Iodine in PDB 4j3u: 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;

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

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

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Iodine 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 Iodine atom.
In total 35 binding sites of Iodine where determined in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin, PDB code: 4j3u:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I910 b:27.0 occ:0.85 O A:HOH1512 3.3 25.1 1.0 CG A:MET4 3.5 44.4 1.0 CA A:GLY423 3.8 17.4 1.0 NE A:ARG428 3.8 19.6 1.0 CZ A:ARG428 3.9 20.4 1.0 N A:GLY423 4.0 16.4 1.0 CB A:MET4 4.2 47.2 1.0 NH2 A:ARG428 4.2 20.3 1.0 CB A:PRO198 4.2 28.7 1.0 CD A:ARG428 4.3 19.3 1.0 CG A:PRO198 4.3 28.5 1.0 CG2 A:THR199 4.3 27.4 1.0 O A:HOH1622 4.4 32.9 1.0 NH1 A:ARG428 4.4 21.6 1.0 O A:GLY432 4.5 21.6 1.0 O A:HOH1161 4.6 20.2 1.0 CD1 A:ILE434 4.6 15.5 1.0 CG1 A:ILE434 4.6 16.2 1.0 CD A:PRO198 4.8 27.6 1.0 C A:PRO422 4.8 17.2 1.0 CG A:ARG428 4.9 18.1 1.0

Iodine binding site 2 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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:I911 b:44.3 occ:0.60 O A:HOH1439 3.5 23.0 1.0 N A:THR495 3.5 19.3 1.0 OG1 A:THR495 3.6 22.8 1.0 CG A:ASP501 3.9 17.2 1.0 CA A:THR494 3.9 17.5 1.0 OD1 A:ASP501 3.9 16.2 1.0 CG2 A:THR495 3.9 22.0 1.0 CB A:THR494 4.0 17.4 1.0 CB A:ASP501 4.1 16.2 1.0 CB A:THR495 4.2 21.8 1.0 OD2 A:ASP501 4.2 19.2 1.0 C A:THR494 4.2 19.1 1.0 CA A:ASP501 4.2 14.5 1.0 CA A:THR495 4.4 21.7 1.0 CG2 A:THR494 4.5 18.1 1.0 O A:LEU493 4.9 15.6 1.0 O A:VAL500 5.0 16.1 1.0 O A:HOH1205 5.0 29.1 1.0

Iodine binding site 3 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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 A:I912 b:42.5 occ:0.60 O A:HOH1606 2.8 35.1 1.0 N A:GLY874 3.3 13.2 1.0 N A:GLU831 3.9 13.4 1.0 O A:HOH1114 4.0 20.9 1.0 CA A:PRO873 4.0 13.4 1.0 CB A:PRO873 4.0 13.7 1.0 CA A:GLY874 4.2 13.5 1.0 C A:PRO873 4.2 12.9 1.0 O A:HOH1182 4.2 19.9 1.0 CB A:GLU831 4.3 14.8 1.0 CA A:GLU831 4.4 14.4 1.0 CD2 A:LEU857 4.5 22.7 1.0 C A:HIS830 4.5 13.5 1.0 O A:HOH1393 4.6 19.5 1.0 O A:HOH1550 4.7 27.4 1.0 CD1 A:LEU857 4.7 24.1 1.0 CA A:HIS830 4.7 14.0 1.0

Iodine binding site 4 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I 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 A:I913 b:35.8 occ:0.60 O A:HOH1509 2.9 28.3 1.0 O A:HOH1289 3.6 23.7 1.0 CB A:ASP661 3.9 21.7 1.0 C A:ASP661 3.9 15.7 1.0 N A:GLU662 4.0 13.7 1.0 CD A:ARG665 4.0 11.5 1.0 O A:ASP661 4.1 14.8 1.0 CG A:GLU662 4.1 15.9 1.0 CA A:GLU662 4.2 13.6 1.0 CG A:ARG665 4.5 10.7 1.0 O A:HOH1273 4.6 21.4 1.0 CA A:ASP661 4.6 18.7 1.0 CB A:GLU662 4.8 14.6 1.0 O A:HOH1393 4.9 19.5 1.0

Iodine binding site 5 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 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:I914 b:35.1 occ:0.60 O A:HOH1468 2.7 29.0 1.0 O A:HOH1604 3.9 46.0 1.0 CD2 A:HIS830 4.1 12.1 1.0 O A:PRO829 4.1 21.5 1.0 CB A:HIS830 4.2 12.5 1.0 CG A:PRO829 4.2 16.2 1.0 CG A:HIS830 4.5 12.1 1.0 C A:PRO829 4.6 16.5 1.0 O A:HOH1550 4.7 27.4 1.0 CB A:PRO829 4.7 16.9 1.0 O A:HOH1461 4.9 37.7 1.0 N A:HIS830 5.0 14.6 1.0

