Iodine in PDB 7k9c: Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A

The structure of Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A, PDB code: 7k9c was solved by Y.Yang, R.R.Breaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.64 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.904, 34.912, 49.637, 90, 90.15, 90
R / Rfree (%)	14.8 / 16.3

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A (pdb code 7k9c). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 17 binding sites of Iodine where determined in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A, PDB code: 7k9c:
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 Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:9.8 occ:1.00 H A:ASP21 2.9 11.0 1.0 HZ2 A:LYS53 2.9 19.4 1.0 HH21 A:ARG45 3.1 10.8 1.0 HD13 A:ILE16 3.3 11.1 1.0 HD3 A:LYS51 3.4 27.8 1.0 H A:ARG20 3.4 11.4 1.0 HA3 A:GLY19 3.4 13.6 1.0 HD2 A:LYS51 3.4 27.8 1.0 HG21 A:ILE16 3.4 11.9 1.0 O A:HOH325 3.5 10.8 1.0 HB3 A:ARG20 3.5 12.0 1.0 HB2 A:ASP21 3.5 11.6 1.0 HD3 A:LYS53 3.6 16.1 1.0 HD11 A:ILE39 3.7 11.8 1.0 HE2 A:LYS53 3.7 17.7 1.0 NZ A:LYS53 3.7 16.1 1.0 N A:ASP21 3.8 9.2 1.0 N A:ARG20 3.8 9.5 1.0 NH2 A:ARG45 3.9 9.0 1.0 CD A:LYS51 3.9 23.1 1.0 HE A:ARG45 3.9 12.3 1.0 HZ3 A:LYS53 4.0 19.4 1.0 CE A:LYS53 4.1 14.7 1.0 CA A:GLY19 4.2 11.3 1.0 C A:GLY19 4.2 10.1 1.0 CD1 A:ILE16 4.2 9.2 1.0 HH22 A:ARG45 4.3 10.8 1.0 CD A:LYS53 4.3 13.4 1.0 CB A:ASP21 4.3 9.7 1.0 CB A:ARG20 4.3 10.0 1.0 CG2 A:ILE16 4.3 9.9 1.0 HZ1 A:LYS53 4.4 19.4 1.0 CA A:ARG20 4.4 10.0 1.0 HG23 A:ILE16 4.4 11.9 1.0 OD2 A:ASP21 4.5 11.2 1.0 HD11 A:ILE16 4.5 11.1 1.0 CA A:ASP21 4.6 9.1 1.0 HE3 A:LYS51 4.6 30.7 1.0 NE A:ARG45 4.6 10.2 1.0 C A:ARG20 4.6 9.6 1.0 HA2 A:GLY19 4.6 13.6 1.0 HB2 A:ARG20 4.6 12.0 1.0 CD1 A:ILE39 4.6 9.9 1.0 CZ A:ARG45 4.6 9.9 1.0 CG A:ASP21 4.7 9.6 1.0 HD12 A:ILE16 4.7 11.1 1.0 HG12 A:ILE16 4.8 10.2 1.0 HE A:ARG20 4.8 12.1 1.0 HG2 A:LYS51 4.8 22.1 1.0 HD2 A:LYS53 4.8 16.1 1.0 CE A:LYS51 4.9 25.6 1.0 HG22 A:ILE16 4.9 11.9 1.0 HB3 A:LYS51 4.9 17.9 1.0 CG A:LYS51 4.9 18.4 1.0 O A:LYS18 5.0 11.8 1.0 HD13 A:ILE39 5.0 11.8 1.0 CG1 A:ILE16 5.0 8.5 1.0 HD12 A:ILE39 5.0 11.8 1.0

Iodine binding site 2 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:19.4 occ:0.54 I A:IOD202 0.0 19.4 0.5 HE A:ARG22 2.8 25.8 1.0 I A:IOD202 2.9 27.6 0.5 H A:GLY19 2.9 12.7 1.0 HD3 A:ARG22 3.1 22.5 1.0 HG3 A:LYS18 3.2 18.4 1.0 NE A:ARG22 3.5 21.5 1.0 HA A:LYS18 3.5 14.0 1.0 HB2 A:ARG22 3.7 16.0 1.0 N A:GLY19 3.7 10.6 1.0 CD A:ARG22 3.8 18.7 1.0 O A:GLY19 4.0 10.1 1.0 CG A:LYS18 4.2 15.4 1.0 CA A:LYS18 4.3 11.7 1.0 HD2 A:ARG22 4.4 22.5 1.0 HH21 A:ARG22 4.4 32.4 1.0 CB A:ARG22 4.5 13.4 1.0 HB3 A:ARG22 4.5 16.0 1.0 HG2 A:LYS18 4.5 18.4 1.0 C A:LYS18 4.5 10.5 1.0 C A:GLY19 4.6 10.1 1.0 HE3 A:LYS18 4.6 23.3 1.0 CA A:GLY19 4.6 11.3 1.0 CZ A:ARG22 4.6 25.6 1.0 HA2 A:GLY19 4.6 13.6 1.0 CB A:LYS18 4.7 13.2 1.0 CG A:ARG22 4.7 15.9 1.0 HB2 A:LYS18 4.9 15.9 1.0 NH2 A:ARG22 4.9 27.0 1.0

Iodine binding site 3 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:27.6 occ:0.46 I A:IOD202 0.0 27.6 0.5 HE A:ARG22 2.6 25.8 1.0 HH21 A:ARG22 2.6 32.4 1.0 I A:IOD202 2.9 19.4 0.5 NE A:ARG22 3.4 21.5 1.0 NH2 A:ARG22 3.4 27.0 1.0 CZ A:ARG22 3.8 25.6 1.0 HH22 A:ARG22 4.1 32.4 1.0 HB3 A:ARG22 4.2 16.0 1.0 HB2 A:ARG22 4.5 16.0 1.0 HD3 A:ARG22 4.5 22.5 1.0 O A:GLY19 4.5 10.1 1.0 CD A:ARG22 4.5 18.7 1.0 CB A:ARG22 4.8 13.4 1.0 H A:GLY19 5.0 12.7 1.0

Iodine binding site 4 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:21.1 occ:0.75 HD2 A:LYS18 3.3 20.8 1.0 HD2 A:HIS57 3.5 15.0 1.0 HB2 A:LYS18 3.5 15.9 1.0 O A:HOH410 3.6 25.6 1.0 HD3 A:LYS18 3.8 20.8 1.0 HG12 A:VAL17 3.8 16.2 1.0 O A:HOH350 3.8 37.9 1.0 CD A:LYS18 4.0 17.3 1.0 CD2 A:HIS57 4.2 12.5 1.0 CB A:LYS18 4.3 13.2 1.0 HB3 A:LYS18 4.3 15.9 1.0 HG11 A:VAL17 4.5 16.2 1.0 CG1 A:VAL17 4.6 13.5 1.0 O A:ASN56 4.6 11.5 1.0 NE2 A:HIS57 4.7 13.4 1.0 HA A:HIS57 4.7 12.8 1.0 HZ2 A:LYS18 4.7 25.6 1.0 CG A:LYS18 4.8 15.4 1.0

Iodine binding site 5 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:20.7 occ:0.29 HD2 A:ARG35 3.7 29.0 1.0 HD3 A:ARG35 3.9 29.0 1.0 HH11 A:ARG35 3.9 35.7 1.0 CD A:ARG35 4.2 24.2 1.0 NH1 A:ARG35 4.5 29.8 1.0 HH12 A:ARG35 4.9 35.7 1.0 NE A:ARG35 4.9 26.4 1.0

Iodine binding site 6 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:18.5 occ:0.38 HH12 A:ARG20 2.6 12.3 1.0 O A:HOH389 2.9 28.0 0.6 HG3 A:ARG49 3.1 18.4 1.0 HH11 A:ARG49 3.3 27.4 1.0 NH1 A:ARG20 3.5 10.2 1.0 O A:HOH374 3.5 14.9 1.0 NH1 A:ARG49 3.8 22.8 1.0 HH11 A:ARG20 3.9 12.3 1.0 HH22 A:ARG20 3.9 11.9 1.0 HH12 A:ARG49 4.0 27.4 1.0 HB3 A:ARG49 4.0 14.8 1.0 CG A:ARG49 4.0 15.3 1.0 HD2 A:ARG49 4.2 21.2 1.0 HB2 A:ARG49 4.3 14.8 1.0 O A:LYS44 4.3 10.8 1.0 O A:HOH347 4.3 10.5 1.0 CB A:ARG49 4.3 12.3 1.0 CZ A:ARG20 4.5 10.0 1.0 NH2 A:ARG20 4.5 9.9 1.0 HA A:ARG45 4.5 10.8 1.0 CD A:ARG49 4.6 17.7 1.0 HG2 A:ARG49 4.7 18.4 1.0 HH12 A:ARG45 4.7 12.1 1.0 CZ A:ARG49 4.7 23.1 1.0

