 A:HIS89 4.2 21.8 1.0 CG A:HIS50 4.2 21.4 1.0 CG A:HIS48 4.3 25.9 1.0 CG A:HIS89 4.3 23.0 1.0 CBC A:FLC1114 4.4 50.7 1.0 OB1 A:FLC1114 4.5 54.6 1.0 CE1 A:PHE104 4.5 18.1 1.0 CG A:GLN55 4.5 20.6 1.0 CB A:FLC1114 4.6 49.8 1.0 OHB A:FLC1114 4.6 47.5 1.0 NH1 A:ARG108 4.7 25.0 1.0 OB2 A:FLC1114 4.7 48.6 1.0 CB A:GLN55 4.8 20.6 1.0 CZ A:PHE104 4.9 18.3 1.0

Nickel binding site 2 out of 5 in the The Structure of Kdgf From Halomonas Sp.


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 Halomonas Sp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1113 b:25.7 occ:1.00 OG1 B:FLC1114 2.0 31.6 1.0 NE2 B:HIS50 2.1 21.1 1.0 NE2 B:HIS89 2.1 20.7 1.0 OE1 B:GLN55 2.2 21.9 1.0 NE2 B:HIS48 2.2 30.0 1.0 OG2 B:FLC1114 2.3 31.0 1.0 CGC B:FLC1114 2.4 39.0 1.0 CE1 B:HIS89 2.9 21.9 1.0 CE1 B:HIS50 3.0 22.6 1.0 CE1 B:HIS48 3.1 29.7 1.0 CD2 B:HIS50 3.1 22.2 1.0 CD2 B:HIS89 3.2 19.7 1.0 CD2 B:HIS48 3.2 28.5 1.0 CD B:GLN55 3.2 22.2 1.0 NE2 B:GLN55 3.7 21.3 1.0 CG B:FLC1114 3.9 38.9 1.0 ND1 B:HIS89 4.1 20.8 1.0 ND1 B:HIS50 4.1 23.8 1.0 ND1 B:HIS48 4.2 29.4 1.0 CG B:HIS50 4.2 23.6 1.0 CG B:HIS89 4.2 21.0 1.0 OB1 B:FLC1114 4.3 51.5 1.0 CG B:HIS48 4.3 30.8 1.0 CBC B:FLC1114 4.5 48.5 1.0 CE1 B:PHE104 4.5 22.1 1.0 O B:HOH2077 4.5 41.5 1.0 CG B:GLN55 4.5 20.8 1.0 CB B:FLC1114 4.6 49.1 1.0 OHB B:FLC1114 4.6 46.2 1.0 NH1 B:ARG108 4.7 23.8 1.0 CB B:GLN55 4.8 21.2 1.0 CZ B:PHE104 4.9 23.6 1.0

Nickel binding site 3 out of 5 in the The Structure of Kdgf From Halomonas Sp.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Structure of Kdgf From Halomonas Sp. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1114 b:26.0 occ:1.00 NE2 C:HIS50 2.1 22.2 1.0 OG1 C:FLC1115 2.1 31.3 1.0 OE1 C:GLN55 2.1 24.9 1.0 NE2 C:HIS89 2.1 22.6 1.0 OG2 C:FLC1115 2.2 33.3 1.0 NE2 C:HIS48 2.3 31.0 1.0 CGC C:FLC1115 2.4 40.4 1.0 CE1 C:HIS50 2.8 22.7 1.0 CE1 C:HIS89 3.0 23.2 1.0 CE1 C:HIS48 3.1 32.0 1.0 CD C:GLN55 3.1 23.6 1.0 CD2 C:HIS89 3.2 22.1 1.0 CD2 C:HIS50 3.2 21.5 1.0 CD2 C:HIS48 3.2 32.1 1.0 NE2 C:GLN55 3.5 23.6 1.0 CG C:FLC1115 3.9 42.6 1.0 ND1 C:HIS50 4.0 22.0 1.0 ND1 C:HIS89 4.2 23.8 1.0 CG C:HIS50 4.2 23.3 1.0 ND1 C:HIS48 4.3 30.4 1.0 CG C:HIS89 4.3 23.4 1.0 CG C:HIS48 4.3 30.8 1.0 CBC C:FLC1115 4.5 50.7 1.0 CG C:GLN55 4.5 21.7 1.0 CE1 C:PHE104 4.6 24.1 1.0 CB C:FLC1115 4.6 52.0 1.0 NH1 C:ARG108 4.6 26.1 1.0 OB2 C:FLC1115 4.6 46.1 1.0 OHB C:FLC1115 4.7 49.1 1.0 OB1 C:FLC1115 4.7 54.0 1.0 CB C:GLN55 4.8 21.9 1.0 CZ C:PHE104 5.0 25.5 1.0

