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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5x7s:

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

Nickel Binding Sites:

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 5x7s

Go back to Nickel Binding Sites List in 5x7s
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 5x7s

Go back to Nickel Binding Sites List in 5x7s
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

Reference:

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
Page generated: Wed Dec 16 01:49:54 2020

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