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Calcium in PDB 4j3u: Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin

Enzymatic activity of Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin

All present enzymatic activity of Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin:
3.2.1.41;

Protein crystallography data

The structure of Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin, PDB code: 4j3u was solved by L.Sim, M.S.Windahl, M.S.Moeller, A.Henriksen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.76 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 195.430, 84.610, 121.790, 90.00, 119.91, 90.00
R / Rfree (%) 17.2 / 21.8

Other elements in 4j3u:

The structure of Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin also contains other interesting chemical elements:

Iodine (I) 35 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin (pdb code 4j3u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin, PDB code: 4j3u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4j3u

Go back to Calcium Binding Sites List in 4j3u
Calcium binding site 1 out of 4 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


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 Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca930

b:11.2
occ:1.00
 O A:HOH1315 2.6 26.5 1.0
O A:LEU301 2.7 10.3 1.0
O A:HOH1361 2.7 24.2 1.0
O A:GLY393 2.7 10.3 1.0
OG A:SER297 2.8 9.7 1.0
O A:SER297 2.8 8.8 1.0
C A:SER297 3.6 9.5 1.0
C A:GLY393 3.7 10.2 1.0
O A:HOH1267 3.7 22.8 1.0
CA A:SER297 3.7 9.2 1.0
CB A:SER297 3.8 9.1 1.0
C A:LEU301 3.8 9.0 1.0
O A:HOH1112 4.1 12.0 1.0
CA A:GLY393 4.1 10.1 1.0
C A:GLY300 4.4 7.4 1.0
CA A:THR302 4.4 9.4 1.0
O A:GLY300 4.5 7.5 1.0
N A:LEU301 4.6 7.6 1.0
CD2 A:LEU394 4.6 9.7 1.0
N A:THR302 4.6 9.0 1.0
N A:ASP298 4.7 10.3 1.0
N A:LEU394 4.8 10.4 1.0
O A:HOH1253 4.8 13.0 1.0
CA A:LEU301 4.8 8.8 1.0
CA A:GLY300 4.8 7.1 1.0
O A:ILE392 4.9 12.1 1.0

Calcium binding site 2 out of 4 in 4j3u

Go back to Calcium Binding Sites List in 4j3u
Calcium binding site 2 out of 4 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


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 Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca931

b:12.6
occ:1.00
 O A:GLN348 2.2 16.9 1.0
O A:TYR353 2.3 12.1 1.0
OD1 A:ASN701 2.4 11.4 1.0
O A:HOH1002 2.5 14.0 1.0
OD1 A:ASP351 2.5 15.1 1.0
O A:HOH1001 2.5 11.0 1.0
O A:HOH1225 2.5 12.6 1.0
C A:GLN348 3.4 17.8 1.0
C A:TYR353 3.5 11.5 1.0
CG A:ASP351 3.5 14.9 1.0
CG A:ASN701 3.6 11.3 1.0
OD2 A:ASP351 3.8 15.8 1.0
CA A:GLN348 4.1 17.9 1.0
CA A:TYR353 4.2 12.3 1.0
O A:GLY314 4.2 14.0 1.0
N A:TYR353 4.2 13.2 1.0
ND2 A:ASN701 4.3 12.6 1.0
CB A:TYR353 4.4 12.9 1.0
O A:ASP351 4.4 13.9 1.0
N A:GLU349 4.5 18.7 1.0
CB A:GLN348 4.5 19.0 1.0
N A:ASN354 4.5 10.8 1.0
ND2 A:ASN354 4.6 13.1 1.0
CA A:ASN701 4.6 11.3 1.0
O A:ASN701 4.6 12.1 1.0
O A:HOH1153 4.6 21.0 1.0
CB A:ASN701 4.7 11.2 1.0
CA A:GLU349 4.7 19.2 1.0
CB A:ASN354 4.7 11.8 1.0
N A:ASP351 4.7 15.6 1.0
CB A:ASP351 4.8 14.8 1.0
CA A:ASN354 4.8 10.8 1.0
C A:ASP351 4.8 14.4 1.0
C A:GLU349 4.9 18.3 1.0
C A:ASN701 4.9 12.0 1.0