Nickel binding site 4 out of 5 in the The Structure of Kdgf From Halomonas Sp.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Structure of Kdgf From Halomonas Sp. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1113 b:27.5 occ:1.00 OG1 D:FLC1114 2.0 30.9 1.0 NE2 D:HIS50 2.1 20.3 1.0 NE2 D:HIS89 2.2 25.2 1.0 OE1 D:GLN55 2.2 23.6 1.0 NE2 D:HIS48 2.2 37.0 1.0 OG2 D:FLC1114 2.4 33.3 1.0 CGC D:FLC1114 2.4 39.7 1.0 CD2 D:HIS50 3.1 21.1 1.0 CE1 D:HIS50 3.1 22.2 1.0 CE1 D:HIS89 3.1 28.8 1.0 CD D:GLN55 3.2 24.6 1.0 CD2 D:HIS48 3.2 36.9 1.0 CD2 D:HIS89 3.2 25.3 1.0 CE1 D:HIS48 3.2 36.4 1.0 NE2 D:GLN55 3.5 24.5 1.0 OB1 D:FLC1114 3.7 68.0 1.0 CG D:FLC1114 3.8 45.6 1.0 ND1 D:HIS50 4.2 22.0 1.0 CG D:HIS50 4.2 22.6 1.0 ND1 D:HIS89 4.2 26.8 1.0 ND1 D:HIS48 4.2 37.6 1.0 CG D:HIS48 4.3 35.6 1.0 CBC D:FLC1114 4.3 58.0 1.0 CG D:HIS89 4.3 25.1 1.0 CB D:FLC1114 4.5 55.8 1.0 CG D:GLN55 4.5 25.3 1.0 CE1 D:PHE104 4.5 27.8 1.0 OHB D:FLC1114 4.7 52.7 1.0 O D:HOH2045 4.8 44.3 1.0 NH1 D:ARG108 4.8 26.0 1.0 CZ D:PHE104 4.8 27.8 1.0 CB D:GLN55 4.8 22.7 1.0

Nickel binding site 5 out of 5 in the The Structure of Kdgf From Halomonas Sp.


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Structure of Kdgf From Halomonas Sp. within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni1004 b:34.7 occ:1.00 ND1 H:HIS1 1.9 55.2 1.0 ND1 H:HIS2 2.0 30.9 1.0 N H:HIS2 2.2 38.0 1.0 CG H:HIS1 2.8 45.8 1.0 CE1 H:HIS1 2.9 49.9 1.0 C H:HIS1 3.0 40.5 1.0 CG H:HIS2 3.0 35.3 1.0 CA H:HIS1 3.0 43.9 1.0 CB H:HIS1 3.0 46.1 1.0 CE1 H:HIS2 3.0 32.1 1.0 CA H:HIS2 3.2 36.4 1.0 CB H:HIS2 3.3 33.8 1.0 N H:HIS3 3.6 40.1 1.0 CB C:GLU69 3.6 27.9 1.0 CD2 H:HIS1 3.9 47.2 1.0 NE2 H:HIS1 4.0 59.9 1.0 C H:HIS2 4.0 38.8 1.0 O H:HIS1 4.1 37.3 1.0 NE2 H:HIS2 4.1 35.1 1.0 CD2 H:HIS2 4.1 34.1 1.0 CG C:GLU69 4.2 30.2 1.0 O C:GLU69 4.3 25.7 1.0 N H:HIS1 4.4 39.0 1.0 CA H:HIS3 4.8 43.0 1.0 CA C:GLU69 4.9 28.6 1.0 O C:LEU68 5.0 26.2 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