Atomistry » Calcium » PDB 5wzv-5xiw » 5x7o
Atomistry »
  Calcium »
    PDB 5wzv-5xiw »
      5x7o »

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

Go back to Calcium Binding Sites List in 5x7o
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

Go back to Calcium Binding Sites List in 5x7o
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

Go back to Calcium Binding Sites List in 5x7o
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

Go back to Calcium Binding Sites List in 5x7o
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

Go back to Calcium Binding Sites List in 5x7o
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

Go back to Calcium Binding Sites List in 5x7o
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: Mon Jul 15 14:46:15 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy