Nickel in PDB 5by3: A Novel Family GH115 4-O-Methyl-Alpha-Glucuronidase, BTGH115A, with Specificity For Decorated Arabinogalactans

The structure of A Novel Family GH115 4-O-Methyl-Alpha-Glucuronidase, BTGH115A, with Specificity For Decorated Arabinogalactans, PDB code: 5by3 was solved by A.Lammerts Van Bueren, G.J.Davies, J.P.Turkenburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.770, 102.300, 122.400, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 26.6

The binding sites of Nickel atom in the A Novel Family GH115 4-O-Methyl-Alpha-Glucuronidase, BTGH115A, with Specificity For Decorated Arabinogalactans (pdb code 5by3). 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 A Novel Family GH115 4-O-Methyl-Alpha-Glucuronidase, BTGH115A, with Specificity For Decorated Arabinogalactans, PDB code: 5by3:

Nickel binding site 1 out of 1 in the A Novel Family GH115 4-O-Methyl-Alpha-Glucuronidase, BTGH115A, with Specificity For Decorated Arabinogalactans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A Novel Family GH115 4-O-Methyl-Alpha-Glucuronidase, BTGH115A, with Specificity For Decorated Arabinogalactans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni802 b:63.6 occ:1.00 O A:LEU404 2.4 34.9 1.0 OD2 A:ASP436 2.4 44.2 1.0 O A:HOH973 2.5 47.8 1.0 O A:HOH959 2.5 34.7 1.0 O A:HOH905 2.7 8.5 0.5 O A:HOH952 2.8 42.7 1.0 C A:LEU404 3.5 36.8 1.0 CG A:ASP436 3.6 42.8 1.0 O A:HOH905 4.1 10.4 0.5 CA A:LEU404 4.2 37.8 1.0 N A:ASP436 4.2 42.8 1.0 CB A:ASP436 4.3 41.8 1.0 CB A:LEU404 4.4 43.5 1.0 O A:TRP405 4.4 34.0 1.0 OD1 A:ASP436 4.5 46.9 1.0 N A:TRP405 4.6 34.1 1.0 OG A:SER395 4.7 45.5 1.0 O A:LYS438 4.7 40.4 1.0 CA A:TRP405 4.7 35.5 1.0 CA A:GLY435 4.8 39.6 1.0 C A:TRP405 4.9 36.5 1.0 O A:ASP169 4.9 45.7 1.0 CA A:ASP436 4.9 41.2 1.0 CD2 A:LEU404 4.9 45.6 1.0

F.Aalbers, J.P.Turkenburg, G.J.Davies, L.Dijkhuizen, A.Lammerts Van Bueren. Structural and Functional Characterization of A Novel Family GH115 4-O-Methyl-Alpha-Glucuronidase with Specificity For Decorated Arabinogalactans. J.Mol.Biol. V. 427 3935 2015.
ISSN: ESSN 1089-8638
PubMed: 26186997
DOI: 10.1016/J.JMB.2015.07.006