Iodine in PDB 4h8r: Imipenem Complex of Ges-5 Carbapenemase

The structure of Imipenem Complex of Ges-5 Carbapenemase, PDB code: 4h8r was solved by C.A.Smith, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.82 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.940, 81.240, 71.930, 90.00, 102.04, 90.00
R / Rfree (%)	14.8 / 17

The structure of Imipenem Complex of Ges-5 Carbapenemase also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Iodine atom in the Imipenem Complex of Ges-5 Carbapenemase (pdb code 4h8r). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 17 binding sites of Iodine where determined in the Imipenem Complex of Ges-5 Carbapenemase, PDB code: 4h8r:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:I502 b:16.9 occ:0.38 O B:HOH732 3.1 35.9 1.0 O B:HOH812 3.2 38.9 1.0 O B:HOH817 3.2 45.4 1.0 NH1 A:ARG204 3.6 9.9 1.0 CD1 A:ILE207 4.1 9.8 1.0 CD A:ARG204 4.1 10.3 1.0 CB B:SER109 4.2 10.0 1.0 CE1 A:HIS200 4.4 21.2 1.0 CE1 B:HIS111 4.5 13.8 1.0 CZ A:ARG204 4.7 9.6 1.0 CG1 A:VAL225 4.8 12.5 1.0 OG B:SER109 4.8 9.8 1.0 NE A:ARG204 4.9 9.7 1.0 ND1 A:HIS200 4.9 20.6 1.0 O B:HOH816 5.0 38.7 1.0

Iodine binding site 2 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:I503 b:26.4 occ:0.65 O A:HOH767 3.2 26.4 1.0 O A:HOH673 3.3 26.1 1.0 O A:HOH700 3.6 40.0 1.0 CA A:GLY139 4.0 20.3 1.0 CD A:PRO140 4.0 18.0 1.0 O A:LEU134 4.1 20.2 1.0 C A:LEU134 4.1 17.9 1.0 N A:ARG135 4.1 18.7 1.0 CB A:LEU134 4.2 16.1 1.0 CA A:ARG135 4.3 20.2 1.0 N A:GLY139 4.8 21.1 1.0 CG A:ARG135 4.8 25.2 1.0 CA A:LEU134 4.8 16.0 1.0 CB A:LYS160 4.9 17.1 1.0 CD A:LYS160 4.9 21.4 1.0 N A:PRO140 5.0 18.2 1.0

Iodine binding site 3 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:I504 b:17.9 occ:0.29 O A:HOH631 3.2 23.2 1.0 CE A:MET56 3.6 18.2 0.5 N A:ARG55 3.7 9.3 1.0 N A:MET56 3.8 9.6 1.0 CG A:MET56 4.0 13.7 0.5 CG A:MET56 4.0 15.0 0.5 CA A:HIS54 4.0 9.3 1.0 CB A:MET56 4.1 11.9 0.5 C A:HIS54 4.2 8.9 1.0 O A:GLY53 4.2 12.5 1.0 N A:HIS54 4.2 9.7 1.0 O A:HOH790 4.3 34.0 1.0 C A:GLY53 4.3 10.6 1.0 CB A:MET56 4.4 12.9 0.5 CA A:ARG55 4.5 9.5 1.0 CA A:MET56 4.6 10.3 0.5 SD A:MET56 4.6 17.9 0.5 SD A:MET56 4.6 15.7 0.5 C A:ARG55 4.7 9.0 1.0 CA A:MET56 4.7 10.5 0.5 CE A:MET56 4.8 17.0 0.5

Iodine binding site 4 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:I505 b:23.0 occ:0.27 O B:HOH813 3.2 35.9 1.0 NH2 A:ARG105 3.4 13.9 1.0 NH1 A:ARG105 3.5 13.5 1.0 OE1 B:GLN210 3.5 14.9 1.0 CB A:PRO101 3.9 13.9 1.0 CZ A:ARG105 3.9 13.2 1.0 CD2 A:LEU124 4.1 16.1 1.0 CD B:GLN210 4.2 12.6 1.0 CG A:PRO101 4.3 13.8 1.0 CB B:GLN210 4.4 9.0 1.0 CG B:GLN210 4.5 10.3 1.0 CD1 A:LEU124 4.6 15.4 1.0 O A:HOH852 4.6 39.6 1.0 CH2 A:TRP99 4.8 25.9 1.0 CG A:LEU124 5.0 13.9 1.0 CZ2 A:TRP99 5.0 25.0 1.0

