Iodine in PDB 7jwf: Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose

The structure of Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose, PDB code: 7jwf was solved by A.G.Hettle, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.76 / 2.19
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	98.517, 124.763, 142.423, 90.00, 93.86, 90.00
R / Rfree (%)	20.5 / 23.7

The structure of Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose also contains other interesting chemical elements:

Chlorine	(Cl)	10 atoms
Calcium	(Ca)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose (pdb code 7jwf). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 120 binding sites of Iodine where determined in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose, PDB code: 7jwf:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I714 b:33.0 occ:0.96 ND2 A:ASN327 3.5 27.6 1.0 NZ A:LYS433 3.7 37.2 1.0 CD A:LYS433 3.8 32.4 1.0 CB A:PHE379 3.9 26.3 1.0 CE A:LYS433 4.0 32.1 1.0 CG A:ARG297 4.0 28.7 1.0 CB A:ASN327 4.2 31.3 1.0 CD A:ARG297 4.2 26.1 1.0 CB A:ARG297 4.3 32.3 1.0 O A:PHE379 4.3 34.1 1.0 CG A:ASN327 4.3 28.0 1.0 CD A:ARG435 4.4 31.9 1.0 O A:ASN327 4.4 32.7 1.0 CA A:PHE379 4.5 30.1 1.0 CA A:ARG297 4.8 29.2 1.0 C A:PHE379 4.9 32.4 1.0 CG A:PHE379 4.9 31.2 1.0 O A:HOH1070 5.0 42.8 1.0 CG A:ARG435 5.0 31.9 1.0

Iodine binding site 2 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I715 b:47.4 occ:0.57 O A:HOH951 3.4 39.0 1.0 CE1 A:PHE33 4.1 34.0 1.0 CZ A:PHE33 4.2 30.0 1.0 CG1 A:ILE28 4.3 36.5 1.0 CG A:GLU53 4.6 33.9 1.0 CD1 A:ILE28 4.6 32.6 1.0 O A:HOH1172 4.7 44.2 1.0 CG2 A:ILE28 4.8 33.3 1.0 N A:ASP25 4.8 49.5 1.0 CB A:ILE28 5.0 32.9 1.0 OE2 A:GLU53 5.0 43.0 1.0

Iodine binding site 3 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I716 b:51.3 occ:0.61 O A:HOH1049 3.7 47.7 1.0 CB A:ARG575 3.9 32.4 1.0 CG A:LYS577 3.9 43.8 1.0 CA A:ARG575 4.2 41.2 1.0 CG A:ARG575 4.2 34.0 1.0 N A:LYS576 4.2 40.0 1.0 CE A:LYS577 4.3 42.1 1.0 CD A:LYS577 4.3 47.2 1.0 N A:LYS577 4.4 40.2 1.0 C A:ARG575 4.5 38.6 1.0 CB A:LYS577 4.5 43.1 1.0 O A:HOH1068 4.7 45.6 1.0 CG A:LYS576 4.8 44.1 1.0 CE A:MET222 4.8 30.3 1.0 CD A:ARG575 5.0 34.1 1.0

Iodine binding site 4 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I717 b:33.3 occ:1.00 O A:HOH1021 3.6 34.0 1.0 N A:GLU427 3.7 32.0 1.0 CD A:LYS426 4.1 32.9 1.0 CG A:GLU427 4.2 29.5 1.0 CA A:LYS426 4.2 34.6 1.0 CB A:GLU427 4.3 29.1 1.0 CB A:LYS426 4.3 31.6 1.0 CD1 A:ILE359 4.4 30.5 1.0 CD A:GLU427 4.4 31.6 1.0 C A:LYS426 4.5 32.4 1.0 OE1 A:GLU427 4.6 28.1 1.0 CA A:GLU427 4.6 31.8 1.0 CG A:LYS426 4.9 34.7 1.0 OE2 A:GLU427 5.0 33.2 1.0

Iodine binding site 5 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I718 b:48.3 occ:0.52 N A:ILE168 3.7 33.5 1.0 CB A:ILE168 4.0 33.6 1.0 CG1 A:ILE168 4.2 31.5 1.0 CE1 A:TYR166 4.2 36.9 1.0 CA A:ILE168 4.4 34.8 1.0 C A:LYS167 4.5 35.4 1.0 CA A:LYS167 4.5 38.0 1.0 O A:ILE168 4.5 33.4 1.0 CD1 A:ILE168 4.6 35.2 1.0 CD1 A:TYR166 4.7 36.1 1.0 C A:ILE168 4.9 32.7 1.0

