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Calcium in PDB 5x7p: Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose

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

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

Protein crystallography data

The structure of Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose, PDB code: 5x7p 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) 152.48 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 184.287, 271.517, 133.630, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 23.7

Other elements in 5x7p:

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

Nickel (Ni) 2 atoms
Magnesium (Mg) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose (pdb code 5x7p). 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 Complexed with Acarbose, PDB code: 5x7p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5x7p

Go back to Calcium Binding Sites List in 5x7p
Calcium binding site 1 out of 6 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose


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

b:47.6
occ:1.00
 OD1 A:ASP979 2.2 43.7 1.0
OE1 A:GLU855 2.2 45.6 1.0
OE1 A:GLU857 2.5 45.2 1.0
O A:GLY883 2.5 47.4 1.0
O A:ASP979 2.5 42.1 1.0
O A:SER880 2.5 54.0 1.0
OE2 A:GLU857 2.5 41.6 1.0
CD A:GLU857 2.8 42.0 1.0
CD A:GLU855 3.3 49.3 1.0
CG A:ASP979 3.4 46.1 1.0
C A:ASP979 3.4 43.7 1.0
C A:SER880 3.5 48.6 1.0
C A:GLY883 3.6 46.1 1.0
CA A:ASP979 3.9 42.3 1.0
CB A:GLU855 4.1 42.1 1.0
OE2 A:GLU855 4.2 50.5 1.0
OD2 A:ASP979 4.2 45.5 1.0
CG A:GLU855 4.2 46.8 1.0
CB A:ASP979 4.2 44.8 1.0
CG A:GLU857 4.3 43.2 1.0
N A:GLY883 4.3 47.2 1.0
CA A:SER880 4.3 50.2 1.0
CA A:PHE884 4.4 47.9 1.0
N A:GLY881 4.4 48.9 1.0
N A:SER880 4.4 51.5 1.0
N A:PHE884 4.4 49.2 1.0
CA A:GLU855 4.4 41.2 1.0
CB A:SER880 4.5 44.7 1.0
CA A:GLY881 4.5 49.7 1.0
CA A:GLY883 4.5 46.0 1.0
N A:TYR980 4.6 45.4 1.0
N A:VAL856 4.7 38.2 1.0
CB A:TYR980 4.8 43.8 1.0
CB A:TYR879 4.8 48.1 1.0
N A:SER882 4.9 46.2 1.0
CB A:PHE884 4.9 49.4 1.0
C A:GLU855 4.9 42.7 1.0
C A:GLY881 4.9 47.7 1.0

Calcium binding site 2 out of 6 in 5x7p

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


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

b:52.6
occ:1.00
 OD1 A:ASP1111 2.1 43.9 1.0
O A:ALA1016 2.4 35.4 1.0
OE1 A:GLU995 2.5 40.3 1.0
O A:LYS1013 2.5 42.2 1.0
OE2 A:GLU995 2.6 37.8 1.0
O A:HOH2372 2.7 39.4 1.0
CD A:GLU995 2.9 39.7 1.0
O A:ASP1111 3.0 39.4 1.0
CG A:ASP1111 3.3 43.1 1.0
C A:LYS1013 3.4 39.2 1.0
C A:ALA1016 3.6 38.8 1.0
C A:ASP1111 3.8 36.1 1.0
OD2 A:ASP1111 4.0 45.5 1.0
CA A:ASP1111 4.1 38.8 1.0
N A:GLY1014 4.2 38.8 1.0
N A:LYS1013 4.2 36.2 1.0
CA A:LYS1013 4.2 42.0 1.0
CA A:GLY1014 4.3 37.5 1.0
CB A:ASP1111 4.3 40.2 1.0
N A:ALA1016 4.5 36.6 1.0
CB A:LYS1013 4.5 44.1 1.0
CG A:GLU995 4.5 37.9 1.0
CA A:PHE1017 4.5 37.2 1.0
N A:PHE1017 4.5 37.0 1.0
CA A:ALA1016 4.7 38.4 1.0
C A:GLY1014 4.7 38.4 1.0
CB A:ALA993 4.8 35.6 1.0
N A:ALA994 4.8 35.2 1.0
N A:ARG1112 4.9 37.6 1.0
N A:ALA1015 4.9 37.0 1.0
CB A:PHE1017 4.9 35.0 1.0
CB A:TYR1012 4.9 34.8 1.0

