Calcium in PDB 5x7o: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase

Enzymatic activity of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase

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

Protein crystallography data

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase, PDB code: 5x7o was solved by Z.Fujimoto, N.Suzuki, N.Kishine, 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 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 184.159, 271.934, 133.998, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.9

Other elements in 5x7o:

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

Nickel (Ni) 2 atoms
Magnesium (Mg) 15 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase (pdb code 5x7o). 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, PDB code: 5x7o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5x7o

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1301

b:35.5
occ:1.00
 OD1 A:ASP979 2.2 32.6 1.0
OE1 A:GLU855 2.2 31.2 1.0
O A:GLY883 2.4 33.6 1.0
O A:SER880 2.5 39.1 1.0
OE1 A:GLU857 2.5 36.2 1.0
OE2 A:GLU857 2.6 35.5 1.0
O A:ASP979 2.6 29.3 1.0
CD A:GLU857 2.9 35.1 1.0
CG A:ASP979 3.4 32.9 1.0
CD A:GLU855 3.4 35.1 1.0
C A:SER880 3.5 38.0 1.0
C A:ASP979 3.5 28.8 1.0
C A:GLY883 3.5 33.3 1.0
CA A:ASP979 3.9 29.9 1.0
CB A:GLU855 4.1 34.0 1.0
OD2 A:ASP979 4.2 32.8 1.0
CB A:ASP979 4.2 30.9 1.0
OE2 A:GLU855 4.3 35.2 1.0
CA A:SER880 4.3 38.1 1.0
CG A:GLU855 4.3 35.2 1.0
N A:SER880 4.3 39.2 1.0
N A:GLY883 4.3 35.5 1.0
N A:PHE884 4.4 31.6 1.0
CA A:PHE884 4.4 32.9 1.0
N A:GLY881 4.4 39.1 1.0
CB A:SER880 4.4 38.7 1.0
CG A:GLU857 4.4 34.7 1.0
CA A:GLY881 4.5 40.0 1.0
CA A:GLY883 4.5 34.6 1.0
CA A:GLU855 4.5 33.2 1.0
N A:TYR980 4.6 28.9 1.0
N A:VAL856 4.8 32.3 1.0
C A:GLY881 4.8 39.4 1.0
CB A:TYR879 4.8 36.9 1.0
CB A:TYR980 4.9 32.1 1.0
CB A:PHE884 4.9 33.9 1.0
N A:SER882 4.9 38.2 1.0
CD2 A:TYR980 5.0 35.4 1.0

Calcium binding site 2 out of 6 in 5x7o

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1302

b:40.0
occ:1.00
 O A:HOH2467 2.1 33.2 1.0
OD1 A:ASP1111 2.2 30.8 1.0
O A:ALA1016 2.3 26.4 1.0
O A:LYS1013 2.4 33.2 1.0
OE1 A:GLU995 2.4 26.7 1.0
OE2 A:GLU995 2.7 29.0 1.0
CD A:GLU995 2.9 28.2 1.0
O A:ASP1111 2.9 27.4 1.0
CG A:ASP1111 3.3 31.2 1.0
C A:LYS1013 3.5 34.3 1.0
C A:ALA1016 3.5 25.4 1.0
C A:ASP1111 3.8 27.1 1.0
CA A:ASP1111 4.1 27.3 1.0
OD2 A:ASP1111 4.1 32.1 1.0
N A:LYS1013 4.2 30.3 1.0
CA A:PHE1017 4.2 24.2 1.0
CB A:ASP1111 4.3 29.4 1.0
CA A:LYS1013 4.3 31.7 1.0
N A:PHE1017 4.3 24.1 1.0
N A:ALA1016 4.4 27.6 1.0
N A:GLY1014 4.4 33.3 1.0
CG A:GLU995 4.4 26.6 1.0
CA A:GLY1014 4.5 33.5 1.0
CB A:LYS1013 4.6 34.1 1.0
CA A:ALA1016 4.6 27.2 1.0
CB A:PHE1017 4.7 24.5 1.0
C A:GLY1014 4.7 32.3 1.0
CB A:TYR1012 4.8 26.7 1.0
N A:ALA1015 4.9 30.4 1.0
N A:ALA994 4.9 26.4 1.0
N A:ARG1112 5.0 27.0 1.0

Calcium binding site 3 out of 6 in 5x7o

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1303

b:34.9
occ:1.00
 OD1 A:ASP1273 2.3 25.4 1.0
OE2 A:GLU1136 2.3 26.4 1.0
O A:GLN1176 2.4 24.9 1.0
O A:ASP1134 2.5 27.4 1.0
O A:ARG1173 2.8 25.9 1.0
OD2 A:ASP1273 2.8 24.6 1.0
CG A:ASP1273 2.9 26.7 1.0
CD A:GLU1136 3.4 29.6 1.0
C A:GLN1176 3.6 26.1 1.0
C A:ASP1134 3.6 27.2 1.0
CG A:GLU1136 3.8 28.3 1.0
C A:ARG1173 3.9 26.2 1.0
CB A:ASP1134 4.0 28.5 1.0
N A:GLN1176 4.1 25.2 1.0
CA A:ASP1134 4.1 27.7 1.0
OE2 A:GLU1274 4.2 36.3 1.0
CB A:PRO1171 4.3 31.7 1.0
CA A:GLN1176 4.4 24.9 1.0
CB A:ASP1273 4.4 26.0 1.0
N A:ARG1173 4.5 28.6 1.0
OE1 A:GLU1136 4.5 26.4 1.0
N A:ARG1177 4.5 26.7 1.0
CA A:ARG1173 4.7 29.2 1.0
CA A:ARG1177 4.7 28.2 1.0
N A:PHE1135 4.7 25.9 1.0
N A:ASN1175 4.8 25.1 1.0
CB A:ARG1174 4.8 26.8 1.0
N A:GLU1274 4.8 26.4 1.0
CB A:ARG1173 4.9 29.8 1.0
C A:PHE1135 4.9 26.6 1.0
CG A:GLU1274 4.9 32.6 1.0
N A:GLU1136 4.9 26.6 1.0
CG A:ASP1134 5.0 30.0 1.0
N A:ARG1174 5.0 26.8 1.0

Calcium binding site 4 out of 6 in 5x7o

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1301

b:32.2
occ:1.00
 OE1 B:GLU855 2.2 32.2 1.0
OD1 B:ASP979 2.3 33.9 1.0
O B:GLY883 2.3 29.6 1.0
O B:SER880 2.4 34.8 1.0
OE1 B:GLU857 2.4 32.9 1.0
O B:ASP979 2.6 25.6 1.0
OE2 B:GLU857 2.7 31.4 1.0
CD B:GLU857 2.9 33.4 1.0
CD B:GLU855 3.4 34.5 1.0
CG B:ASP979 3.4 32.5 1.0
C B:SER880 3.5 34.9 1.0
C B:ASP979 3.5 28.2 1.0
C B:GLY883 3.5 29.6 1.0
CA B:ASP979 3.9 28.6 1.0
CB B:GLU855 4.1 33.6 1.0
CA B:SER880 4.2 35.2 1.0
N B:SER880 4.2 35.3 1.0
CB B:ASP979 4.3 30.9 1.0
CG B:GLU855 4.3 33.3 1.0
OE2 B:GLU855 4.3 34.1 1.0
OD2 B:ASP979 4.3 33.3 1.0
N B:GLY883 4.3 32.7 1.0
N B:PHE884 4.4 30.5 1.0
N B:GLY881 4.4 36.1 1.0
CB B:SER880 4.4 34.1 1.0
CG B:GLU857 4.4 32.3 1.0
CA B:PHE884 4.4 30.3 1.0
CA B:GLU855 4.5 32.3 1.0
CA B:GLY883 4.5 29.6 1.0
CA B:GLY881 4.6 37.3 1.0
N B:TYR980 4.6 27.3 1.0
CB B:TYR980 4.8 29.0 1.0
N B:VAL856 4.8 29.8 1.0
CB B:TYR879 4.8 34.2 1.0
CD2 B:TYR980 4.9 30.7 1.0
CB B:PHE884 4.9 31.4 1.0
C B:GLY881 4.9 38.1 1.0
C B:GLU855 5.0 32.4 1.0

