Iodine in PDB 9nwf: Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine

The structure of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine, PDB code: 9nwf was solved by A.B.Boraston, B.Alvarez, O.Canil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.543, 105.84, 179.944, 90, 90, 90
R / Rfree (%)	19.1 / 26.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Iodine atom in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine (pdb code 9nwf). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 27 binding sites of Iodine where determined in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine, PDB code: 9nwf:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:128.8 occ:1.00 N A:GLN130 3.5 36.8 1.0 N A:ALA129 3.8 47.1 1.0 CE A:MET70 3.9 42.2 1.0 CB A:GLN130 4.1 34.9 1.0 CB A:ALA129 4.1 41.3 1.0 CA A:ALA129 4.3 44.0 1.0 CA A:GLN130 4.3 36.3 1.0 C A:ALA129 4.3 43.3 1.0 CB A:HIS128 4.3 46.9 1.0 CH2 A:TRP178 4.7 45.5 1.0 OE1 A:GLN130 4.8 39.6 1.0 C A:HIS128 4.8 45.6 1.0 ND1 A:HIS128 4.9 59.4 1.0 CA A:HIS128 5.0 48.4 1.0 CG A:HIS128 5.0 56.7 1.0

Iodine binding site 2 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:59.0 occ:1.00 CD A:ARG60 3.9 35.5 1.0 CA A:SER61 3.9 37.9 1.0 N A:SER61 3.9 43.8 1.0 CG A:ARG60 4.0 31.6 1.0 CB A:SER61 4.2 40.1 1.0 C A:ARG60 4.2 42.0 1.0 O A:ARG60 4.4 38.4 1.0 NE A:ARG60 4.4 38.7 1.0 CB A:ARG60 4.4 26.4 1.0

Iodine binding site 3 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:71.7 occ:1.00 O A:HOH666 3.6 46.0 1.0 CB A:GLU96 3.9 42.5 1.0 CG1 A:VAL32 4.1 42.1 1.0 CA A:GLU96 4.1 47.6 1.0 N A:GLU96 4.2 53.8 1.0 CD1 A:LEU99 4.3 44.1 1.0 CG A:GLU96 4.3 41.0 1.0 CB A:VAL32 4.4 47.6 1.0 CA A:ALA29 4.6 50.5 1.0 CG2 A:VAL32 4.6 42.6 1.0 CB A:ALA29 4.6 40.2 1.0 C A:GLU95 4.7 58.3 1.0 O A:GLU95 4.8 55.7 1.0 OE1 A:GLU96 5.0 43.3 1.0

Iodine binding site 4 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:94.0 occ:1.00 NH1 D:ARG60 3.7 53.0 1.0 N A:LYS399 3.8 44.5 1.0 NH2 D:ARG60 3.8 51.8 1.0 O D:GLU349 3.9 43.0 1.0 CB A:LYS399 4.0 30.1 1.0 CZ D:ARG60 4.3 53.5 1.0 ND1 A:HIS398 4.3 56.6 1.0 NE2 A:HIS309 4.4 59.1 1.0 CA A:LYS399 4.4 36.8 1.0 CE A:LYS399 4.6 31.2 1.0 CA A:HIS398 4.6 47.5 1.0 O A:LYS399 4.7 37.9 1.0 C A:HIS398 4.7 46.8 1.0 CB A:HIS398 4.7 52.0 1.0 CE1 A:HIS309 5.0 60.7 1.0

Iodine binding site 5 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:112.4 occ:1.00 O A:HOH656 3.9 49.4 1.0 CD2 A:TYR40 4.1 54.2 1.0 CD2 A:HIS44 4.2 49.0 1.0 CE2 A:TYR40 4.2 53.7 1.0 CA A:PRO41 4.3 38.2 1.0 CG A:PRO41 4.6 41.9 1.0 CB A:PRO41 4.6 40.2 1.0 ND2 A:ASN45 4.7 42.1 1.0 N A:PRO41 4.7 44.5 1.0 CG A:HIS44 5.0 50.2 1.0

