Iodine in PDB 2dgm: Crystal Structure of Escherichia Coli Gadb in Complex with Iodide

All present enzymatic activity of Crystal Structure of Escherichia Coli Gadb in Complex with Iodide:
4.1.1.15;

The structure of Crystal Structure of Escherichia Coli Gadb in Complex with Iodide, PDB code: 2dgm was solved by M.G.Gruetter, G.Capitani, H.Gut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	91.336, 91.804, 93.914, 76.65, 76.94, 78.04
R / Rfree (%)	22.7 / 26.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide (pdb code 2dgm). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 32 binding sites of Iodine where determined in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide, PDB code: 2dgm:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I2331 b:20.5 occ:0.91 OG A:SER16 3.5 19.6 1.0 CD F:ARG427 3.5 17.5 1.0 CB A:SER16 3.5 19.3 1.0 NH1 F:ARG427 3.6 17.9 1.0 O F:HOH2788 3.7 18.8 1.0 CD2 A:PHE18 4.1 17.7 1.0 CZ3 F:TRP67 4.1 12.8 1.0 N A:PHE18 4.2 18.7 1.0 CG2 F:VAL342 4.3 11.9 1.0 O A:HOH2813 4.3 22.4 1.0 CG F:ARG427 4.4 17.0 1.0 CB A:PHE18 4.4 18.2 1.0 N A:ARG17 4.4 19.6 1.0 NE F:ARG427 4.4 17.7 1.0 CZ F:ARG427 4.5 17.8 1.0 CA A:SER16 4.7 19.1 1.0 CG A:PHE18 4.8 17.8 1.0 CA A:PHE18 4.8 18.5 1.0 C A:SER16 4.8 19.3 1.0 CH2 F:TRP67 4.9 12.7 1.0 CE3 F:TRP67 4.9 12.7 1.0

Iodine binding site 2 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I2337 b:36.1 occ:0.73 CD1 A:ILE418 3.7 25.7 1.0 NZ A:LYS381 3.7 24.2 1.0 N A:GLY185 4.0 25.0 1.0 CE A:LYS381 4.1 23.6 1.0 CD1 A:LEU187 4.2 22.4 1.0 CD2 A:LEU187 4.2 22.4 1.0 CD1 A:ILE366 4.3 23.2 1.0 CA A:PRO184 4.3 24.7 1.0 CD A:LYS381 4.4 23.3 1.0 O A:HOH2853 4.5 43.1 1.0 CG A:LEU187 4.5 22.5 1.0 OE2 A:GLU364 4.6 28.2 1.0 C A:PRO184 4.7 24.9 1.0 CG1 A:ILE366 4.8 22.6 1.0 CG2 A:ILE418 4.9 25.6 1.0 CB A:PRO184 4.9 24.7 1.0 CA A:GLY185 5.0 25.2 1.0

Iodine binding site 3 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I2343 b:47.4 occ:0.47 CB A:LYS453 3.3 42.9 1.0 N A:LYS453 3.7 42.1 1.0 CA A:HIS451 3.8 38.9 1.0 C A:HIS451 4.0 39.7 1.0 CB A:HIS451 4.0 39.0 1.0 CA A:LYS453 4.1 42.6 1.0 CG A:LYS453 4.2 43.1 1.0 N A:PRO452 4.2 40.4 1.0 CD A:PRO452 4.2 40.6 1.0 CD A:LYS453 4.3 43.4 1.0 O A:HIS451 4.5 39.8 1.0 CD2 A:HIS451 4.5 39.2 1.0 CG A:HIS451 4.5 39.2 1.0 CG A:PRO452 4.8 40.8 1.0 C A:PRO452 4.8 41.5 1.0 O A:ASP450 4.8 37.1 1.0

Iodine binding site 4 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I2349 b:97.5 occ:0.72 NE2 A:HIS73 3.3 14.3 1.0 CD1 A:TRP67 3.6 15.1 1.0 N A:ASP68 3.7 15.4 1.0 O A:ASP68 3.9 15.5 1.0 CA A:TRP67 3.9 15.1 1.0 O A:HOH2668 3.9 41.5 1.0 CE1 A:HIS73 3.9 14.3 1.0 OD1 B:ASN81 4.0 17.7 1.0 CG A:TRP67 4.1 14.9 1.0 NE1 A:TRP67 4.1 15.0 1.0 O A:HOH2710 4.1 32.8 1.0 C A:TRP67 4.3 15.2 1.0 O B:HOH2770 4.4 19.7 1.0 CB A:TRP67 4.5 15.0 1.0 CD2 A:HIS73 4.5 14.2 1.0 O A:HOH2759 4.6 42.8 1.0 O A:THR66 4.6 14.8 1.0 OD2 A:ASP68 4.7 17.2 1.0 CE2 A:TRP67 4.7 15.3 1.0 CD2 A:TRP67 4.7 15.0 1.0 C A:ASP68 4.7 15.4 1.0 CA A:ASP68 4.8 15.5 1.0 N A:TRP67 4.9 15.0 1.0

Iodine binding site 5 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I2355 b:48.5 occ:0.55 O A:HOH2652 3.3 26.5 1.0 N A:LEU392 3.3 24.1 1.0 CD1 A:LEU382 3.6 25.9 1.0 CB A:THR391 3.7 25.3 1.0 CA A:THR391 3.7 25.2 1.0 CB A:VAL419 3.9 22.7 1.0 C A:THR391 4.0 24.7 1.0 CG A:LEU392 4.1 23.1 1.0 CG1 A:VAL419 4.1 22.6 1.0 CB A:LEU392 4.2 23.3 1.0 CG A:LEU382 4.2 25.9 1.0 CA A:LEU392 4.3 23.6 1.0 CG2 A:THR391 4.4 25.2 1.0 CG2 A:VAL419 4.4 22.7 1.0 CD1 A:LEU392 4.7 23.1 1.0 O A:HOH2669 4.8 29.7 1.0 OG1 A:THR391 4.8 25.7 1.0 O A:HOH2877 4.8 26.7 1.0 CB A:LEU382 4.9 25.8 1.0 O A:VAL419 5.0 21.6 1.0

Iodine binding site 6 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I2361 b:39.0 occ:0.43 CB A:ALA232 4.0 22.5 1.0 CA A:LYS229 4.1 20.4 1.0 CB A:LYS229 4.4 20.8 1.0 CG A:LYS229 4.5 21.7 1.0 N A:LYS229 4.7 19.9 1.0 O A:HOH2838 4.7 33.2 1.0 O A:ASP228 4.8 19.8 1.0 C A:ASP228 4.9 19.5 1.0

Iodine binding site 7 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ B:I2332 b:24.1 occ:0.91 OG B:SER16 3.2 20.2 1.0 O C:HOH2814 3.5 24.5 1.0 CD C:ARG427 3.5 17.7 1.0 CB B:SER16 3.6 19.9 1.0 NH1 C:ARG427 3.7 18.1 1.0 N B:PHE18 4.0 20.0 1.0 CZ3 C:TRP67 4.1 14.0 1.0 CD2 B:PHE18 4.2 18.1 1.0 CG2 C:VAL342 4.2 14.9 1.0 CG C:ARG427 4.3 17.1 1.0 N B:ARG17 4.3 20.4 1.0 O B:HOH2881 4.4 26.5 1.0 CB B:PHE18 4.4 19.0 1.0 NE C:ARG427 4.5 17.7 1.0 CZ C:ARG427 4.5 17.6 1.0 C B:SER16 4.7 20.1 1.0 CA B:PHE18 4.7 19.7 1.0 CB B:ARG17 4.7 21.0 1.0 CA B:SER16 4.7 19.8 1.0 CG B:PHE18 4.8 18.4 1.0 CH2 C:TRP67 4.9 14.0 1.0 CA B:ARG17 4.9 20.7 1.0 C B:ARG17 4.9 20.5 1.0 CE3 C:TRP67 4.9 14.0 1.0 N B:GLY19 5.0 19.9 1.0

Iodine binding site 8 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ B:I2333 b:22.0 occ:0.91 OG C:SER16 3.4 18.5 1.0 CD B:ARG427 3.5 15.5 1.0 CB C:SER16 3.6 18.4 1.0 NH1 B:ARG427 3.6 15.7 1.0 O B:HOH2874 3.7 16.6 1.0 CZ3 B:TRP67 4.1 12.9 1.0 N C:PHE18 4.1 18.2 1.0 CD2 C:PHE18 4.3 17.3 1.0 CG2 B:VAL342 4.3 11.1 1.0 CG B:ARG427 4.4 15.1 1.0 N C:ARG17 4.4 18.4 1.0 CB C:PHE18 4.5 17.9 1.0 NE B:ARG427 4.5 15.3 1.0 CZ B:ARG427 4.5 15.7 1.0 CB C:ARG17 4.8 19.0 1.0 C C:SER16 4.8 18.3 1.0 CA C:SER16 4.8 18.1 1.0 CA C:PHE18 4.8 18.1 1.0 CE3 B:TRP67 4.9 13.0 1.0 CG C:PHE18 4.9 17.6 1.0 CH2 B:TRP67 4.9 13.1 1.0 CA C:ARG17 5.0 18.8 1.0

Iodine binding site 9 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ B:I2338 b:35.0 occ:0.60 CD1 B:ILE418 3.5 26.9 1.0 CE B:LYS381 3.7 23.3 1.0 N B:GLY185 3.9 24.1 1.0 CD1 B:LEU187 4.2 20.9 1.0 CA B:PRO184 4.2 23.9 1.0 CD B:LYS381 4.3 23.0 1.0 CD2 B:LEU187 4.3 20.9 1.0 CG B:LEU187 4.5 21.2 1.0 C B:PRO184 4.6 23.9 1.0 CG2 B:ILE418 4.7 26.7 1.0 CD1 B:ILE366 4.8 21.5 1.0 CG1 B:ILE418 4.8 26.7 1.0 CA B:GLY185 4.9 24.0 1.0 CB B:PRO184 4.9 24.0 1.0 NZ B:LYS381 4.9 23.4 1.0

Iodine binding site 10 out of 32 in the Crystal Structure of Escherichia Coli Gadb in Complex with Iodide


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 Escherichia Coli Gadb in Complex with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ B:I2344 b:39.6 occ:0.48 CA B:HIS451 3.8 38.6 1.0 CB B:LYS453 4.0 41.9 1.0 CB B:HIS451 4.0 38.7 1.0 N B:LYS453 4.1 41.1 1.0 C B:HIS451 4.1 39.2 1.0 CD2 B:HIS451 4.4 39.0 1.0 N B:PRO452 4.4 39.8 1.0 CA B:LYS453 4.5 41.6 1.0 CG B:HIS451 4.5 38.9 1.0 CD B:PRO452 4.6 40.0 1.0 O B:HIS451 4.6 39.3 1.0 CG B:LYS453 4.6 42.3 1.0 C B:LYS453 4.7 41.8 1.0 O B:ASP450 4.7 37.1 1.0 CD B:LYS453 4.8 42.6 1.0

H.Gut, E.Pennacchietti, R.A.John, F.Bossa, G.Capitani, D.De Biase, M.G.Gruetter. Escherichia Coli Acid Resistance: pH-Sensing, Activation By Chloride and Autoinhibition in Gadb Embo J. V. 25 2643 2006.
ISSN: ISSN 0261-4189
PubMed: 16675957
DOI: 10.1038/SJ.EMBOJ.7601107