Iodine in PDB 4mdx: Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna

The structure of Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna, PDB code: 4mdx was solved by D.K.Simanshu, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.55 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.793, 69.885, 79.209, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 17.8

The structure of Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iodine atom in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna (pdb code 4mdx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna, PDB code: 4mdx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna


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 Subtilis Mazf in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:19.3 occ:0.55 N A:ASP97 3.6 13.1 1.0 CG A:ASP97 3.8 23.1 1.0 OD2 A:ASP97 3.9 27.7 1.0 CB A:ASP96 4.0 13.8 1.0 O A:HOH402 4.0 40.9 1.0 O A:HOH319 4.0 22.6 1.0 CB A:ASP97 4.1 17.5 1.0 OD1 A:ASP97 4.1 26.5 1.0 CA A:ASP96 4.2 12.6 1.0 O A:HOH404 4.3 48.6 1.0 C A:ASP96 4.5 12.7 1.0 CA A:ASP97 4.5 16.1 1.0 O A:HOH387 4.7 32.8 1.0 O A:HOH390 4.8 36.4 1.0

Iodine binding site 2 out of 6 in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna


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 Subtilis Mazf in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:38.8 occ:0.31 O A:HOH444 3.4 48.5 1.0 O A:HOH420 3.4 34.7 1.0 N A:GLU70 3.4 23.2 1.0 CB A:GLU70 3.9 29.0 1.0 CA A:PHE69 4.0 22.0 1.0 CZ A:PHE10 4.1 20.6 1.0 C A:PHE69 4.2 22.9 1.0 CA A:GLU70 4.3 23.1 1.0 CD2 A:PHE69 4.3 19.3 1.0 CD1 A:ILE92 4.3 16.4 1.0 CG2 A:ILE92 4.3 18.9 1.0 CE2 A:PHE10 4.3 19.5 1.0 CB A:PHE69 4.5 18.0 1.0 CG A:PHE69 4.6 20.2 1.0 CG1 A:ILE92 4.7 12.8 1.0 O A:GLY68 4.7 30.8 1.0 OE1 A:GLU70 4.9 45.9 1.0

Iodine binding site 3 out of 6 in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna


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 Subtilis Mazf in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:21.5 occ:0.56 O B:HOH435 3.0 21.2 1.0 N A:ASP33 3.7 9.2 1.0 O B:HOH449 4.1 37.7 1.0 CB A:ASN32 4.2 9.0 1.0 CG1 A:ILE34 4.2 13.0 1.0 CB A:ASP33 4.2 11.5 1.0 N A:ILE34 4.4 11.0 1.0 CA A:ASP33 4.4 9.6 1.0 O B:HOH389 4.5 35.0 1.0 CD1 A:ILE34 4.5 17.8 1.0 C A:ASN32 4.6 11.0 1.0 CA A:ASN32 4.6 9.1 1.0 OD1 A:ASN32 4.7 10.4 1.0 C A:ASP33 4.8 11.6 1.0 CG A:ASN32 4.9 10.8 1.0

Iodine binding site 4 out of 6 in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna


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 Subtilis Mazf in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:I201 b:21.7 occ:0.32 O B:HOH316 3.7 19.7 1.0 N B:ASP97 3.8 15.1 1.0 O B:HOH388 3.8 33.0 1.0 O B:HOH442 3.9 44.0 1.0 CB B:ASP96 3.9 12.8 1.0 CG B:ASP97 4.1 24.4 1.0 OD2 B:ASP97 4.1 27.8 1.0 CB B:ASP97 4.2 18.8 1.0 CA B:ASP96 4.4 10.8 1.0 O B:HOH444 4.6 43.9 1.0 OD1 B:ASP97 4.6 28.2 1.0 C B:ASP96 4.6 12.3 1.0 CA B:ASP97 4.7 15.8 1.0 O B:HOH441 4.9 44.9 1.0

Iodine binding site 5 out of 6 in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna


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 Subtilis Mazf in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:I202 b:18.9 occ:0.60 O B:HOH302 3.0 16.2 1.0 N B:ASP33 3.8 9.9 1.0 CB B:ASN32 4.2 9.8 1.0 CB B:ASP33 4.3 9.9 1.0 CG1 B:ILE34 4.4 15.7 1.0 CA B:ASP33 4.5 10.4 1.0 N B:ILE34 4.5 11.2 1.0 O A:HOH392 4.7 44.1 1.0 C B:ASN32 4.7 11.9 1.0 CA B:ASN32 4.7 9.6 1.0 CD1 B:ILE34 4.7 21.2 1.0 OD1 B:ASN32 4.8 12.1 1.0 O A:HOH401 4.9 41.3 1.0 CG B:ASN32 4.9 12.7 1.0 C B:ASP33 5.0 10.9 1.0 OD2 B:ASP33 5.0 13.9 1.0 CG B:ASP33 5.0 12.8 1.0

Iodine binding site 6 out of 6 in the Crystal Structure of Bacillus Subtilis Mazf in Complex with Rna


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 Subtilis Mazf in Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:I101 b:25.9 occ:0.49 O B:HOH417 3.1 30.8 1.0 O B:HOH391 3.5 41.5 1.0 N9 C:A4 3.6 12.1 1.0 C8 C:A4 3.7 13.3 1.0 C B:GLY22 3.8 10.2 1.0 O B:GLY22 3.8 10.4 1.0 C1' C:A4 3.9 14.3 1.0 N B:GLY23 4.0 10.3 1.0 C4 C:A4 4.1 12.6 1.0 CA B:GLY23 4.1 10.8 1.0 N7 C:A4 4.1 10.1 1.0 O4' C:A4 4.2 14.3 1.0 CA B:GLY22 4.3 10.7 1.0 O B:HOH406 4.3 40.4 1.0 C5 C:A4 4.3 9.3 1.0 O B:HOH370 4.4 36.6 1.0 NH2 B:ARG25 4.7 9.6 1.0 N3 C:A4 4.7 15.2 1.0 N B:GLY22 4.8 9.8 1.0 O C:HOH248 4.9 47.7 1.0 O C:HOH219 4.9 38.6 1.0

D.K.Simanshu, Y.Yamaguchi, J.H.Park, M.Inouye, D.J.Patel. Structural Basis of Mrna Recognition and Cleavage By Toxin Mazf and Its Regulation By Antitoxin Maze in Bacillus Subtilis. Mol.Cell V. 52 447 2013.
ISSN: ISSN 1097-2765
PubMed: 24120662
DOI: 10.1016/J.MOLCEL.2013.09.006