Iodine in PDB 3v3r: Crystal Structure of Ges-11

All present enzymatic activity of Crystal Structure of Ges-11:
3.5.2.6;

The structure of Crystal Structure of Ges-11, PDB code: 3v3r was solved by H.Delbruck, K.M.V.Hoffmann, C.Bebrone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.680, 85.240, 85.120, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.2

The structure of Crystal Structure of Ges-11 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Ges-11 (pdb code 3v3r). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 25 binding sites of Iodine where determined in the Crystal Structure of Ges-11, PDB code: 3v3r:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I288 b:15.8 occ:0.85 CG A:GLN145 3.3 19.4 0.5 O A:HOH322 3.6 14.7 1.0 CG A:GLN145 3.7 19.9 0.5 CB A:GLN145 3.9 19.5 0.5 CB A:GLN145 3.9 19.5 0.5 CD A:GLN145 4.0 19.6 0.5 CA A:ALA142 4.2 17.4 1.0 NE2 A:GLN145 4.5 19.3 0.5 O A:ALA141 4.6 17.6 1.0 OE1 A:GLN145 4.6 20.1 0.5 N A:ALA142 4.6 17.4 1.0 NZ A:LYS149 4.6 22.4 0.5 CB A:ALA142 4.7 17.4 1.0 C A:ALA141 4.7 17.6 1.0

Iodine binding site 2 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I289 b:37.4 occ:0.90 CD A:LYS160 3.7 28.6 1.0 CA A:GLY139 4.0 18.1 1.0 CG A:LYS160 4.1 26.4 1.0 CD A:PRO140 4.1 17.5 1.0 N A:ARG135 4.2 18.3 1.0 CA A:ARG135 4.3 19.0 1.0 C A:LEU134 4.3 17.9 1.0 O A:LEU134 4.4 18.1 1.0 CB A:LEU134 4.4 17.1 1.0 N A:GLY139 4.8 18.4 1.0 CB A:ARG135 4.9 19.1 1.0

Iodine binding site 3 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I290 b:24.4 occ:0.73 OG1 A:THR177 3.5 15.6 1.0 I A:IOD298 3.8 53.0 0.5 CG2 A:ILE179 3.9 15.2 1.0 CB A:ALA57 3.9 19.3 1.0 CG2 A:VAL154 3.9 20.6 1.0 CG2 A:THR177 4.1 15.9 1.0 CA A:ALA57 4.3 18.9 1.0 CB A:THR177 4.3 15.6 1.0 CG1 A:VAL154 4.6 19.6 1.0 O A:ALA57 4.7 19.5 1.0 O A:HOH331 4.7 35.6 1.0 CB A:VAL154 4.8 19.2 1.0 C A:ALA57 4.9 18.9 1.0 CB A:ALA180 5.0 15.1 1.0

Iodine binding site 4 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I291 b:31.1 occ:0.69 NH1 A:ARG204 3.5 17.2 1.0 O A:HOH422 3.9 33.3 1.0 CD A:ARG204 4.0 16.0 1.0 CE1 A:HIS200 4.2 20.6 1.0 CB B:SER109 4.2 19.2 1.0 CD1 A:ILE207 4.2 15.0 1.0 CE1 B:HIS111 4.3 19.6 1.0 CZ A:ARG204 4.5 17.1 1.0 NE A:ARG204 4.7 16.5 1.0 ND1 A:HIS200 4.8 20.2 1.0 OG B:SER109 4.9 19.0 1.0

Iodine binding site 5 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I292 b:26.9 occ:0.78 I A:IOD292 0.0 26.9 0.8 I A:IOD292 2.0 27.4 0.2 OG1 A:THR230 3.3 14.8 1.0 OG A:SER125 3.6 14.6 1.0 N A:THR232 3.9 16.6 1.0 CA A:GLY231 3.9 15.4 1.0 CB A:SER125 3.9 14.8 1.0 OG1 A:THR232 4.0 17.9 1.0 O A:HOH348 4.0 13.7 1.0 CB A:THR230 4.1 14.6 1.0 O A:THR230 4.1 14.1 1.0 C A:THR230 4.1 14.4 1.0 C A:GLY231 4.1 16.1 1.0 N A:GLY231 4.2 15.0 1.0 NH1 A:ARG238 4.2 18.2 1.0 NZ A:LYS229 4.3 14.1 1.0 CB A:SER64 4.4 17.4 1.0 OG A:SER64 4.4 18.1 1.0 CB A:THR232 4.5 17.8 1.0 CA A:THR230 4.8 14.1 1.0 CA A:THR232 4.8 17.2 1.0 O A:HOH376 4.9 20.0 1.0 OG1 A:THR211 4.9 17.0 1.0 O A:GLY231 4.9 16.4 1.0 CB A:THR211 5.0 17.3 1.0

