Atomistry » Calcium » PDB 4ixo-4jml » 4j3u
Atomistry »
  Calcium »
    PDB 4ixo-4jml »
      4j3u »

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

Last articles

Hg in 2QO8
Hg in 2PGV
Hg in 2Q38
Hg in 2Q1Q
Hg in 2Q1B
Hg in 2P4E
Hg in 2O9G
Hg in 2O1G
Hg in 2O1H
Hg in 2O9E
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy