Iodine in PDB 4ebk: Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound

The structure of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound, PDB code: 4ebk was solved by P.J.Stogios, A.Dong, G.Minasov, E.Evdokimova, O.Egorova, V.Yim, M.Kudritska, P.Courvalin, A.Savchenko, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.89 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.906, 84.451, 98.762, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.1

The structure of Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound also contains other interesting chemical elements:

Chlorine

(Cl)

17 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound (pdb code 4ebk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 14 binding sites of Iodine where determined in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound, PDB code: 4ebk:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:I16 b:45.7 occ:0.09 IE A:IYR16 0.0 45.7 0.1 CE A:IYR16 2.1 40.0 1.0 CF A:IYR16 3.0 37.0 1.0 OF A:IYR16 3.1 34.6 1.0 CD A:IYR16 3.1 42.1 1.0 NH1 A:ARG54 3.2 32.8 1.0 CD2 A:LEU12 3.4 31.3 1.0 CH2 A:TRP56 3.6 30.0 1.0 CD A:GLU15 3.7 56.2 1.0 CZ2 A:TRP56 3.7 26.6 1.0 OE1 A:GLU15 3.8 53.9 1.0 OE2 A:GLU15 4.0 62.1 1.0 CG A:ARG54 4.0 32.7 1.0 CG A:GLU15 4.1 54.4 1.0 CZ A:ARG54 4.2 39.3 1.0 CG A:IYR16 4.3 39.4 1.0 CB A:GLU15 4.4 52.3 1.0 CC A:IYR16 4.4 42.0 1.0 CB A:ARG54 4.6 28.4 1.0 CD A:ARG54 4.7 33.8 1.0 CG A:LEU12 4.7 32.2 1.0 CG2 A:VAL71 4.8 35.6 1.0 NE A:ARG54 4.8 35.8 1.0 CH A:IYR16 4.9 41.2 1.0 CZ3 A:TRP56 4.9 28.9 1.0 CA A:LEU12 4.9 35.7 1.0 CB A:LEU12 5.0 33.2 1.0 NH2 A:ARG54 5.0 39.0 1.0

Iodine binding site 2 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:I16 b:65.7 occ:0.10 IE B:IYR16 0.0 65.7 0.1 CE B:IYR16 2.1 50.4 1.0 CF B:IYR16 3.0 50.0 1.0 CD B:IYR16 3.1 51.6 1.0 OF B:IYR16 3.1 47.8 1.0 NH1 B:ARG54 3.3 47.7 1.0 OE1 B:GLU15 3.3 64.5 1.0 CD2 B:LEU12 3.4 46.0 1.0 CZ2 B:TRP56 3.5 44.0 1.0 CD B:GLU15 3.5 65.7 1.0 CH2 B:TRP56 3.6 39.8 1.0 OE2 B:GLU15 3.9 67.5 1.0 CG B:ARG54 4.1 37.9 1.0 CG B:GLU15 4.1 63.0 1.0 CZ B:ARG54 4.2 43.8 1.0 CB B:GLU15 4.3 59.0 1.0 CG B:IYR16 4.3 51.5 1.0 CC B:IYR16 4.4 48.7 1.0 CD B:ARG54 4.7 36.2 1.0 CB B:ARG54 4.7 36.1 1.0 CG B:LEU12 4.8 45.6 1.0 NE B:ARG54 4.8 37.0 1.0 CE2 B:TRP56 4.8 40.3 1.0 CH B:IYR16 4.9 49.6 1.0 CZ3 B:TRP56 4.9 37.6 1.0

Iodine binding site 3 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:63.6 occ:0.52 CG1 A:VAL74 4.0 37.7 1.0 CB A:SER46 4.0 41.4 1.0 CA A:SER46 4.4 42.2 1.0 CG1 A:VAL20 4.5 38.4 1.0

Iodine binding site 4 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:30.7 occ:0.71 O A:HOH466 3.7 34.3 1.0 NH2 A:ARG175 3.8 23.8 1.0 NH1 A:ARG175 3.8 26.9 1.0 CA A:GLU179 4.0 24.4 1.0 CD1 A:LEU182 4.0 23.4 1.0 CB A:GLU179 4.2 28.0 1.0 CZ A:ARG175 4.3 31.2 1.0 CG A:GLU179 4.4 35.1 1.0 N A:GLU179 4.5 24.8 1.0 CD1 B:LEU145 4.5 32.2 1.0 CG2 A:ILE178 4.8 25.3 1.0 C A:ILE178 4.9 27.8 1.0 CB A:LEU182 4.9 27.2 1.0 O A:ILE178 4.9 25.5 1.0

Iodine binding site 5 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:35.2 occ:0.78 O A:HOH488 3.2 49.0 1.0 CG A:ARG219 3.9 47.8 1.0 CG1 A:VAL249 4.0 34.8 1.0 NE2 A:GLN250 4.0 62.2 1.0 CB A:VAL249 4.1 32.1 1.0 CA A:GLU246 4.2 41.2 1.0 CA A:ARG219 4.3 34.3 1.0 CB A:ARG219 4.3 39.2 1.0 O A:HOH599 4.4 56.5 1.0 CD1 A:LEU222 4.4 35.4 1.0 CG A:GLU246 4.5 55.2 1.0 CG2 A:VAL249 4.5 30.0 1.0 CB A:GLU246 4.5 46.9 1.0 O A:HOH633 4.5 45.4 1.0 CG A:GLN250 4.6 46.4 1.0 O A:GLU246 4.7 32.2 1.0 CD A:GLN250 4.8 54.7 1.0 CB A:LEU222 4.8 33.2 1.0 O A:ARG219 4.9 31.0 1.0 C A:GLU246 5.0 36.1 1.0

