Iodine in PDB 4s2v: E. Coli Rpph Structure, Ki Soak

The structure of E. Coli Rpph Structure, Ki Soak, PDB code: 4s2v was solved by N.Vasilyev, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.54 / 1.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.693, 59.693, 81.778, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 19.9

The structure of E. Coli Rpph Structure, Ki Soak also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Iodine atom in the E. Coli Rpph Structure, Ki Soak (pdb code 4s2v). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 27 binding sites of Iodine where determined in the E. Coli Rpph Structure, Ki Soak, PDB code: 4s2v:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:52.6 occ:0.28 O A:HOH316 2.3 28.8 1.0 I A:IOD202 2.9 43.1 0.3 NZ A:LYS97 3.6 20.2 1.0 CE A:LYS97 3.7 20.3 1.0 CG A:PRO10 4.1 20.1 1.0 CB A:ASP4 4.4 23.8 1.0 CB A:PRO10 4.4 19.1 1.0 CD A:PRO10 4.8 18.7 1.0 O A:MET2 4.9 40.6 1.0

Iodine binding site 2 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:43.1 occ:0.32 I A:IOD201 2.9 52.6 0.3 CB A:PRO10 3.9 19.1 1.0 CZ2 A:TRP75 4.0 19.6 1.0 CH2 A:TRP75 4.0 18.7 1.0 CG2 A:ILE41 4.1 20.4 1.0 CG A:PRO10 4.1 20.1 1.0 I A:IOD203 4.1 45.6 0.4 O A:HOH316 4.5 28.8 1.0 CB A:ILE41 4.6 21.9 1.0 CD1 A:ILE41 4.8 22.8 1.0 CE A:LYS97 4.9 20.3 1.0 O A:GLU45 4.9 36.7 1.0

Iodine binding site 3 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:45.6 occ:0.43 N A:ALA47 3.6 23.6 1.0 CA A:SER46 4.1 28.0 1.0 I A:IOD202 4.1 43.1 0.3 CZ2 A:TRP75 4.2 19.6 1.0 O A:GLU45 4.2 36.7 1.0 C A:SER46 4.2 25.1 1.0 CH2 A:TRP75 4.2 18.7 1.0 CB A:ALA47 4.3 23.3 1.0 CE A:LYS99 4.3 31.0 1.0 CA A:ALA47 4.4 22.6 1.0 CD A:LYS99 4.6 29.2 1.0 CD1 A:ILE41 4.9 22.8 1.0 CB A:SER46 4.9 29.8 1.0 CG2 A:ILE41 5.0 20.4 1.0

Iodine binding site 4 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:58.4 occ:0.44 N A:GLU48 3.9 20.1 1.0 CB A:ALA47 4.0 23.3 1.0 N A:ALA47 4.2 23.6 1.0 CB A:GLU48 4.3 24.3 1.0 CA A:ALA47 4.5 22.6 1.0 CZ A:PHE101 4.6 20.0 1.0 C A:ALA47 4.6 20.9 1.0 CA A:GLU48 4.6 19.8 1.0 CB A:SER46 4.7 29.8 1.0 OE1 A:GLU48 5.0 46.2 1.0

Iodine binding site 5 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:56.1 occ:0.44 CB A:ARG73 4.3 41.8 1.0 CA A:ARG73 4.8 40.9 1.0

Iodine binding site 6 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:47.0 occ:0.40 N A:ASN74 3.6 34.0 1.0 N A:ARG73 3.8 38.9 1.0 CB A:ASN74 4.1 33.4 1.0 I A:IOD207 4.1 66.1 0.4 OD1 A:ASN74 4.2 41.0 1.0 O A:HOH327 4.2 32.2 1.0 CB A:THR72 4.2 41.7 1.0 CA A:ASN74 4.2 31.2 1.0 CA A:THR72 4.2 35.9 1.0 C A:THR72 4.3 37.3 1.0 C A:ASN74 4.3 29.3 1.0 O A:ASN74 4.4 35.8 1.0 CG2 A:THR72 4.5 44.5 1.0 CG A:ASN74 4.5 36.8 1.0 CA A:ARG73 4.6 40.9 1.0 C A:ARG73 4.6 39.6 1.0 CB A:ARG73 4.8 41.8 1.0

Iodine binding site 7 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I207 b:66.1 occ:0.44 O A:HOH368 3.5 40.3 1.0 O A:HOH327 3.6 32.2 1.0 O A:HOH382 3.6 40.1 1.0 CG2 A:THR72 4.0 44.5 1.0 I A:IOD206 4.1 47.0 0.4 CB A:LEU76 4.1 19.1 1.0 CG A:LEU76 4.2 23.4 1.0 CG A:GLU151 4.2 37.4 1.0 CD1 A:LEU76 4.2 26.1 1.0 CA A:LEU76 4.4 16.5 1.0 CD A:GLU151 4.5 45.8 1.0 OE2 A:GLU151 4.6 49.4 1.0 O A:TRP75 4.8 18.8 1.0 N A:LEU76 4.8 16.7 1.0 CB A:THR72 4.9 41.7 1.0 NH2 A:ARG147 5.0 37.3 1.0

Iodine binding site 8 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I208 b:46.4 occ:0.39 O A:HOH403 3.3 44.4 1.0 O A:HOH392 3.4 38.2 1.0 NZ A:LYS79 3.6 31.8 1.0 O A:HOH335 3.8 25.8 1.0 CG1 A:ILE94 3.9 20.0 1.0 CE A:LYS79 4.1 30.5 1.0 CB A:ILE94 4.2 18.1 1.0 CD1 A:ILE94 4.3 22.4 1.0 CG2 A:ILE94 4.4 18.1 1.0 CD A:LYS79 4.4 27.5 1.0

Iodine binding site 9 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I209 b:31.0 occ:0.26 OH A:TYR8 2.9 22.7 1.0 I A:IOD210 3.5 27.2 0.1 CA A:TYR78 3.8 20.2 1.0 CB A:ARG77 3.9 16.4 1.0 CZ A:TYR8 3.9 19.7 1.0 C A:ARG77 3.9 16.6 1.0 O A:ARG77 3.9 16.8 1.0 CG A:LYS79 4.0 24.9 1.0 N A:TYR78 4.0 16.9 1.0 CE A:LYS79 4.0 30.5 1.0 CE1 A:TYR8 4.1 14.9 1.0 C A:TYR78 4.1 19.7 1.0 N A:LYS79 4.1 21.0 1.0 CD A:LYS79 4.1 27.5 1.0 O A:HOH334 4.2 23.9 1.0 O A:HOH329 4.3 28.6 1.0 CA A:ARG77 4.6 15.2 1.0 NZ A:LYS79 4.7 31.8 1.0 O A:TYR78 4.8 16.5 1.0 CD A:ARG77 5.0 18.6 1.0

Iodine binding site 10 out of 27 in the E. Coli Rpph Structure, Ki Soak


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of E. Coli Rpph Structure, Ki Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:I210 b:27.2 occ:0.14 O A:HOH341 3.5 19.0 1.0 I A:IOD209 3.5 31.0 0.3 CB A:ARG77 3.9 16.4 1.0 CD A:ARG77 4.4 18.6 1.0 O A:HOH334 4.4 23.9 1.0 O A:ARG77 4.5 16.8 1.0 CG A:ARG77 4.7 17.6 1.0 C A:ARG77 4.9 16.6 1.0 CA A:ARG77 4.9 15.2 1.0

N.Vasilyev, A.Serganov. Structures of Escherichia Coli Rpph-Rna Complexes Unveil the Basis For Specific 5-End-Dependent Mrna Decay To Be Published.