Calcium binding site 3 out of 6 in 5x7p

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


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

b:50.0
occ:1.00
 OE2 A:GLU1136 2.3 37.2 1.0
OD1 A:ASP1273 2.4 44.9 1.0
O A:GLN1176 2.5 37.8 1.0
O A:ASP1134 2.6 33.8 1.0
O A:ARG1173 2.6 35.2 1.0
OD2 A:ASP1273 3.0 39.3 1.0
CG A:ASP1273 3.1 40.9 1.0
CD A:GLU1136 3.3 34.7 1.0
OE2 A:GLU1274 3.6 44.9 1.0
C A:ASP1134 3.7 35.8 1.0
C A:GLN1176 3.7 33.0 1.0
CG A:GLU1136 3.7 37.0 1.0
C A:ARG1173 3.8 36.1 1.0
CB A:ASP1134 4.0 33.8 1.0
N A:GLN1176 4.1 32.6 1.0
CA A:ASP1134 4.2 33.9 1.0
N A:ARG1173 4.4 35.2 1.0
OE1 A:GLU1136 4.4 40.1 1.0
CA A:GLN1176 4.4 34.0 1.0
CB A:PRO1171 4.5 43.5 1.0
CA A:ARG1173 4.5 37.9 1.0
CB A:ASP1273 4.6 39.6 1.0
CD A:GLU1274 4.6 45.2 1.0
CB A:ARG1174 4.7 36.2 1.0
N A:ASN1175 4.7 31.3 1.0
CB A:ARG1173 4.7 35.1 1.0
N A:ARG1177 4.7 34.7 1.0
N A:ARG1174 4.8 35.0 1.0
N A:PHE1135 4.8 36.8 1.0
N A:GLU1274 4.9 38.7 1.0
CG A:GLU1274 4.9 39.8 1.0
N A:GLU1136 4.9 35.5 1.0
CA A:ARG1177 4.9 39.3 1.0
CG A:ASP1134 4.9 37.5 1.0

Calcium binding site 4 out of 6 in 5x7p

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


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

b:39.4
occ:1.00
 OD1 B:ASP979 2.2 40.6 1.0
OE1 B:GLU855 2.3 41.2 1.0
O B:GLY883 2.3 36.7 1.0
O B:SER880 2.3 37.8 1.0
OE1 B:GLU857 2.4 39.5 1.0
O B:ASP979 2.5 35.0 1.0
OE2 B:GLU857 2.7 43.3 1.0
CD B:GLU857 2.9 42.2 1.0
C B:SER880 3.4 40.0 1.0
CG B:ASP979 3.4 40.1 1.0
CD B:GLU855 3.4 45.0 1.0
C B:GLY883 3.5 41.1 1.0
C B:ASP979 3.5 34.6 1.0
CA B:ASP979 3.9 37.1 1.0
CB B:GLU855 4.2 40.1 1.0
N B:GLY883 4.3 43.7 1.0
N B:GLY881 4.3 45.0 1.0
CB B:ASP979 4.3 38.1 1.0
OE2 B:GLU855 4.3 47.6 1.0
OD2 B:ASP979 4.3 44.5 1.0
N B:PHE884 4.3 39.7 1.0
CG B:GLU855 4.3 39.6 1.0
CA B:SER880 4.4 41.7 1.0
N B:SER880 4.4 44.2 1.0
CA B:GLY881 4.4 45.7 1.0
CG B:GLU857 4.4 39.9 1.0
CA B:PHE884 4.4 36.7 1.0
CA B:GLY883 4.4 39.0 1.0
CA B:GLU855 4.4 41.6 1.0
N B:TYR980 4.6 31.9 1.0
CB B:SER880 4.7 41.3 1.0
CB B:TYR980 4.7 39.8 1.0
N B:VAL856 4.7 34.5 1.0
OG B:SER880 4.8 40.0 1.0
CD2 B:TYR980 4.8 42.1 1.0
C B:GLY881 4.9 50.5 1.0
CB B:PHE884 4.9 34.5 1.0
C B:GLU855 4.9 40.0 1.0
CB B:TYR879 4.9 40.2 1.0
N B:SER882 5.0 48.5 1.0

