Nickel in PDB 5x7q: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Maltohexaose

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

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Maltohexaose, PDB code: 5x7q 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)	152.51 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	184.267, 271.760, 133.677, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.5

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Maltohexaose 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 Maltohexaose (pdb code 5x7q). 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 Maltohexaose, PDB code: 5x7q:
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 Maltohexaose


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 Maltohexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1501 b:45.0 occ:1.00 OD2 A:ASP196 2.2 26.2 1.0 O A:HOH2079 2.2 28.9 1.0 O A:HOH2095 2.2 27.1 1.0 O A:HOH2379 2.2 25.8 1.0 NE2 A:HIS187 2.3 25.9 1.0 NE2 A:HIS190 2.4 30.7 1.0 CG A:ASP196 3.1 26.5 1.0 CD2 A:HIS187 3.2 26.7 1.0 CE1 A:HIS187 3.3 26.7 1.0 CE1 A:HIS190 3.3 31.3 1.0 CD2 A:HIS190 3.3 30.7 1.0 OD1 A:ASP196 3.4 26.2 1.0 O A:HOH2197 4.0 25.9 1.0 OE2 A:GLU175 4.2 36.2 1.0 OE1 A:GLU175 4.3 33.2 1.0 O A:SER170 4.4 25.5 1.0 ND1 A:HIS187 4.4 27.0 1.0 O A:HOH2233 4.4 24.3 1.0 CG A:HIS187 4.4 27.4 1.0 NH2 A:ARG169 4.4 27.0 1.0 ND1 A:HIS190 4.4 31.8 1.0 CG A:HIS190 4.5 30.6 1.0 O A:HOH2700 4.5 36.4 1.0 CB A:ASP196 4.5 26.1 1.0 CD A:GLU175 4.7 35.7 1.0 CB A:ARG169 4.9 24.8 1.0 NE A:ARG169 4.9 27.1 1.0

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


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 Maltohexaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1501 b:45.4 occ:1.00 O B:HOH2155 2.2 29.8 1.0 OD2 B:ASP196 2.2 28.4 1.0 O B:HOH2420 2.2 26.8 1.0 O B:HOH2213 2.3 25.7 1.0 NE2 B:HIS187 2.3 29.2 1.0 NE2 B:HIS190 2.4 33.0 1.0 CG B:ASP196 3.1 28.4 1.0 CD2 B:HIS187 3.2 29.2 1.0 CE1 B:HIS187 3.2 30.5 1.0 CD2 B:HIS190 3.3 33.0 1.0 OD1 B:ASP196 3.4 27.8 1.0 CE1 B:HIS190 3.4 33.7 1.0 O B:HOH2150 4.0 27.3 1.0 OE2 B:GLU175 4.1 36.7 1.0 O B:HOH2136 4.3 26.8 1.0 OE1 B:GLU175 4.3 33.1 1.0 O B:SER170 4.3 29.0 1.0 ND1 B:HIS187 4.3 30.5 1.0 CG B:HIS187 4.4 30.8 1.0 NH2 B:ARG169 4.4 30.0 1.0 ND1 B:HIS190 4.5 31.7 1.0 CG B:HIS190 4.5 31.9 1.0 CB B:ASP196 4.5 26.7 1.0 O B:HOH2742 4.6 44.3 1.0 CD B:GLU175 4.7 36.9 1.0 CB B:ARG169 4.9 27.1 1.0 NE B:ARG169 4.9 28.4 1.0 CZ B:ARG169 5.0 29.6 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