Iodine binding site 6 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I719 b:63.2 occ:0.51 I A:IOD725 3.6 90.9 1.0 CG A:PRO611 3.8 46.7 1.0 CG2 A:ILE584 3.8 36.6 1.0 CD1 A:ILE584 3.9 42.7 1.0 CB A:PRO611 3.9 42.7 1.0 CB A:ILE584 4.0 36.2 1.0 CG1 A:ILE584 4.6 38.7 1.0 CB A:ILE590 4.6 43.2 1.0 CD A:PRO611 4.8 40.9 1.0 CG2 A:ILE590 4.9 41.0 1.0

Iodine binding site 7 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I720 b:53.3 occ:0.39 O A:HOH1195 3.4 43.2 1.0 N A:SER436 3.6 30.8 1.0 O A:HOH1066 3.7 44.7 1.0 CA A:ARG435 3.9 32.5 1.0 CB A:ARG435 4.0 32.7 1.0 CG2 A:THR329 4.0 34.8 1.0 C A:ARG435 4.3 34.1 1.0 CG A:ARG435 4.4 31.9 1.0 CB A:SER436 4.4 31.3 1.0 CA A:SER436 4.6 37.2 1.0 O A:HOH852 4.9 38.1 1.0 O A:VAL434 4.9 34.6 1.0 CB A:THR329 5.0 30.2 1.0

Iodine binding site 8 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I721 b:62.3 occ:0.39 CE A:LYS426 4.1 36.1 1.0 O A:SER423 4.3 42.5 1.0 NZ A:LYS426 4.4 38.5 1.0 CA A:ARG424 4.5 40.9 1.0 CG A:ARG424 4.9 42.5 1.0

Iodine binding site 9 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I722 b:51.9 occ:0.37 NH2 A:ARG68 3.3 36.9 1.0 CB A:SER139 3.7 32.5 1.0 CE1 A:HIS115 3.9 31.8 1.0 CA A:SER139 4.2 32.6 1.0 CZ A:ARG68 4.4 41.4 1.0 CG2 A:ILE113 4.5 31.3 1.0 O A:HOH1146 4.5 42.3 1.0 NH1 A:ARG68 4.6 41.4 1.0 ND1 A:HIS115 4.6 34.1 1.0 NE2 A:HIS115 4.8 34.7 1.0 O A:SER139 4.8 36.0 1.0 OG A:SER139 4.9 41.7 1.0

Iodine binding site 10 out of 120 in the Crystal Structure of PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose


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 PDGH110B D344N in Complex with Alpha-(1,3)- Galactobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:I723 b:56.1 occ:0.37 N A:GLU603 3.3 43.0 1.0 OE1 A:GLU603 3.3 61.5 1.0 OG A:SER602 3.3 53.9 1.0 CB A:GLU603 3.5 46.4 1.0 CE A:LYS547 3.5 50.9 1.0 I A:IOD726 3.6 0.8 1.0 N A:SER602 3.6 42.7 1.0 CG A:GLU603 3.8 55.5 1.0 CD A:GLU603 3.9 61.3 1.0 CD2 A:LEU608 4.0 39.5 1.0 CA A:GLU603 4.0 42.8 1.0 NZ A:LYS547 4.1 55.5 1.0 CB A:PHE601 4.1 37.2 1.0 CD1 A:PHE601 4.2 42.4 1.0 C A:SER602 4.2 43.6 1.0 CA A:SER602 4.2 42.0 1.0 CB A:SER602 4.4 45.4 1.0 CD A:LYS547 4.4 46.3 1.0 C A:PHE601 4.5 45.3 1.0 CA A:PHE601 4.6 39.3 1.0 CG A:PHE601 4.6 43.4 1.0 CG A:LEU608 4.8 40.0 1.0 CD1 A:LEU608 4.9 39.9 1.0

B.E.Mcguire, A.Hettle, C.Vickers, D.T.King, D.J.Vocadlo, A.B.Boraston. The Structure of A Family 110 Glycoside Hydrolase Provides Insight Into the Hydrolysis of Alpha-(1,3)-Galactosidic Linkages in Lambda-Carrageenan and Blood Group Antigens. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33127644
DOI: 10.1074/JBC.RA120.015776