Iodine binding site 7 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:18.0 occ:0.37 H A:VAL78 3.0 12.1 1.0 HB A:VAL47 3.1 13.5 1.0 HA A:LYS77 3.2 11.6 1.0 HB2 A:LYS77 3.3 12.9 1.0 HZ A:PHE72 3.3 18.9 1.0 HG12 A:VAL78 3.3 18.1 1.0 O A:HOH379 3.4 35.7 1.0 HE1 A:PHE72 3.5 18.4 1.0 HD12 A:ILE29 3.5 15.5 1.0 N A:VAL78 3.8 10.1 1.0 HG11 A:VAL47 3.8 15.0 1.0 CZ A:PHE72 3.9 15.7 1.0 CB A:LYS77 3.9 10.7 1.0 CB A:VAL47 3.9 11.3 1.0 CA A:LYS77 3.9 9.7 1.0 HG21 A:VAL47 4.0 16.4 1.0 O A:VAL78 4.0 13.6 1.0 CE1 A:PHE72 4.0 15.3 1.0 HB3 A:LYS77 4.0 12.9 1.0 HG12 A:VAL47 4.2 15.0 1.0 CG1 A:VAL47 4.2 12.5 1.0 CG1 A:VAL78 4.3 15.1 1.0 C A:LYS77 4.4 9.1 1.0 CD1 A:ILE29 4.4 12.9 1.0 CG2 A:VAL47 4.4 13.6 1.0 HD13 A:ILE29 4.6 15.5 1.0 HG23 A:VAL47 4.6 16.4 1.0 HG13 A:VAL78 4.7 18.1 1.0 HD11 A:ILE29 4.7 15.5 1.0 HG11 A:VAL78 4.7 18.1 1.0 CA A:VAL78 4.8 11.6 1.0 O A:GLY76 4.8 10.9 1.0 C A:VAL78 4.8 12.0 1.0 O A:HOH321 4.9 17.1 1.0 HB A:ILE29 4.9 12.0 1.0

Iodine binding site 8 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:10.4 occ:1.00 HZ2 B:LYS53 2.9 21.0 1.0 HH21 B:ARG45 3.0 12.2 1.0 H B:ASP21 3.0 11.5 1.0 HD13 B:ILE16 3.2 11.2 1.0 H B:ARG20 3.3 11.7 1.0 HG21 B:ILE16 3.3 11.9 1.0 HA3 B:GLY19 3.3 12.9 1.0 O B:HOH316 3.5 10.3 1.0 HB3 B:ARG20 3.5 10.3 1.0 HD3 B:LYS53 3.5 17.3 1.0 HD11 B:ILE39 3.6 11.7 1.0 NH2 B:ARG45 3.7 10.1 1.0 NZ B:LYS53 3.7 17.5 1.0 HZ1 B:LYS51 3.7 18.2 0.1 N B:ARG20 3.7 9.7 1.0 HZ3 B:LYS51 3.7 18.2 0.1 HG2 B:LYS51 3.8 18.0 0.8 HB2 B:ASP21 3.8 12.8 1.0 HE B:ARG45 3.9 11.4 1.0 N B:ASP21 3.9 9.6 1.0 HE2 B:LYS53 3.9 18.8 1.0 HG2 B:LYS51 3.9 14.9 0.1 HZ3 B:LYS53 4.0 21.0 1.0 CA B:GLY19 4.1 10.8 1.0 HH22 B:ARG45 4.1 12.2 1.0 NZ B:LYS51 4.1 15.2 0.1 CD1 B:ILE16 4.2 9.3 1.0 CE B:LYS53 4.2 15.7 1.0 CG2 B:ILE16 4.2 9.9 1.0 C B:GLY19 4.2 9.1 1.0 CB B:ARG20 4.3 8.6 1.0 CD B:LYS53 4.3 14.4 1.0 HZ1 B:LYS53 4.3 21.0 1.0 HG23 B:ILE16 4.3 11.9 1.0 HA2 B:GLY19 4.4 12.9 1.0 HD11 B:ILE16 4.4 11.2 1.0 HZ2 B:LYS51 4.4 18.2 0.1 NE B:ARG45 4.4 9.5 1.0 CA B:ARG20 4.4 9.3 1.0 HG12 B:ILE16 4.5 10.1 1.0 CZ B:ARG45 4.5 8.5 1.0 CD1 B:ILE39 4.5 9.7 1.0 CB B:ASP21 4.5 10.6 1.0 HB2 B:ARG20 4.5 10.3 1.0 OD2 B:ASP21 4.6 11.3 1.0 I B:IOD204 4.6 17.2 0.3 C B:ARG20 4.7 9.3 1.0 CA B:ASP21 4.7 10.4 1.0 CG B:LYS51 4.7 15.0 0.8 HB3 B:LYS51 4.7 14.9 0.8 HB3 B:LYS51 4.7 13.8 0.1 HE2 B:LYS51 4.7 23.1 0.8 HG22 B:ILE16 4.7 11.9 1.0 HD12 B:ILE16 4.8 11.2 1.0 CG1 B:ILE16 4.8 8.4 1.0 CG B:ASP21 4.8 10.8 1.0 HD12 B:ILE39 4.8 11.7 1.0 HE B:ARG20 4.8 9.6 1.0 CG B:LYS51 4.8 12.4 0.1 HD13 B:ILE39 4.9 11.7 1.0 HD2 B:LYS53 4.9 17.3 1.0