Calcium binding site 3 out of 4 in 4j3u

Go back to Calcium Binding Sites List in 4j3u
Calcium binding site 3 out of 4 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


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 Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca922

b:12.3
occ:1.00
 O B:GLN348 2.2 16.9 1.0
O B:TYR353 2.3 10.7 1.0
O B:HOH1805 2.3 13.9 1.0
OD1 B:ASN701 2.4 12.9 1.0
O B:HOH1784 2.4 13.5 1.0
O B:HOH1206 2.5 13.9 1.0
OD1 B:ASP351 2.5 14.0 1.0
C B:GLN348 3.4 17.4 1.0
C B:TYR353 3.4 9.6 1.0
CG B:ASP351 3.5 13.4 1.0
CG B:ASN701 3.6 13.3 1.0
OD2 B:ASP351 3.8 14.8 1.0
CA B:GLN348 4.1 17.4 1.0
CA B:TYR353 4.1 10.0 1.0
N B:TYR353 4.2 10.9 1.0
ND2 B:ASN701 4.3 14.9 1.0
O B:GLY314 4.3 13.7 1.0
CB B:TYR353 4.3 9.6 1.0
CB B:GLN348 4.5 17.7 1.0
N B:GLU349 4.5 17.3 1.0
N B:ASN354 4.5 10.3 1.0
O B:ASP351 4.5 12.4 1.0
CA B:ASN701 4.6 13.5 1.0
O B:ASN701 4.6 12.7 1.0
ND2 B:ASN354 4.6 11.5 1.0
O B:HOH1060 4.7 22.1 1.0
CB B:ASN354 4.7 10.8 1.0
CB B:ASN701 4.7 13.6 1.0
CA B:GLU349 4.7 18.1 1.0
N B:ASP351 4.8 14.0 1.0
CA B:ASN354 4.8 10.0 1.0
CB B:ASP351 4.8 13.3 1.0
C B:ASP351 4.9 12.9 1.0
C B:ASN701 4.9 12.9 1.0

Calcium binding site 4 out of 4 in 4j3u

Go back to Calcium Binding Sites List in 4j3u
Calcium binding site 4 out of 4 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


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 Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca923

b:10.9
occ:1.00
 O B:HOH1326 2.5 29.6 1.0
O B:LEU301 2.6 9.5 1.0
OG B:SER297 2.7 9.7 1.0
O B:GLY393 2.7 10.7 1.0
O B:HOH1145 2.8 15.8 1.0
O B:SER297 2.9 8.5 1.0
C B:SER297 3.6 10.1 1.0
C B:GLY393 3.7 10.2 1.0
C B:LEU301 3.8 8.4 1.0
CA B:SER297 3.8 9.8 1.0
CB B:SER297 3.8 9.9 1.0
O B:HOH1244 3.9 16.0 1.0
O B:HOH1097 4.1 13.9 1.0
CA B:GLY393 4.1 10.7 1.0
C B:GLY300 4.4 8.6 1.0
CA B:THR302 4.4 8.3 1.0
O B:GLY300 4.4 7.7 1.0
O B:HOH1187 4.5 12.5 1.0
N B:THR302 4.5 7.7 1.0
CD2 B:LEU394 4.6 8.6 1.0
N B:LEU301 4.6 8.5 1.0
N B:ASP298 4.7 10.4 1.0
N B:LEU394 4.8 9.8 1.0
CA B:LEU301 4.8 8.6 1.0
CA B:GLY300 4.8 9.7 1.0
O B:HOH1511 4.8 27.6 1.0
O B:ILE392 4.9 12.6 1.0
O B:HOH1533 5.0 22.6 1.0

Reference:

L.Sim, M.S.Windahl, M.S.Moeller, A.Henriksen. Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl-S-Betacyclodextrin To Be Published.
Page generated: Tue Jul 8 23:05:46 2025

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