Iodine binding site 6 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I292 b:27.4 occ:0.22 I A:IOD292 0.0 27.4 0.2 I A:IOD292 2.0 26.9 0.8 OG A:SER64 2.8 18.1 1.0 OG A:SER125 2.9 14.6 1.0 CB A:SER64 3.3 17.4 1.0 CB A:SER125 3.7 14.8 1.0 N A:THR232 3.9 16.6 1.0 O A:THR232 4.2 17.6 1.0 CA A:GLY231 4.3 15.4 1.0 C A:GLY231 4.6 16.1 1.0 CB A:THR232 4.6 17.8 1.0 CA A:SER64 4.6 17.0 1.0 NZ A:LYS67 4.7 21.1 1.0 O A:SER125 4.7 14.9 1.0 CA A:THR232 4.7 17.2 1.0 NZ A:LYS229 4.7 14.1 1.0 O A:HOH342 4.8 26.1 1.0 O A:THR230 4.8 14.1 1.0 N A:SER64 4.8 16.9 1.0 OG1 A:THR232 4.8 17.9 1.0 C A:THR232 5.0 17.4 1.0

Iodine binding site 7 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I293 b:29.9 occ:0.75 N A:GLY92 3.5 22.4 1.0 N A:MET95 3.9 23.3 1.0 O A:GLY92 4.0 22.4 1.0 CB A:ASP94 4.0 26.1 1.0 CB A:MET95 4.1 22.4 1.0 CE A:MET95 4.2 24.0 1.0 CA A:GLY92 4.2 22.9 1.0 CA A:TYR91 4.3 21.0 1.0 C A:GLY92 4.4 22.8 1.0 CA A:MET95 4.4 22.6 1.0 C A:TYR91 4.4 21.7 1.0 CB A:TYR91 4.4 19.8 1.0 C A:ASP94 4.4 23.9 1.0 CA A:ASP94 4.6 24.9 1.0 NH1 A:ARG135 4.6 20.9 1.0 N A:ASP94 4.7 24.3 1.0

Iodine binding site 8 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I294 b:37.6 occ:0.65 NH2 A:ARG84 3.6 25.5 1.0 N A:LYS88 3.7 22.4 1.0 CG A:LYS88 4.1 23.6 1.0 CB A:LYS88 4.1 23.1 1.0 NH1 A:ARG84 4.3 25.9 1.0 CA A:ARG87 4.3 22.2 1.0 CZ A:ARG84 4.4 25.7 1.0 CG A:ARG87 4.5 23.2 1.0 CA A:LYS88 4.5 22.0 1.0 C A:ARG87 4.6 21.8 1.0 CD A:LYS88 4.6 24.6 1.0 O A:ASP86 4.8 22.2 1.0 CE A:LYS88 4.9 25.9 1.0 O A:LYS88 5.0 22.2 1.0 CB A:ARG87 5.0 22.3 1.0 O A:HOH366 5.0 21.7 1.0

Iodine binding site 9 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I295 b:30.7 occ:0.50 OE1 B:GLN210 3.5 23.0 1.0 NH2 A:ARG105 3.5 20.5 1.0 NH1 A:ARG105 3.6 19.3 1.0 CD2 A:LEU124 3.9 15.9 1.0 CZ A:ARG105 4.0 19.6 1.0 CB A:PRO101 4.1 19.0 1.0 CD1 A:LEU124 4.1 15.9 1.0 CD B:GLN210 4.2 21.3 1.0 CG A:PRO101 4.4 19.1 1.0 CB B:GLN210 4.4 19.4 1.0 CG B:GLN210 4.5 19.5 1.0 CG A:LEU124 4.6 15.7 1.0 CH2 A:TRP99 4.9 24.2 1.0 O B:GLN210 4.9 19.1 1.0

Iodine binding site 10 out of 25 in the Crystal Structure of Ges-11


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 Ges-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:I296 b:38.3 occ:0.50 CE A:LYS261 3.2 24.0 0.5 NZ A:LYS261 3.9 23.4 0.5 CG A:LYS261 4.1 24.1 0.5 CD A:LYS261 4.1 23.7 0.5 CG A:LYS261 4.2 24.4 0.5 CD A:LYS261 4.5 24.7 0.5 CB A:PRO260 4.6 21.7 1.0 CG A:PRO260 4.8 21.1 1.0

H.Delbruck, P.Bogaerts, M.B.Kupper, R.Rezende De Castro, S.Bennink, Y.Glupczynski, M.Galleni, K.M.Hoffmann, C.Bebrone. Kinetic and Crystallographic Studies of Extended-Spectrum Ges-11, Ges-12, and Ges-14 Beta-Lactamases. Antimicrob.Agents Chemother. V. 56 5618 2012.
ISSN: ISSN 0066-4804
PubMed: 22908160
DOI: 10.1128/AAC.01272-12