Nickel in PDB 5x7p: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose

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

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose, PDB code: 5x7p 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)	152.48 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	184.287, 271.517, 133.630, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 23.7

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

Magnesium	(Mg)	12 atoms
Calcium	(Ca)	6 atoms

The binding sites of Nickel atom in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose (pdb code 5x7p). 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 Complexed with Acarbose, PDB code: 5x7p:
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 Complexed with Acarbose


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 Complexed with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1501 b:63.8 occ:1.00 O A:HOH2133 2.1 39.7 1.0 O A:HOH2069 2.2 37.0 1.0 OD2 A:ASP196 2.2 36.7 1.0 NE2 A:HIS187 2.3 37.1 1.0 O A:HOH2234 2.3 32.6 1.0 NE2 A:HIS190 2.4 42.0 1.0 CG A:ASP196 3.1 36.2 1.0 CD2 A:HIS187 3.3 37.0 1.0 CE1 A:HIS187 3.3 36.5 1.0 CD2 A:HIS190 3.4 43.5 1.0 CE1 A:HIS190 3.4 45.4 1.0 OD1 A:ASP196 3.4 31.7 1.0 O A:HOH2028 3.9 36.5 1.0 OE2 A:GLU175 4.1 53.9 1.0 OE1 A:GLU175 4.3 42.9 1.0 O A:HOH2091 4.3 27.7 1.0 O A:SER170 4.4 33.4 1.0 ND1 A:HIS187 4.4 36.0 1.0 CG A:HIS187 4.4 38.8 1.0 ND1 A:HIS190 4.5 46.2 1.0 CG A:HIS190 4.5 41.6 1.0 CB A:ASP196 4.5 35.3 1.0 NH2 A:ARG169 4.6 36.3 1.0 CD A:GLU175 4.7 50.9 1.0 NE A:ARG169 4.9 39.1 1.0 CB A:ARG169 5.0 37.7 1.0

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


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 Complexed with Acarbose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1501 b:63.2 occ:1.00 O B:HOH2373 2.2 44.6 1.0 NE2 B:HIS187 2.2 42.5 1.0 OD2 B:ASP196 2.2 45.5 1.0 O B:HOH2181 2.3 38.2 1.0 O B:HOH2073 2.4 34.2 1.0 NE2 B:HIS190 2.5 41.6 1.0 CG B:ASP196 3.2 37.4 1.0 CD2 B:HIS187 3.2 37.9 1.0 CE1 B:HIS187 3.2 35.1 1.0 OD1 B:ASP196 3.4 36.3 1.0 CE1 B:HIS190 3.4 42.1 1.0 CD2 B:HIS190 3.4 41.8 1.0 O B:HOH2087 3.9 34.8 1.0 OE2 B:GLU175 4.2 50.4 1.0 ND1 B:HIS187 4.3 40.1 1.0 CG B:HIS187 4.3 39.2 1.0 O B:SER170 4.3 32.4 1.0 O B:HOH2049 4.4 29.9 1.0 OE1 B:GLU175 4.4 47.9 1.0 NH2 B:ARG169 4.4 37.6 1.0 ND1 B:HIS190 4.5 43.0 1.0 CG B:HIS190 4.5 44.5 1.0 CB B:ASP196 4.5 35.4 1.0 O B:HOH2395 4.7 46.2 1.0 CD B:GLU175 4.7 51.2 1.0 NE B:ARG169 4.8 39.5 1.0 CB B:ARG169 4.9 34.7 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