Nickel in PDB 5x7s: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative

All present enzymatic activity of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative:
3.2.1.20;

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative, PDB code: 5x7s was solved by Z.Fujimoto, N.Kishine, N.Suzuki, M.Momma, H.Ichinose, A.Kimura, K.Funane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	151.54 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	182.815, 270.920, 133.341, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.9

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Terbium	(Tb)	7 atoms
Calcium	(Ca)	6 atoms

The binding sites of Nickel atom in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative (pdb code 5x7s). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative, PDB code: 5x7s:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1501 b:70.2 occ:1.00 O A:HOH2133 2.0 55.6 1.0 O A:HOH2195 2.2 32.8 1.0 NE2 A:HIS187 2.3 45.7 1.0 O A:HOH2225 2.3 42.0 1.0 OD2 A:ASP196 2.3 39.8 1.0 NE2 A:HIS190 2.4 46.4 1.0 CD2 A:HIS187 3.2 38.3 1.0 CG A:ASP196 3.3 40.6 1.0 CE1 A:HIS190 3.3 49.3 1.0 CE1 A:HIS187 3.3 41.4 1.0 CD2 A:HIS190 3.3 46.8 1.0 OD1 A:ASP196 3.5 36.9 1.0 O A:HOH2135 4.1 37.8 1.0 O A:HOH2073 4.3 30.6 1.0 OE2 A:GLU175 4.3 60.9 1.0 OE1 A:GLU175 4.3 42.5 1.0 CG A:HIS187 4.4 42.1 1.0 ND1 A:HIS187 4.4 41.0 1.0 ND1 A:HIS190 4.4 49.7 1.0 CG A:HIS190 4.5 47.2 1.0 O A:SER170 4.5 37.1 1.0 CB A:ASP196 4.6 40.8 1.0 NH2 A:ARG169 4.7 40.9 1.0 CD A:GLU175 4.7 54.6 1.0 NE A:ARG169 4.9 41.3 1.0 CB A:ARG169 4.9 37.9 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1501 b:76.0 occ:1.00 O B:HOH2052 2.1 54.1 1.0 OD2 B:ASP196 2.2 41.9 1.0 O B:HOH2378 2.2 33.1 1.0 NE2 B:HIS187 2.3 46.4 1.0 O B:HOH2113 2.4 40.2 1.0 NE2 B:HIS190 2.6 42.0 1.0 CG B:ASP196 3.1 38.5 1.0 CD2 B:HIS187 3.2 43.0 1.0 CE1 B:HIS187 3.3 42.1 1.0 OD1 B:ASP196 3.3 36.0 1.0 CD2 B:HIS190 3.4 45.8 1.0 CE1 B:HIS190 3.5 46.3 1.0 OE2 B:GLU175 4.0 68.3 1.0 O B:HOH2218 4.0 37.8 1.0 O B:HOH2133 4.2 30.1 1.0 OE1 B:GLU175 4.4 50.3 1.0 CG B:HIS187 4.4 43.7 1.0 ND1 B:HIS187 4.4 48.5 1.0 NH2 B:ARG169 4.5 42.1 1.0 O B:SER170 4.5 37.8 1.0 CB B:ASP196 4.5 38.1 1.0 CG B:HIS190 4.5 43.2 1.0 ND1 B:HIS190 4.5 44.8 1.0 CD B:GLU175 4.6 59.5 1.0 CB B:ARG169 4.7 35.0 1.0 NE B:ARG169 4.8 44.9 1.0 CZ B:ARG169 5.0 45.2 1.0

Z.Fujimoto, N.Suzuki, N.Kishine, H.Ichinose, M.Momma, A.Kimura, K.Funane. Carbohydrate-Binding Architecture of the Multi-Modular Alpha-1,6-Glucosyltransferase From Paenibacillus Sp. 598K, Which Produces Alpha-1,6-Glucosyl-Alpha-Glucosaccharides From Starch Biochem. J. V. 474 2763 2017.
ISSN: ESSN 1470-8728
PubMed: 28698247
DOI: 10.1042/BCJ20170152