Nickel in PDB 5xgz: Metagenomic Glucose-Tolerant Glycosidase

The structure of Metagenomic Glucose-Tolerant Glycosidase, PDB code: 5xgz was solved by M.Watanabe, T.Matsuzawa, K.Yaoi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.75
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	202.427, 202.427, 202.427, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.5

The binding sites of Nickel atom in the Metagenomic Glucose-Tolerant Glycosidase (pdb code 5xgz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Metagenomic Glucose-Tolerant Glycosidase, PDB code: 5xgz:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Metagenomic Glucose-Tolerant Glycosidase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Metagenomic Glucose-Tolerant Glycosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni508 b:75.5 occ:1.00 O A:HOH834 3.4 38.9 1.0 NH1 A:ARG196 3.6 18.3 1.0 NH2 A:ARG196 4.0 16.5 1.0 CZ A:ARG196 4.3 17.9 1.0 CB A:PRO278 4.6 22.0 1.0 O A:HOH663 4.8 30.9 1.0

Nickel binding site 2 out of 4 in the Metagenomic Glucose-Tolerant Glycosidase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Metagenomic Glucose-Tolerant Glycosidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni509 b:80.2 occ:1.00 NE2 A:HIS8 2.3 74.2 1.0 CD2 A:HIS8 3.2 69.5 1.0 CE1 A:HIS8 3.3 70.5 1.0 ND1 A:HIS8 4.4 60.1 1.0 CG A:HIS8 4.4 70.7 1.0

Nickel binding site 3 out of 4 in the Metagenomic Glucose-Tolerant Glycosidase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Metagenomic Glucose-Tolerant Glycosidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni509 b:77.9 occ:1.00 NE2 B:HIS8 2.1 76.9 1.0 CE1 B:HIS8 3.1 74.6 1.0 CD2 B:HIS8 3.2 67.2 1.0 ND1 B:HIS8 4.2 58.1 1.0 CG B:HIS8 4.3 70.6 1.0

Nickel binding site 4 out of 4 in the Metagenomic Glucose-Tolerant Glycosidase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Metagenomic Glucose-Tolerant Glycosidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni510 b:23.5 occ:1.00 NE2 B:HIS63 2.0 25.5 1.0 CE1 B:HIS63 3.0 27.3 1.0 CD2 B:HIS63 3.0 19.9 1.0 O2 B:GOL508 4.1 52.3 1.0 ND1 B:HIS63 4.1 22.7 1.0 CG B:HIS63 4.2 20.3 1.0 C3 B:GOL508 4.9 57.0 1.0 C2 B:GOL508 4.9 48.0 1.0

T.Matsuzawa, M.Watanabe, K.Yaoi. Improved Thermostability of A Metagenomic Glucose-Tolerant Beta-Glycosidase Based on Its X-Ray Crystal Structure. Appl.Microbiol.Biotechnol. V. 101 8353 2017.
ISSN: ESSN 1432-0614
PubMed: 29063172
DOI: 10.1007/S00253-017-8525-9