Iodine binding site 6 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:129.4 occ:1.00 CD2 A:HIS52 3.9 40.9 1.0 CE1 A:HIS72 4.1 44.9 1.0 CB A:HIS52 4.3 40.8 1.0 O A:HIS52 4.3 54.4 1.0 CG A:HIS52 4.5 43.1 1.0 NE2 A:HIS72 4.5 46.9 1.0 O A:HOH604 4.5 41.5 1.0 O A:LYS68 4.7 49.1 1.0 CB A:LYS68 4.7 51.8 1.0 CA A:HIS52 4.9 46.5 1.0 C A:HIS52 4.9 49.7 1.0

Iodine binding site 7 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:115.8 occ:1.00 CE3 A:TRP250 3.4 73.3 1.0 O A:TRP250 3.6 64.7 1.0 CG2 A:ILE201 3.8 42.7 1.0 NZ A:LYS205 3.9 56.2 1.0 CA A:ARG202 4.0 52.6 1.0 CE A:LYS205 4.0 53.9 1.0 CZ3 A:TRP250 4.1 70.6 1.0 N A:ARG202 4.1 43.2 1.0 CD1 A:LEU245 4.3 43.2 1.0 CB A:ARG202 4.3 56.7 1.0 CB A:TRP250 4.3 64.6 1.0 CD2 A:TRP250 4.4 83.0 1.0 C A:TRP250 4.4 63.3 1.0 C A:ILE201 4.6 47.6 1.0 CD A:LYS205 4.6 49.2 1.0 O A:ILE201 4.7 50.5 1.0 CA A:TRP250 4.8 61.4 1.0 CB A:ILE201 4.8 61.6 1.0 CG A:TRP250 4.9 79.5 1.0 CG A:ARG202 4.9 67.9 1.0

Iodine binding site 8 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:162.9 occ:1.00 CD1 A:LEU99 4.5 44.1 1.0 CG A:TRP36 4.5 41.6 1.0 CD1 A:TRP36 4.6 42.2 1.0 CB A:TRP36 4.7 38.0 1.0 O A:HOH666 4.8 46.0 1.0 CD2 A:TRP36 4.9 42.9 1.0 CA A:LYS33 5.0 36.8 1.0 CD2 A:LEU99 5.0 47.4 1.0

Iodine binding site 9 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:98.3 occ:1.00 CG A:GLU328 3.6 59.1 1.0 NH2 A:ARG324 3.8 64.7 1.0 NZ A:LYS33 3.8 47.4 1.0 CB A:GLU328 3.9 46.0 1.0 CD A:GLU328 4.0 62.8 1.0 CG2 A:ILE30 4.0 45.1 1.0 NE A:ARG324 4.2 49.1 1.0 CD2 A:LEU34 4.3 37.6 1.0 OE1 A:GLU328 4.3 69.1 1.0 CD A:LYS33 4.3 52.3 1.0 CG1 A:ILE30 4.4 44.1 1.0 CZ A:ARG324 4.5 64.2 1.0 CD1 A:LEU34 4.5 42.5 1.0 CE A:LYS33 4.5 63.5 1.0 CG A:LEU34 4.6 45.2 1.0 OE2 A:GLU328 4.6 68.8 1.0 CB A:ILE30 4.7 46.1 1.0 CA A:GLU328 4.7 47.5 1.0 CB A:ARG324 4.7 49.2 1.0 CA A:ILE30 5.0 44.7 1.0

Iodine binding site 10 out of 27 in the Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of An Inactive Beta-D-Glucuronate Dehydratase Mutant in Complex with Chondrosine within 5.0Å range: probe atom residue distance (Å) B Occ B:I501 b:100.6 occ:1.00 CB B:GLU96 3.8 53.5 1.0 CA B:GLU96 4.1 58.5 1.0 CG1 B:VAL32 4.1 38.7 1.0 OE1 B:GLU96 4.3 47.5 1.0 N B:GLU96 4.3 66.3 1.0 CB B:VAL32 4.3 50.8 1.0 CG B:GLU96 4.4 47.9 1.0 CD1 B:LEU99 4.4 39.8 1.0 CG2 B:VAL32 4.5 50.6 1.0 CA B:ALA29 4.7 44.9 1.0 CD B:GLU96 4.8 51.4 1.0 C B:GLU95 4.8 65.4 1.0 CB B:ALA29 4.8 35.7 1.0

B.Alvarez, O.Canil, K.Low, D.W.Abbott, A.B.Boraston. Analysis of Chondroitin Degradation By Components of A Bacteroides Caccae Polysaccharide Utilization Locus To Be Published.