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Terbium 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:

Nickel (Ni) 2 atoms
Magnesium (Mg) 7 atoms
Calcium (Ca) 6 atoms

Terbium Binding Sites:

The binding sites of Terbium 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 Terbium atom.
In total 7 binding sites of Terbium where determined in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative, PDB code: 5x7s:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7;

Terbium binding site 1 out of 7 in 5x7s

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Terbium binding site 1 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb 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:Tb1605

b:39.8
occ:1.00
 O B:HOH2053 2.1 36.8 1.0
OE1 B:GLN571 2.1 39.5 1.0
OE2 A:GLU290 2.2 46.5 1.0
OE2 A:GLU283 2.3 49.3 1.0
O A:GLY285 2.3 42.8 1.0
O B:HOH2083 2.3 45.2 1.0
OE1 A:GLU290 2.3 39.0 1.0
O A:HOH2012 2.6 45.1 1.0
CD A:GLU290 2.6 41.8 1.0
CD B:GLN571 3.2 39.7 1.0
CD A:GLU283 3.4 46.6 1.0
C A:GLY285 3.5 43.9 1.0
NE2 B:GLN571 3.7 35.1 1.0
CG A:GLU283 4.1 49.7 1.0
CG A:GLU290 4.1 40.1 1.0
OE1 A:GLU283 4.4 40.0 1.0
N A:ILE286 4.4 39.2 1.0
CA A:ILE286 4.4 40.1 1.0
O B:GLN570 4.5 38.3 1.0
CA A:GLY285 4.6 39.5 1.0
CB A:ILE286 4.6 44.9 1.0
CG B:GLN571 4.6 39.4 1.0
NE2 A:HIS294 4.7 47.5 1.0
O A:TRP284 4.7 36.0 1.0
O B:ASN569 4.8 44.7 1.0
C B:ASN569 4.9 45.4 1.0
CA B:ASN569 4.9 44.6 1.0

Terbium binding site 2 out of 7 in 5x7s

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Terbium binding site 2 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb 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
A:Tb1606

b:42.9
occ:0.30
 O A:HOH2035 2.2 55.8 1.0
OE1 A:GLU605 2.4 64.8 1.0
OE1 A:GLU608 2.5 75.3 1.0
CD A:GLU605 3.4 60.5 1.0
OE2 A:GLU605 3.5 57.1 1.0
CD A:GLU608 3.7 74.3 1.0
OE2 A:GLU608 4.1 81.2 1.0
O2 A:EDO1802 4.5 52.9 1.0
O A:HOH2314 4.6 50.6 1.0
CG A:GLU605 4.8 55.1 1.0
CG A:GLU608 4.9 60.1 1.0

Terbium binding site 3 out of 7 in 5x7s

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Terbium binding site 3 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 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:Tb1607

b:50.2
occ:0.50
 OE2 A:GLU726 2.0 59.2 1.0
OE2 A:GLU763 2.4 57.5 1.0
CD A:GLU726 2.9 55.6 1.0
OE1 A:GLU763 3.0 77.1 1.0
CD A:GLU763 3.1 78.8 1.0
OE1 A:GLU726 3.2 62.4 1.0
CG A:GLU726 4.4 51.2 1.0
CG A:GLU763 4.6 74.1 1.0
NH2 A:ARG750 4.7 69.2 1.0
NH2 A:ARG761 4.8 70.5 1.0

Terbium binding site 4 out of 7 in 5x7s

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Terbium binding site 4 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 4 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:Tb1608

b:37.5
occ:0.50
 OD1 A:ASP376 2.3 60.4 1.0
OD2 A:ASP376 2.3 51.1 1.0
O A:HOH2204 2.4 51.5 1.0
OD2 A:ASP1183 2.5 54.8 1.0
CG A:ASP376 2.6 53.6 1.0
OD1 A:ASP1183 2.8 55.6 1.0
CG A:ASP1183 3.0 59.7 1.0
O1 A:SO41708 3.9 88.3 1.0
CB A:ASP376 4.2 47.2 1.0
O A:HOH2080 4.3 48.7 1.0
O A:HOH2334 4.3 54.9 1.0
OH A:TYR372 4.4 55.8 1.0
CB A:ASP1183 4.6 56.1 1.0
NE2 A:HIS1181 4.7 50.0 1.0
OH A:TYR1267 4.9 76.8 1.0
CD2 A:HIS1181 5.0 51.4 1.0

Terbium binding site 5 out of 7 in 5x7s

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Terbium binding site 5 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 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:Tb1606

b:40.0
occ:1.00
 O B:GLY285 2.0 48.7 1.0
OE2 B:GLU290 2.2 43.4 1.0
OE1 A:GLN571 2.3 40.5 1.0
OE1 B:GLU290 2.3 45.7 1.0
OE2 B:GLU283 2.4 45.8 1.0
O B:HOH2108 2.4 47.3 1.0
O A:HOH2146 2.4 38.4 1.0
O A:HOH2138 2.5 34.1 1.0
CD B:GLU290 2.6 46.8 1.0
C B:GLY285 3.3 51.0 1.0
CD A:GLN571 3.3 36.5 1.0
CD B:GLU283 3.5 43.9 1.0
NE2 A:GLN571 3.6 31.1 1.0
CG B:GLU283 4.1 42.9 1.0
N B:ILE286 4.1 47.1 1.0
CG B:GLU290 4.2 47.4 1.0
CA B:GLY285 4.3 50.4 1.0
CA B:ILE286 4.3 47.6 1.0
O B:HOH2020 4.3 45.0 1.0
OE1 B:GLU283 4.5 36.5 1.0
CB B:ILE286 4.5 48.9 1.0
O A:GLN570 4.5 45.6 1.0
OD1 A:ASN569 4.6 49.3 1.0
NE2 B:HIS294 4.6 39.5 1.0
O A:ASN569 4.6 47.5 1.0
O B:TRP284 4.7 40.9 1.0
CG A:GLN571 4.7 33.9 1.0
C A:ASN569 4.9 51.9 1.0
CA A:ASN569 5.0 48.4 1.0

Terbium binding site 6 out of 7 in 5x7s

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Terbium binding site 6 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 6 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:Tb1604

b:44.2
occ:0.30
 O B:HOH2206 2.1 53.6 1.0
O B:HOH2251 2.1 56.7 1.0
OE1 B:GLU605 2.6 55.9 1.0
OE1 B:GLU608 2.7 78.5 1.0
CD B:GLU605 3.6 61.8 1.0
CD B:GLU608 3.8 66.1 1.0
OE2 B:GLU605 3.9 60.6 1.0
OE2 B:GLU608 4.3 76.9 1.0
CG B:GLU605 5.0 61.3 1.0

Terbium binding site 7 out of 7 in 5x7s

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Terbium binding site 7 out of 7 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 7 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:Tb1605

b:46.7
occ:0.65
 OE1 B:GLU763 2.0 63.1 1.0
OE2 B:GLU726 2.5 64.2 1.0
OE1 B:GLU726 2.7 68.4 1.0
CD B:GLU763 2.8 64.7 1.0
OE2 B:GLU763 2.8 78.5 1.0
CD B:GLU726 2.9 58.2 1.0
O B:HOH2291 4.1 44.7 1.0
NH1 B:ARG761 4.1 78.9 1.0
CG B:GLU763 4.3 56.0 1.0
CG B:GLU726 4.5 53.5 1.0
NH1 B:ARG750 4.7 52.7 1.0
NH2 B:ARG750 4.8 47.4 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 02:26:45 2020

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