Calcium binding site 5 out of 6 in 5x7o

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1302

b:40.9
occ:1.00
 O B:HOH2547 2.1 36.2 1.0
O B:LYS1013 2.2 29.9 1.0
OD1 B:ASP1111 2.3 28.4 1.0
O B:ALA1016 2.4 24.9 1.0
OE1 B:GLU995 2.5 25.8 1.0
OE2 B:GLU995 2.6 28.4 1.0
CD B:GLU995 2.9 27.4 1.0
O B:ASP1111 3.0 28.1 1.0
C B:LYS1013 3.3 32.6 1.0
CG B:ASP1111 3.4 29.1 1.0
C B:ALA1016 3.6 24.6 1.0
C B:ASP1111 3.9 26.9 1.0
OD2 B:ASP1111 4.0 30.6 1.0
CA B:ASP1111 4.1 27.9 1.0
N B:LYS1013 4.2 27.9 1.0
N B:GLY1014 4.2 33.3 1.0
CA B:LYS1013 4.2 29.9 1.0
N B:ALA1016 4.3 27.9 1.0
CB B:ASP1111 4.3 28.2 1.0
CA B:GLY1014 4.3 33.7 1.0
CA B:PHE1017 4.4 24.2 1.0
CG B:GLU995 4.4 26.2 1.0
N B:PHE1017 4.4 24.6 1.0
CB B:LYS1013 4.5 32.5 1.0
CA B:ALA1016 4.6 27.5 1.0
C B:GLY1014 4.7 33.6 1.0
N B:ALA1015 4.8 31.0 1.0
CB B:PHE1017 4.8 25.6 1.0
CB B:ALA993 4.9 26.5 1.0
CB B:TYR1012 4.9 24.1 1.0
N B:ALA994 5.0 24.7 1.0

Calcium binding site 6 out of 6 in 5x7o

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1303

b:37.0
occ:1.00
 O B:GLN1176 2.3 24.9 1.0
OD1 B:ASP1273 2.4 25.1 1.0
OE2 B:GLU1136 2.4 26.8 1.0
O B:ASP1134 2.5 29.5 1.0
OD2 B:ASP1273 2.7 26.6 1.0
OE2 B:GLU1274 2.7 47.3 1.0
O B:ARG1173 2.8 27.7 1.0
CG B:ASP1273 2.9 25.3 1.0
CD B:GLU1136 3.5 28.1 1.0
C B:GLN1176 3.5 25.7 1.0
C B:ASP1134 3.6 28.2 1.0
CG B:GLU1136 3.9 26.4 1.0
CD B:GLU1274 4.0 37.6 1.0
C B:ARG1173 4.0 29.8 1.0
CB B:ASP1134 4.1 29.8 1.0
N B:GLN1176 4.1 26.2 1.0
CA B:ASP1134 4.1 30.2 1.0
CA B:GLN1176 4.4 26.0 1.0
CB B:ASP1273 4.4 25.0 1.0
CB B:PRO1171 4.4 33.0 1.0
N B:ARG1177 4.5 26.5 1.0
N B:ARG1173 4.5 30.5 1.0
OE1 B:GLU1136 4.6 26.7 1.0
CA B:ARG1177 4.6 27.3 1.0
CA B:ARG1173 4.7 31.1 1.0
CG B:GLU1274 4.7 33.6 1.0
N B:PHE1135 4.7 25.5 1.0
N B:GLU1274 4.8 26.6 1.0
N B:ASN1175 4.8 26.5 1.0
OE1 B:GLU1274 4.8 39.2 1.0
C B:PHE1135 4.9 27.4 1.0
CB B:ARG1174 4.9 27.7 1.0
CB B:GLN1176 5.0 26.4 1.0
CB B:ARG1173 5.0 31.1 1.0
N B:GLU1136 5.0 26.8 1.0
CG B:ASP1134 5.0 32.4 1.0
CB B:ARG1177 5.0 28.1 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: Sat Dec 12 05:50:35 2020

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