Calcium binding site 5 out of 6 in 5x7p

Go back to Calcium Binding Sites List in 5x7p
Calcium binding site 5 out of 6 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose


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

b:59.6
occ:1.00
 O B:LYS1013 2.3 44.3 1.0
OD1 B:ASP1111 2.3 41.7 1.0
O B:HOH2371 2.4 41.9 1.0
O B:ALA1016 2.5 32.4 1.0
OE1 B:GLU995 2.6 39.9 1.0
OE2 B:GLU995 2.8 38.5 1.0
O B:ASP1111 3.0 32.3 1.0
CD B:GLU995 3.1 39.7 1.0
CG B:ASP1111 3.3 40.9 1.0
C B:LYS1013 3.3 37.8 1.0
C B:ALA1016 3.7 34.8 1.0
OD2 B:ASP1111 3.8 41.1 1.0
C B:ASP1111 3.8 33.0 1.0
N B:GLY1014 4.1 37.0 1.0
N B:LYS1013 4.1 39.3 1.0
CA B:ASP1111 4.1 36.4 1.0
CA B:LYS1013 4.2 38.3 1.0
CA B:GLY1014 4.2 34.8 1.0
CB B:ASP1111 4.3 40.0 1.0
CB B:LYS1013 4.4 42.3 1.0
CA B:PHE1017 4.5 36.2 1.0
N B:ALA1016 4.5 38.2 1.0
N B:PHE1017 4.6 35.9 1.0
CG B:GLU995 4.6 40.7 1.0
C B:GLY1014 4.6 39.4 1.0
CB B:ALA993 4.7 31.4 1.0
CA B:ALA1016 4.8 38.4 1.0
CB B:PHE1017 4.9 38.1 1.0
CB B:TYR1012 4.9 37.3 1.0
N B:ALA1015 4.9 39.2 1.0
N B:ARG1112 5.0 33.3 1.0
N B:ALA994 5.0 34.0 1.0

Calcium binding site 6 out of 6 in 5x7p

Go back to Calcium Binding Sites List in 5x7p
Calcium binding site 6 out of 6 in the Crystal Structure of Paenibacillus Sp. 598K Alpha-1,6- Glucosyltransferase Complexed with Acarbose


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

b:44.7
occ:1.00
 O B:GLN1176 2.4 35.7 1.0
O B:ASP1134 2.4 37.0 1.0
OD1 B:ASP1273 2.4 35.5 1.0
OE2 B:GLU1136 2.4 40.7 1.0
OD2 B:ASP1273 2.7 31.2 1.0
O B:ARG1173 2.8 30.9 1.0
CG B:ASP1273 2.9 34.0 1.0
OE2 B:GLU1274 3.0 48.4 1.0
CD B:GLU1136 3.5 34.4 1.0
C B:ASP1134 3.5 36.1 1.0
C B:GLN1176 3.6 34.5 1.0
CG B:GLU1136 3.9 36.5 1.0
C B:ARG1173 4.0 34.6 1.0
CB B:ASP1134 4.0 34.9 1.0
CA B:ASP1134 4.1 33.1 1.0
N B:GLN1176 4.1 32.0 1.0
CD B:GLU1274 4.2 47.5 1.0
CA B:GLN1176 4.4 33.4 1.0
CB B:ASP1273 4.4 34.5 1.0
N B:ARG1173 4.5 34.3 1.0
OE1 B:GLU1136 4.5 36.3 1.0
CB B:PRO1171 4.5 46.0 1.0
N B:ARG1177 4.6 35.2 1.0
CA B:ARG1173 4.6 35.5 1.0
CG B:GLU1274 4.6 43.9 1.0
N B:PHE1135 4.7 31.9 1.0
CB B:ARG1173 4.7 34.7 1.0
CB B:ARG1174 4.8 33.6 1.0
CA B:ARG1177 4.8 37.9 1.0
N B:ASN1175 4.8 35.2 1.0
N B:GLU1274 4.8 36.9 1.0
CG B:ASP1134 4.9 35.8 1.0
CB B:GLN1176 4.9 32.7 1.0
N B:GLU1136 4.9 40.0 1.0
C B:PHE1135 5.0 38.1 1.0
N B:ARG1174 5.0 36.4 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: Mon Jul 15 14:46:16 2024

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