Iodine binding site 9 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:32.5 occ:0.65 HH22 B:ARG31 3.1 20.6 1.0 HH21 B:ARG31 3.5 20.6 1.0 H B:ASP34 3.6 18.4 1.0 NH2 B:ARG31 3.7 17.1 1.0 HB2 B:ASP33 3.7 26.0 1.0 HA B:ASP33 3.9 23.6 1.0 OD2 B:ASP34 4.1 17.8 1.0 CG B:ASP34 4.1 15.9 1.0 N B:ASP34 4.2 15.3 1.0 OD1 B:ASP34 4.2 16.5 1.0 CB B:ASP33 4.4 21.6 1.0 CA B:ASP33 4.5 19.6 1.0 HB2 B:ASP34 4.5 17.9 1.0 HB3 B:ASP33 4.6 26.0 1.0 C B:ASP33 4.7 17.2 1.0 CB B:ASP34 4.8 14.9 1.0 CZ B:ARG31 5.0 15.9 1.0

Iodine binding site 10 out of 17 in the Crystal Structure of Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A


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 Bacillus Halodurans Oapb (Iodine-Derivative) at 1.0 A within 5.0Å range: probe atom residue distance (Å) B Occ B:I203 b:12.1 occ:0.72 HH12 B:ARG20 2.7 10.4 1.0 HA A:GLU93 3.0 10.1 1.0 HH21 B:ARG49 3.2 17.8 1.0 HG3 B:ARG49 3.3 15.2 1.0 O B:HOH366 3.5 14.1 1.0 NH1 B:ARG20 3.5 8.7 1.0 HH22 B:ARG20 3.7 10.9 1.0 HB3 B:ARG49 3.7 13.8 1.0 NH2 B:ARG49 3.8 14.8 1.0 O B:LYS44 3.8 9.9 1.0 CA A:GLU93 3.8 8.4 1.0 HB2 A:GLU93 3.8 12.1 1.0 HH22 B:ARG49 3.9 17.8 1.0 HH11 B:ARG20 3.9 10.4 1.0 HA B:ARG45 4.1 10.2 1.0 CG B:ARG49 4.1 12.7 1.0 HG3 A:GLU93 4.2 13.0 1.0 N A:GLU93 4.2 7.7 1.0 HB2 B:ARG49 4.2 13.8 1.0 CB B:ARG49 4.2 11.5 1.0 HD2 B:ARG49 4.3 16.5 1.0 HB3 A:GLU92 4.3 9.3 1.0 CB A:GLU93 4.3 10.1 1.0 NH2 B:ARG20 4.4 9.1 1.0 CZ B:ARG20 4.4 8.1 1.0 O A:GLU92 4.5 8.8 1.0 C A:GLU92 4.5 8.4 1.0 O A:HOH323 4.5 30.4 1.0 H A:GLU93 4.6 9.3 1.0 HG3 B:ARG45 4.6 12.2 1.0 O B:HOH386 4.6 19.1 1.0 CD B:ARG49 4.7 13.8 1.0 HB2 A:GLU92 4.7 9.3 1.0 CG A:GLU93 4.7 10.8 1.0 CZ B:ARG49 4.8 14.1 1.0 O B:HOH303 4.8 30.3 1.0 O A:HOH357 4.9 26.7 0.6 H B:LYS46 4.9 9.5 0.5 HG2 B:ARG49 4.9 15.2 1.0 H B:LYS46 4.9 9.6 0.5 C B:LYS44 4.9 8.6 1.0 CB A:GLU92 4.9 7.8 1.0

Y.Yang, K.A.Harris, D.L.Widner, R.R.Breaker. Structure of A Bacterial Oapb Protein with Its Ole Rna Target Gives Insights Into the Architecture of the Ole Ribonucleoprotein Complex Proc.Natl.Acad.Sci.Usa 2021.
ISSN: ESSN 1091-6490