Iodine binding site 6 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:42.8 occ:0.54 OG1 A:THR153 3.2 24.4 1.0 OG A:SER150 3.3 29.2 1.0 O A:HOH617 3.8 66.0 1.0 CB A:THR153 3.9 25.9 1.0 CL A:CL312 3.9 67.8 1.0 CA A:SER150 3.9 24.8 1.0 CB A:SER150 4.1 25.7 1.0 CG2 A:THR153 4.2 25.7 1.0 CG A:LYS134 4.5 36.5 1.0 O A:HOH427 4.6 34.1 1.0 N A:SER150 4.7 23.8 1.0 CB A:LYS134 4.7 31.3 1.0 CB A:ALA131 4.8 23.0 1.0 O A:GLN149 4.9 22.6 1.0 O A:SER150 4.9 26.6 1.0 C A:SER150 5.0 23.7 1.0

Iodine binding site 7 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:79.3 occ:0.58 CD A:ARG7 3.5 44.6 0.5 CD A:ARG11 3.5 68.1 1.0 CD A:ARG7 3.6 45.4 0.5 CG A:ARG7 3.6 41.8 0.5 CG A:ARG7 3.6 41.0 0.5 NE A:ARG7 4.0 45.9 0.5 CG A:ARG11 4.0 58.5 1.0 NH1 A:ARG7 4.1 45.3 0.5 NH1 A:ARG11 4.4 70.0 1.0 NE A:ARG7 4.6 46.5 0.5 NE A:ARG11 4.6 71.0 1.0 CZ A:ARG7 4.8 47.2 0.5 CZ A:ARG11 5.0 71.8 1.0

Iodine binding site 8 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:34.4 occ:0.83 SE A:MSE217 3.2 62.2 0.4 CG A:MSE217 3.4 31.5 0.4 SG A:CYS198 3.4 28.3 1.0 CB A:CYS198 3.5 26.7 1.0 CB A:MSE217 3.7 26.2 0.4 CG A:MSE217 3.7 35.4 0.6 CE A:MSE217 3.7 34.6 0.6 CB A:MSE217 3.8 27.3 0.6 CG1 A:VAL154 3.9 24.7 1.0 CA A:ALA155 4.0 21.6 1.0 CB A:ALA155 4.0 21.5 1.0 N A:ALA155 4.2 23.9 1.0 CA A:TRP195 4.2 27.6 1.0 O A:ASP194 4.3 22.5 1.0 CD1 A:TRP195 4.4 22.2 1.0 CG2 A:VAL158 4.5 25.9 1.0 C A:VAL154 4.6 24.6 1.0 CA A:ALA214 4.6 16.3 1.0 C A:ASP194 4.6 29.8 1.0 N A:TRP195 4.7 25.1 1.0 CB A:VAL154 4.7 26.5 1.0 SE A:MSE217 4.7 44.5 0.6 O A:VAL154 4.8 23.8 1.0 O A:ALA213 4.9 26.4 1.0 CA A:CYS198 5.0 25.0 1.0 CE A:MSE217 5.0 44.8 0.4 CB A:TRP195 5.0 22.0 1.0 O A:TRP195 5.0 21.9 1.0

Iodine binding site 9 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:I304 b:59.9 occ:0.37 O B:HOH622 3.4 55.1 1.0 CG B:ARG208 3.7 42.9 1.0 CA B:SER209 3.7 27.1 1.0 NE B:ARG208 3.8 57.9 1.0 N B:SER209 3.9 28.7 1.0 CD B:ARG208 4.0 50.1 1.0 CB B:SER209 4.0 30.2 1.0 C B:ARG208 4.2 27.8 1.0 O B:HOH608 4.2 47.3 1.0 O B:ARG208 4.2 30.1 1.0 CB B:ARG208 4.5 39.1 1.0 CB B:ALA212 4.7 27.1 1.0 CZ B:ARG208 4.8 70.6 1.0

Iodine binding site 10 out of 14 in the Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound


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 Aminoglycoside 4'-O-Adenylyltransferase Ant(4')- Iib, Tobramycin-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:I305 b:45.2 occ:0.87 CG B:MSE217 3.4 38.6 1.0 CB B:CYS198 3.6 22.5 1.0 CE B:MSE217 3.6 87.7 1.0 SG B:CYS198 3.6 27.4 1.0 CB B:MSE217 3.7 26.6 1.0 CG1 B:VAL154 3.9 23.8 1.0 CA B:ALA155 4.1 22.3 1.0 CB B:ALA155 4.1 20.6 1.0 SE B:MSE217 4.2 84.3 1.0 O B:ASP194 4.3 25.7 1.0 CA B:TRP195 4.3 22.8 1.0 N B:ALA155 4.4 25.6 1.0 CD1 B:TRP195 4.5 22.5 1.0 CG2 B:VAL158 4.6 29.1 1.0 C B:ASP194 4.7 26.8 1.0 CA B:ALA214 4.7 25.5 1.0 N B:TRP195 4.7 24.9 1.0 C B:VAL154 4.7 25.4 1.0 CB B:VAL154 4.8 23.6 1.0 O B:VAL154 5.0 22.1 1.0 CA B:CYS198 5.0 22.7 1.0

P.J.Stogios, A.Dong, G.Minasov, E.Evdokimova, O.Egorova, V.Yim, M.Kudritska, P.Courvalin, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Aminoglycoside 4'-O-Adenylyltransferase Ant(4')-Iib, Tobramycin-Bound To Be Published.