Nickel in PDB 5x7o: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase

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

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, PDB code: 5x7o was solved by Z.Fujimoto, N.Suzuki, N.Kishine, 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)	152.48 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	184.159, 271.934, 133.998, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.9

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

Magnesium	(Mg)	15 atoms
Calcium	(Ca)	6 atoms

The binding sites of Nickel atom in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase (pdb code 5x7o). 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, PDB code: 5x7o:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1501 b:51.0 occ:1.00 OD2 A:ASP196 2.2 26.5 1.0 O A:HOH2342 2.2 25.3 1.0 O A:HOH2018 2.2 31.3 1.0 O A:HOH2193 2.3 28.6 1.0 NE2 A:HIS187 2.4 27.6 1.0 NE2 A:HIS190 2.5 29.9 1.0 CG A:ASP196 3.1 26.5 1.0 CE1 A:HIS187 3.3 30.2 1.0 OD1 A:ASP196 3.3 24.9 1.0 CD2 A:HIS187 3.4 28.9 1.0 CD2 A:HIS190 3.4 31.2 1.0 CE1 A:HIS190 3.5 31.7 1.0 O A:HOH2147 4.0 27.2 1.0 OE2 A:GLU175 4.2 41.1 1.0 O A:HOH2220 4.3 25.8 1.0 OE1 A:GLU175 4.4 35.1 1.0 ND1 A:HIS187 4.4 29.5 1.0 CB A:ASP196 4.4 27.2 1.0 O A:SER170 4.5 26.1 1.0 CG A:HIS187 4.5 29.8 1.0 CG A:HIS190 4.5 31.0 1.0 ND1 A:HIS190 4.5 32.8 1.0 NH2 A:ARG169 4.6 26.8 1.0 O A:HOH2910 4.6 34.0 1.0 CD A:GLU175 4.7 40.1 1.0 NE A:ARG169 4.9 26.9 1.0 CB A:ARG169 4.9 24.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1501 b:49.1 occ:1.00 OD2 B:ASP196 2.2 27.4 1.0 O B:HOH2478 2.2 26.7 1.0 O B:HOH2016 2.3 30.0 1.0 O B:HOH2178 2.3 26.7 1.0 NE2 B:HIS187 2.3 28.5 1.0 NE2 B:HIS190 2.5 32.5 1.0 CG B:ASP196 3.1 27.5 1.0 CD2 B:HIS187 3.3 28.9 1.0 CE1 B:HIS187 3.3 29.7 1.0 OD1 B:ASP196 3.3 26.0 1.0 CE1 B:HIS190 3.4 34.1 1.0 CD2 B:HIS190 3.4 33.3 1.0 O B:HOH2147 4.0 26.5 1.0 OE2 B:GLU175 4.1 40.9 1.0 O B:HOH2309 4.3 21.5 1.0 OE1 B:GLU175 4.4 37.0 1.0 O B:SER170 4.4 27.7 1.0 ND1 B:HIS187 4.4 29.1 1.0 CG B:HIS187 4.4 29.6 1.0 CB B:ASP196 4.5 26.8 1.0 NH2 B:ARG169 4.5 28.7 1.0 O B:HOH2895 4.5 43.9 1.0 ND1 B:HIS190 4.5 34.1 1.0 CG B:HIS190 4.6 31.5 1.0 CD B:GLU175 4.7 40.9 1.0 CB B:ARG169 4.8 25.3 1.0 NE B:ARG169 4.9 27.3 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