Iodine binding site 5 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:I506 b:20.4 occ:0.15 O A:HOH713 3.1 37.5 1.0 O A:LYS222 3.3 15.3 1.0 C A:LYS222 3.9 12.5 1.0 CA A:ASP223 4.0 13.2 1.0 CD2 B:LEU107 4.1 14.6 1.0 CG B:LEU107 4.1 12.4 1.0 N A:ASP223 4.2 11.9 1.0 CB A:ASP223 4.3 16.0 1.0 CA B:ALA108 4.4 10.7 1.0 O A:HOH780 4.6 25.7 1.0 CB A:LYS222 4.7 14.5 1.0 N B:ALA108 4.7 10.0 1.0 CB B:ALA108 4.8 11.1 1.0 O A:HOH675 4.8 17.4 1.0 O B:LEU107 4.9 10.1 1.0 C B:LEU107 4.9 9.4 1.0 CA A:LYS222 4.9 12.0 1.0 CD1 B:LEU107 5.0 13.0 1.0

Iodine binding site 6 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:I507 b:23.1 occ:0.24 NA A:NA509 3.7 8.5 1.0 N A:ASP94 4.1 16.6 1.0 CB A:ASP94 4.2 24.9 1.0 CG A:PRO93 4.3 14.7 1.0 CA A:ASP94 4.3 20.0 1.0 CB A:PRO93 4.7 15.0 1.0 C A:PRO93 4.7 14.8 1.0

Iodine binding site 7 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:I508 b:21.9 occ:0.28 O A:HOH614 3.9 19.9 1.0 CA A:LEU22 4.1 13.4 1.0 N A:LEU22 4.1 12.1 1.0 O A:LYS21 4.2 11.8 1.0 C A:LYS21 4.2 11.7 1.0 CD A:LYS25 4.4 18.8 1.0 CB A:LEU22 4.4 15.5 1.0 CD1 A:LEU22 4.5 18.6 1.0 CB A:LYS21 4.6 12.5 1.0 CB A:LYS25 4.8 12.2 1.0

Iodine binding site 8 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:82.5 occ:0.45 CG2 A:ILE150 3.9 21.2 1.0 CE A:LYS187 4.1 26.1 1.0 O A:HOH692 4.1 22.7 1.0 CA A:ALA193 4.2 15.1 1.0 CB A:ALA193 4.3 16.0 1.0 NZ A:LYS187 4.4 27.7 1.0 CB A:ILE150 4.6 21.0 1.0 CA A:ILE150 4.6 20.8 1.0 O A:LYS149 4.8 22.0 1.0 O A:ALA193 4.9 15.4 1.0

Iodine binding site 9 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ B:I502 b:18.9 occ:0.60 O B:HOH677 3.2 27.2 1.0 CA B:GLY139 4.1 14.7 1.0 CD B:PRO140 4.1 13.4 1.0 CB B:LEU134 4.2 11.9 1.0 N B:ARG135 4.2 12.6 1.0 C B:LEU134 4.3 13.0 1.0 CA B:ARG135 4.3 14.1 0.3 CA B:ARG135 4.4 13.8 0.7 O B:LEU134 4.5 13.8 1.0 CD B:LYS160 4.5 20.5 1.0 CB B:LYS160 4.7 16.1 1.0 N B:GLY139 4.8 15.3 1.0 CB B:ARG135 4.8 15.7 0.3 CA B:LEU134 4.9 11.4 1.0 O B:HOH771 5.0 35.9 1.0 CB B:ARG135 5.0 14.6 0.7

Iodine binding site 10 out of 17 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ B:I503 b:13.0 occ:0.38 O A:HOH729 3.3 28.5 1.0 NH1 B:ARG204 3.6 9.6 1.0 CD B:ARG204 4.0 10.4 1.0 CD1 B:ILE207 4.0 9.9 1.0 CB A:SER109 4.2 10.1 1.0 CE1 B:HIS200 4.2 19.1 1.0 CE1 A:HIS111 4.4 13.3 1.0 O A:HOH766 4.5 33.9 1.0 CZ B:ARG204 4.6 9.3 1.0 NE B:ARG204 4.8 9.4 1.0 OG A:SER109 4.8 10.0 1.0 ND1 B:HIS200 4.9 19.3 1.0

C.A.Smith, H.Frase, M.Toth, M.Kumarasiri, K.Wiafe, J.Munoz, S.Mobashery, S.B.Vakulenko. Structural Basis For Progression Toward the Carbapenemase Activity in the Ges Family of Beta-Lactamases. J.Am.Chem.Soc. V. 134 19512 2012.
ISSN: ISSN 0002-7863
PubMed: 23148776
DOI: 10.1021/JA308197J