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Calcium 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
Terbium (Tb) 7 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 5x7s

Go back to Calcium Binding Sites List in 5x7s
Calcium binding site 1 out of 6 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1301

b:50.3
occ:1.00
 OE1 A:GLU855 2.2 58.3 1.0
OD1 A:ASP979 2.2 44.3 1.0
O A:GLY883 2.4 50.3 1.0
O A:ASP979 2.5 42.4 1.0
O A:SER880 2.5 51.1 1.0
OE2 A:GLU857 2.5 50.3 1.0
OE1 A:GLU857 2.5 51.2 1.0
CD A:GLU857 2.8 50.0 1.0
CD A:GLU855 3.3 58.6 1.0
CG A:ASP979 3.4 49.8 1.0
C A:ASP979 3.5 45.8 1.0
C A:GLY883 3.5 50.0 1.0
C A:SER880 3.5 50.1 1.0
CA A:ASP979 3.9 50.1 1.0
CB A:GLU855 4.1 55.3 1.0
OE2 A:GLU855 4.2 55.8 1.0
OD2 A:ASP979 4.2 46.0 1.0
CG A:GLU855 4.2 60.1 1.0
CB A:ASP979 4.3 49.4 1.0
CG A:GLU857 4.3 48.4 1.0
N A:GLY883 4.3 50.5 1.0
N A:PHE884 4.3 48.6 1.0
CA A:PHE884 4.3 53.8 1.0
CA A:SER880 4.4 53.6 1.0
N A:GLY881 4.4 50.9 1.0
N A:SER880 4.4 56.3 1.0
CA A:GLY883 4.5 52.0 1.0
CA A:GLY881 4.5 55.7 1.0
CA A:GLU855 4.5 54.6 1.0
CB A:SER880 4.5 52.6 1.0
N A:TYR980 4.6 44.4 1.0
CB A:TYR980 4.8 49.2 1.0
N A:VAL856 4.8 54.5 1.0
CB A:PHE884 4.9 61.0 1.0
C A:GLY881 4.9 57.9 1.0
N A:SER882 4.9 53.4 1.0
C A:GLU855 5.0 55.3 1.0

Calcium binding site 2 out of 6 in 5x7s

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1302

b:59.8
occ:1.00
 OD1 A:ASP1111 2.3 55.1 1.0
OE1 A:GLU995 2.5 45.9 1.0
O A:HOH2488 2.5 46.9 1.0
O A:ALA1016 2.5 35.5 1.0
O A:LYS1013 2.6 46.8 1.0
O A:ASP1111 2.8 45.4 1.0
OE2 A:GLU995 2.8 44.5 1.0
CD A:GLU995 3.0 46.6 1.0
CG A:ASP1111 3.2 48.3 1.0
C A:LYS1013 3.4 44.7 1.0
C A:ASP1111 3.7 42.4 1.0
C A:ALA1016 3.8 43.5 1.0
OD2 A:ASP1111 3.9 48.6 1.0
CA A:ASP1111 4.0 43.4 1.0
N A:LYS1013 4.1 42.4 1.0
CA A:LYS1013 4.1 45.2 1.0
CB A:LYS1013 4.2 49.8 1.0
CB A:ASP1111 4.2 47.0 1.0
N A:GLY1014 4.3 41.6 1.0
CA A:GLY1014 4.5 42.3 1.0
CG A:GLU995 4.5 43.9 1.0
CA A:PHE1017 4.6 40.1 1.0
N A:ALA1016 4.6 46.4 1.0
N A:PHE1017 4.6 38.5 1.0
N A:ALA994 4.7 39.2 1.0
N A:ARG1112 4.8 43.5 1.0
C A:GLY1014 4.8 45.9 1.0
CA A:ALA1016 4.8 48.2 1.0
CB A:ALA993 4.9 41.0 1.0
CB A:PHE1017 4.9 38.8 1.0
O A:HOH2016 4.9 46.1 1.0
CB A:ARG1112 4.9 48.6 1.0
N A:ALA1015 5.0 43.7 1.0