Iodine binding site 6 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 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:I915 b:66.3 occ:0.80 N A:GLU810 3.6 43.2 1.0 CA A:PRO809 3.8 47.8 1.0 CB A:PRO809 3.8 48.0 1.0 N A:ARG805 3.8 26.9 1.0 O A:HOH1613 3.8 44.5 1.0 O A:ARG805 3.9 34.7 1.0 CA A:ALA804 4.1 20.4 1.0 CG A:MET811 4.1 26.1 1.0 C A:PRO809 4.2 44.6 1.0 CE A:MET811 4.4 25.4 1.0 OE2 A:GLU802 4.4 28.4 1.0 N A:MET811 4.5 34.2 1.0 C A:ALA804 4.5 22.0 1.0 O A:ASP803 4.5 16.0 1.0 CA A:GLU810 4.6 44.6 1.0 SD A:MET811 4.7 24.4 1.0 CB A:GLU810 4.7 47.2 1.0 C A:ARG805 4.8 36.6 1.0 CA A:ARG805 4.8 32.5 1.0 CB A:ALA804 4.8 20.6 1.0 CG A:ARG805 4.8 41.7 1.0 C A:GLU810 4.9 41.5 1.0 N A:ALA804 4.9 18.7 1.0

Iodine binding site 7 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 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:I916 b:63.5 occ:0.70 OG A:SER53 3.6 42.7 1.0 CB A:SER53 3.8 42.0 1.0 CG2 A:VAL87 4.1 38.5 1.0 CB A:VAL55 4.2 42.5 1.0 CG1 A:VAL55 4.2 42.6 1.0 CD1 A:LEU92 4.3 29.7 1.0 CG1 A:VAL87 4.5 39.4 1.0 CD2 A:LEU92 4.5 29.7 1.0 CA A:VAL87 4.6 39.1 1.0 CB A:VAL87 4.6 39.0 1.0 CG A:LEU92 4.8 28.9 1.0 CG2 A:VAL55 4.9 43.0 1.0

Iodine binding site 8 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 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:I917 b:16.3 occ:0.70 O A:HOH1696 3.3 21.0 1.0 NE2 A:GLN850 3.6 15.0 1.0 CD1 A:ILE761 3.6 16.7 0.5 CG2 A:ILE761 3.6 15.0 0.5 CG1 A:ILE761 3.7 15.7 0.5 CE1 A:HIS668 3.8 16.1 1.0 NE2 A:HIS668 3.8 16.8 1.0 O A:HOH1265 4.1 15.6 1.0 CG A:GLN850 4.2 11.6 1.0 O A:HOH1209 4.2 15.3 1.0 O A:SER757 4.2 7.3 0.6 CB A:ASP760 4.3 11.9 1.0 CD A:GLN850 4.4 13.3 1.0 CD1 A:ILE764 4.5 12.9 1.0 N A:ILE761 4.7 12.0 1.0 CB A:SER757 4.8 9.7 0.5 CA A:SER757 4.9 9.8 0.5 CB A:ILE761 4.9 13.8 0.5 OG A:SER853 4.9 13.2 1.0 CA A:SER757 4.9 10.1 0.5

Iodine binding site 9 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 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:I918 b:27.9 occ:0.60 OE2 A:GLU327 3.4 43.6 1.0 O A:HOH1778 3.6 26.9 1.0 O A:HOH1056 3.7 37.4 1.0 CD A:GLU327 3.9 40.3 1.0 N A:TRP705 3.9 14.3 1.0 O A:HOH1775 3.9 21.8 1.0 CG2 A:VAL325 3.9 20.9 1.0 NE2 A:HIS267 3.9 29.9 1.0 CB A:ASP704 4.0 17.1 1.0 CE3 A:TRP705 4.1 17.1 1.0 CA A:TRP705 4.1 14.2 1.0 C A:ASP704 4.3 14.8 1.0 CB A:TRP705 4.4 14.3 1.0 OE1 A:GLU327 4.5 44.5 1.0 CG A:GLU327 4.5 37.0 1.0 CB A:GLU327 4.7 34.7 1.0 CE1 A:HIS267 4.7 28.5 1.0 O A:ASP704 4.7 15.0 1.0 CA A:ASP704 4.7 15.4 1.0 CD2 A:HIS267 4.9 28.4 1.0 CZ3 A:TRP705 4.9 18.3 1.0 CD2 A:TRP705 4.9 15.7 1.0

Iodine binding site 10 out of 35 in the Crystal Structure of Barley Limit Dextrinase in Complex with Maltosyl- S-Betacyclodextrin


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 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:I919 b:41.7 occ:0.60 O A:HOH1150 3.4 19.8 1.0 O A:HOH1310 3.4 16.2 1.0 O A:HOH1355 3.5 20.8 1.0 CD A:ARG452 3.6 13.4 1.0 NE A:ARG452 3.7 14.2 1.0 CG A:ARG452 3.8 12.9 1.0 CB A:THR127 3.9 15.1 1.0 CG2 A:THR127 4.0 16.5 1.0 CA A:THR127 4.0 14.4 1.0 CZ A:ARG452 4.2 13.8 1.0 O A:THR127 4.3 13.3 1.0 NH1 A:ARG452 4.5 13.9 1.0 C A:THR127 4.6 14.2 1.0 CB A:ARG452 4.7 12.2 1.0 O A:TYR126 4.7 14.2 1.0 OD1 A:ASP456 4.8 15.1 1.0 NH2 A:ARG452 4.9 14.2 1.0

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.