Iodine in PDB 5gzh: Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form

The structure of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form, PDB code: 5gzh was solved by K.Abe, M.Nakajima, T.Arakawa, S.Fushinobu, H.Taguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.74 / 1.80
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	90.965, 90.965, 124.086, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 20.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iodine atom in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form (pdb code 5gzh). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 24 binding sites of Iodine where determined in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form, PDB code: 5gzh:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:40.4 occ:1.00 O A:HOH854 2.9 41.7 1.0 NE A:ARG99 3.6 28.7 1.0 NZ A:LYS102 3.8 42.7 1.0 CE A:LYS102 3.9 39.1 1.0 CA A:ARG99 3.9 23.0 1.0 N A:ARG99 4.0 23.6 1.0 CD A:ARG99 4.0 26.2 1.0 CG A:GLU98 4.1 27.0 1.0 CB A:ARG99 4.1 23.8 1.0 CD A:GLU98 4.3 35.2 1.0 C A:GLU98 4.3 24.0 1.0 O A:GLU98 4.4 27.5 1.0 CB A:GLU98 4.5 26.6 1.0 OE2 A:GLU98 4.5 33.4 1.0 CD A:LYS102 4.6 41.5 1.0 CG A:ARG99 4.7 25.9 1.0 CZ A:ARG99 4.7 32.5 1.0 OE1 A:GLU98 4.7 33.0 1.0 CH2 A:TRP42 4.8 28.0 1.0 NH2 A:ARG99 4.9 34.8 1.0 O A:HOH769 5.0 43.4 1.0

Iodine binding site 2 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:29.3 occ:1.00 O A:HOH810 3.4 24.7 1.0 O A:HOH734 3.5 32.2 1.0 CB A:ALA332 4.3 23.2 1.0 CB A:ALA323 4.3 25.7 1.0 CZ A:PHE268 4.4 18.8 1.0 CE1 A:PHE268 4.4 20.4 1.0 O A:HOH704 4.7 22.6 1.0

Iodine binding site 3 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:50.2 occ:1.00 N A:GLU358 3.6 25.8 1.0 N B:GLU358 3.6 25.4 1.0 CB B:GLU358 3.9 26.6 1.0 CD B:PRO357 3.9 27.2 1.0 CB A:GLU358 3.9 25.8 1.0 CG A:GLU358 3.9 29.1 1.0 CG B:GLU358 4.0 29.2 1.0 N B:PRO357 4.0 24.6 1.0 CD A:PRO357 4.0 27.8 1.0 N A:PRO357 4.0 23.9 1.0 CG A:PRO357 4.1 24.4 1.0 CG B:PRO357 4.2 25.5 1.0 CA B:GLU358 4.3 26.0 1.0 CA A:GLU358 4.3 24.4 1.0 C B:THR356 4.3 22.3 1.0 C A:THR356 4.4 22.3 1.0 CA B:THR356 4.5 22.3 1.0 CA A:THR356 4.6 21.0 1.0 C A:PRO357 4.6 19.6 1.0 C B:PRO357 4.6 19.8 1.0 N B:TYR359 4.7 25.6 1.0 N A:TYR359 4.7 24.9 1.0 CA B:PRO357 4.8 23.2 1.0 CA A:PRO357 4.8 21.9 1.0 CB A:PRO357 4.9 21.6 1.0 CB B:PRO357 5.0 22.6 1.0

Iodine binding site 4 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:66.7 occ:1.00 I A:IOD506 3.5 96.8 1.0 N A:GLU124 3.6 33.1 1.0 O A:ASN68 3.7 30.5 1.0 CB A:GLU124 3.7 35.5 1.0 CB A:TYR122 3.8 29.2 1.0 CG A:GLU124 3.8 37.4 1.0 CB A:ASN68 3.8 35.1 1.0 N A:GLY123 3.9 26.2 1.0 CD1 A:TYR122 4.0 31.7 1.0 CD A:GLU124 4.0 45.0 1.0 OE1 A:GLU124 4.1 48.6 1.0 CA A:TYR122 4.1 31.1 1.0 C A:ASN68 4.1 29.8 1.0 C A:TYR122 4.1 25.3 1.0 CA A:GLU124 4.3 37.5 1.0 CG A:TYR122 4.3 27.1 1.0 CA A:ASN68 4.5 31.5 1.0 OE2 A:GLU124 4.6 41.6 1.0 C A:GLY123 4.7 32.2 1.0 CA A:GLY123 4.7 29.7 1.0 N A:VAL69 4.9 29.7 1.0 O A:TYR122 5.0 28.4 1.0

Iodine binding site 5 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:96.8 occ:1.00 I A:IOD505 3.5 66.7 1.0 O A:ASN65 3.6 39.8 1.0 N A:ASN68 3.6 30.3 1.0 O A:HOH826 3.8 47.4 1.0 CG2 A:VAL69 3.8 30.1 1.0 N A:VAL69 3.9 29.7 1.0 C A:ASN68 3.9 29.8 1.0 CB A:ASN68 3.9 35.1 1.0 CA A:ASN68 3.9 31.5 1.0 CA A:ASP66 4.0 43.1 1.0 C A:ASP66 4.1 40.3 1.0 N A:MET67 4.3 38.0 1.0 CD1 A:TYR122 4.4 31.7 1.0 O A:ASN68 4.4 30.5 1.0 O A:ASP66 4.4 37.3 1.0 C A:ASN65 4.5 47.9 1.0 CE1 A:TYR122 4.7 34.4 1.0 N A:ASP66 4.7 45.0 1.0 CA A:VAL69 4.7 25.3 1.0 C A:MET67 4.8 32.8 1.0 CB A:VAL69 4.8 31.1 1.0 CG A:ASN68 4.9 38.5 1.0

Iodine binding site 6 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:68.2 occ:1.00 O A:HOH730 3.3 30.1 1.0 O A:HOH769 3.9 43.4 1.0 CG A:GLU98 4.1 27.0 1.0 CE A:MET101 4.4 39.6 1.0 SD A:MET101 4.5 35.8 1.0 OE2 A:GLU98 4.7 33.4 1.0 CD A:GLU98 4.7 35.2 1.0 O A:HOH872 4.7 31.6 1.0 CB A:GLU98 4.9 26.6 1.0 CA A:GLU98 4.9 23.3 1.0

Iodine binding site 7 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:68.7 occ:1.00 O A:HOH792 2.6 36.3 1.0 I A:IOD513 4.0 82.8 1.0 CD1 A:PHE259 4.0 28.4 1.0 NZ A:LYS261 4.0 36.2 1.0 CA A:PHE259 4.2 24.6 1.0 N A:PHE259 4.3 22.7 1.0 CE A:LYS261 4.4 37.4 1.0 CE1 A:PHE259 4.4 28.4 1.0 CG A:LYS261 4.7 34.3 1.0 CG A:PHE259 4.7 24.4 1.0 CB A:PHE259 4.9 25.3 1.0

Iodine binding site 8 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:75.5 occ:1.00 O A:HOH861 3.0 41.6 1.0 NE1 A:TRP194 3.4 28.2 1.0 CE A:LYS199 3.6 53.6 1.0 CD A:LYS199 3.8 48.8 1.0 CG A:LYS199 3.9 42.0 1.0 NE1 A:TRP200 4.0 30.8 1.0 NZ A:LYS199 4.0 51.7 1.0 CZ2 A:TRP182 4.1 28.5 1.0 CE2 A:TRP194 4.2 29.2 1.0 CZ2 A:TRP194 4.2 28.6 1.0 CH2 A:TRP182 4.5 27.5 1.0 CD1 A:TRP194 4.5 27.7 1.0 CB A:LYS199 4.5 33.0 1.0 CD1 A:TRP200 4.6 27.7 1.0 CE2 A:TRP200 4.7 27.0 1.0 O A:HOH764 4.8 28.0 1.0 CA A:LYS199 4.9 27.0 1.0

Iodine binding site 9 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:73.1 occ:1.00 O5 A:TRE501 3.5 40.2 1.0 NE2 A:HIS449 3.6 43.2 1.0 C1 A:TRE501 3.9 42.6 1.0 O6 A:TRE501 3.9 38.8 1.0 C2 A:TRE501 4.1 39.4 1.0 CD2 A:HIS449 4.1 39.9 1.0 C5 A:TRE501 4.6 38.5 1.0 C4 A:TRE501 4.7 37.1 1.0 CE1 A:HIS449 4.7 42.8 1.0 C6 A:TRE501 4.9 39.5 1.0 O A:HOH605 4.9 40.1 1.0

Iodine binding site 10 out of 24 in the Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Endo-Beta-1,2-Glucanase From Chitinophaga Pinensis - Ligand Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:I511 b:73.6 occ:1.00 O A:HOH714 3.3 30.7 1.0 O A:HOH863 3.3 45.9 1.0 O A:HOH906 3.7 40.5 1.0 O A:ALA168 3.8 25.5 1.0 C A:ALA168 3.8 28.5 1.0 CD A:ARG154 3.9 24.3 1.0 N A:ALA169 4.0 26.6 1.0 CG A:ARG154 4.1 24.1 1.0 CA A:ALA169 4.1 25.9 1.0 CB A:ASP172 4.1 25.7 1.0 CB A:ALA168 4.1 24.3 1.0 O A:HOH632 4.3 40.5 1.0 CG A:ASP172 4.4 26.2 1.0 CA A:ALA168 4.6 27.0 1.0 CB A:ALA169 4.7 27.2 1.0 OD2 A:ASP172 4.7 27.3 1.0 NE A:ARG154 4.7 24.7 1.0 OD1 A:ASP172 4.9 25.6 1.0

K.Abe, M.Nakajima, T.Yamashita, H.Matsunaga, S.Kamisuki, T.Nihira, Y.Takahashi, N.Sugimoto, A.Miyanaga, H.Nakai, T.Arakawa, S.Fushinobu, H.Taguchi. Biochemical and Structural Analyses of A Bacterial Endo-Beta-1,2-Glucanase Reveal A New Glycoside Hydrolase Family J. Biol. Chem. V. 292 7487 2017.
ISSN: ESSN 1083-351X
PubMed: 28270506
DOI: 10.1074/JBC.M116.762724