Calcium binding site 3 out of 6 in 5x7s

Go back to Calcium Binding Sites List in 5x7s
Calcium binding site 3 out of 6 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1303

b:56.4
occ:1.00
 O A:HOH2005 2.2 57.2 1.0
OD1 A:ASP1273 2.3 45.8 1.0
O A:GLN1176 2.3 38.3 1.0
OE2 A:GLU1136 2.5 43.1 1.0
O A:ASP1134 2.6 34.3 1.0
O A:ARG1173 2.9 36.2 1.0
OD2 A:ASP1273 2.9 42.9 1.0
CG A:ASP1273 3.0 47.2 1.0
C A:GLN1176 3.5 41.4 1.0
CD A:GLU1136 3.6 40.2 1.0
C A:ASP1134 3.6 36.5 1.0
CG A:GLU1136 3.9 41.1 1.0
CB A:ASP1134 4.0 34.7 1.0
C A:ARG1173 4.1 42.9 1.0
CA A:ASP1134 4.1 35.7 1.0
N A:GLN1176 4.1 36.2 1.0
OE2 A:GLU1274 4.2 43.9 1.0
CB A:PRO1171 4.2 49.7 1.0
CA A:GLN1176 4.4 40.2 1.0
N A:ARG1177 4.5 43.7 1.0
N A:ARG1173 4.5 40.1 1.0
CB A:ASP1273 4.5 42.5 1.0
CA A:ARG1177 4.6 42.7 1.0
OE1 A:GLU1136 4.7 40.7 1.0
CA A:ARG1173 4.7 43.4 1.0
N A:GLU1274 4.8 41.1 1.0
N A:PHE1135 4.8 35.8 1.0
N A:ASN1175 4.8 32.6 1.0
CG A:GLU1274 4.9 47.4 1.0
N A:GLU1136 4.9 41.4 1.0
CB A:ARG1177 4.9 46.8 1.0
CB A:ARG1174 4.9 42.1 1.0
CD A:GLU1274 5.0 52.4 1.0
CG A:ASP1134 5.0 38.4 1.0
C A:PHE1135 5.0 42.0 1.0

Calcium binding site 4 out of 6 in 5x7s

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca1301

b:43.8
occ:1.00
 OD1 B:ASP979 2.1 52.5 1.0
OE1 B:GLU855 2.2 45.3 1.0
O B:SER880 2.3 37.3 1.0
O B:GLY883 2.3 40.1 1.0
OE1 B:GLU857 2.5 47.6 1.0
O B:ASP979 2.6 40.8 1.0
OE2 B:GLU857 2.7 48.8 1.0
CD B:GLU857 2.9 46.5 1.0
CG B:ASP979 3.3 48.1 1.0
CD B:GLU855 3.4 48.6 1.0
C B:SER880 3.4 42.2 1.0
C B:GLY883 3.5 39.1 1.0
C B:ASP979 3.6 38.6 1.0
CA B:ASP979 3.9 41.5 1.0
OD2 B:ASP979 4.2 48.6 1.0
OE2 B:GLU855 4.2 48.2 1.0
CB B:ASP979 4.2 46.2 1.0
CB B:GLU855 4.2 41.1 1.0
N B:GLY881 4.3 47.8 1.0
N B:SER880 4.3 42.9 1.0
CA B:SER880 4.3 41.4 1.0
N B:GLY883 4.3 41.6 1.0
CG B:GLU855 4.3 43.2 1.0
CA B:GLY881 4.4 48.2 1.0
N B:PHE884 4.4 39.8 1.0
CG B:GLU857 4.4 41.7 1.0
CA B:GLY883 4.5 38.0 1.0
CB B:SER880 4.5 44.8 1.0
CA B:PHE884 4.5 40.6 1.0
CA B:GLU855 4.6 42.7 1.0
N B:TYR980 4.7 33.2 1.0
C B:GLY881 4.8 53.4 1.0
CD2 B:TYR980 4.8 47.3 1.0
N B:VAL856 4.8 42.1 1.0
CB B:TYR879 4.8 45.8 1.0
CB B:TYR980 4.9 41.4 1.0
OG B:SER880 4.9 45.1 1.0
N B:SER882 4.9 54.0 1.0

Calcium binding site 5 out of 6 in 5x7s

Go back to Calcium Binding Sites List in 5x7s
Calcium binding site 5 out of 6 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1302

b:61.6
occ:1.00
 O B:HOH2438 2.2 53.0 1.0
O B:LYS1013 2.2 47.2 1.0
OD1 B:ASP1111 2.3 41.7 1.0
O B:ALA1016 2.5 32.1 1.0
OE1 B:GLU995 2.5 35.3 1.0
OE2 B:GLU995 2.8 42.9 1.0
O B:ASP1111 2.9 35.9 1.0
CD B:GLU995 3.0 41.4 1.0
C B:LYS1013 3.2 45.7 1.0
CG B:ASP1111 3.3 39.0 1.0
C B:ALA1016 3.7 34.8 1.0
OD2 B:ASP1111 3.8 46.9 1.0
C B:ASP1111 3.9 35.0 1.0
N B:LYS1013 4.0 43.3 1.0
CA B:LYS1013 4.1 42.9 1.0
N B:GLY1014 4.1 45.5 1.0
CA B:ASP1111 4.2 35.4 1.0
CA B:GLY1014 4.3 41.6 1.0
CB B:ASP1111 4.3 38.7 1.0
CB B:LYS1013 4.3 46.7 1.0
CA B:PHE1017 4.4 35.6 1.0
N B:PHE1017 4.5 35.3 1.0
CG B:GLU995 4.5 41.0 1.0
N B:ALA1016 4.6 39.4 1.0
C B:GLY1014 4.6 43.0 1.0
CA B:ALA1016 4.8 38.2 1.0
CB B:PHE1017 4.8 37.8 1.0
CB B:TYR1012 4.9 38.8 1.0
N B:ALA1015 4.9 35.6 1.0
N B:ALA994 5.0 37.8 1.0
CB B:ALA993 5.0 39.1 1.0

Calcium binding site 6 out of 6 in 5x7s

Go back to Calcium Binding Sites List in 5x7s
Calcium binding site 6 out of 6 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, Terbium Derivative


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1303

b:52.7
occ:1.00
 O B:GLN1176 2.3 34.3 1.0
OE2 B:GLU1136 2.4 43.3 1.0
O B:ASP1134 2.5 42.9 1.0
OD1 B:ASP1273 2.5 40.1 1.0
OD2 B:ASP1273 2.6 39.1 1.0
OE2 B:GLU1274 2.7 48.8 1.0
O B:ARG1173 2.8 32.8 1.0
CG B:ASP1273 2.9 36.7 1.0
CD B:GLU1136 3.5 42.8 1.0
C B:GLN1176 3.5 36.8 1.0
C B:ASP1134 3.5 40.1 1.0
CD B:GLU1274 3.9 44.6 1.0
CB B:ASP1134 3.9 42.3 1.0
C B:ARG1173 3.9 39.2 1.0
CG B:GLU1136 4.0 41.2 1.0
CA B:ASP1134 4.1 39.5 1.0
N B:GLN1176 4.1 39.6 1.0
CA B:GLN1176 4.3 38.9 1.0
CB B:ASP1273 4.3 39.8 1.0
CB B:PRO1171 4.4 51.2 1.0
N B:ARG1173 4.4 35.9 1.0
N B:ARG1177 4.5 36.3 1.0
OE1 B:GLU1136 4.6 49.2 1.0
CA B:ARG1173 4.7 40.1 1.0
N B:PHE1135 4.7 36.5 1.0
CA B:ARG1177 4.7 38.7 1.0
OE1 B:GLU1274 4.8 41.8 1.0
N B:ASN1175 4.8 39.3 1.0
CG B:GLU1274 4.8 44.0 1.0
CB B:ARG1174 4.8 38.3 1.0
N B:GLU1274 4.8 38.1 1.0
CB B:ARG1173 4.9 39.8 1.0
CB B:GLN1176 4.9 36.5 1.0
CG B:ASP1134 4.9 38.4 1.0
N B:ARG1174 5.0 38.8 1.0
C B:PHE1135 5.0 41.1 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: Mon Jul 15 14:47:42 2024

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