Iodine in PDB 7r9x: Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis

The structure of Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis, PDB code: 7r9x was solved by C.M.Fortinez, T.M.Schmeing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.70 / 2.14
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.94, 106.87, 108.909, 90, 96.25, 90
R / Rfree (%)	19 / 23.2

The structure of Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis also contains other interesting chemical elements:

Sodium

(Na)

12 atoms

The binding sites of Iodine atom in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis (pdb code 7r9x). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis, PDB code: 7r9x:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis


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 A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:I1801 b:111.1 occ:1.00 O A:HOH1997 3.4 30.9 1.0 HA A:PRO1380 3.5 41.9 1.0 HB3 A:SER1374 3.8 45.4 1.0 O A:GLY1378 4.1 40.9 1.0 HB3 A:PRO1468 4.2 41.1 1.0 HE1 A:TRP1471 4.2 47.0 1.0 O A:SER1374 4.2 34.9 1.0 HZ2 A:TRP1471 4.3 50.0 1.0 CA A:PRO1380 4.3 35.0 1.0 N A:PRO1380 4.4 41.1 1.0 HB3 A:PRO1380 4.4 45.6 1.0 O A:ASP1379 4.5 32.6 1.0 O A:HOH1924 4.5 34.4 1.0 C A:ASP1379 4.5 40.8 1.0 HB2 A:PRO1468 4.6 41.1 1.0 O A:HOH1949 4.6 25.4 1.0 HD3 A:PRO1380 4.6 52.7 1.0 C A:GLY1378 4.6 43.0 1.0 HA A:GLU1375 4.7 46.0 1.0 C A:SER1374 4.8 37.4 1.0 CB A:SER1374 4.8 37.9 1.0 HA2 A:GLY1378 4.8 58.2 1.0 CB A:PRO1468 4.8 34.3 1.0 CB A:PRO1380 5.0 38.1 1.0 NE1 A:TRP1471 5.0 39.3 1.0 H A:PHE1469 5.0 28.2 1.0 N A:ASP1379 5.0 33.7 1.0

Iodine binding site 2 out of 5 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis


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 A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:I1802 b:76.0 occ:1.00 HG12 A:VAL1539 3.2 26.5 1.0 HD2 A:PRO1362 3.2 32.3 1.0 HD3 A:ARG1543 3.4 44.7 1.0 HB2 A:ALA1540 3.4 28.4 1.0 HA A:ALA1540 3.6 31.6 1.0 HD3 A:PRO1362 3.9 32.3 1.0 HG2 A:PRO1362 3.9 38.3 1.0 CD A:PRO1362 3.9 27.0 1.0 HG11 A:VAL1539 4.0 26.5 1.0 CG1 A:VAL1539 4.0 22.2 1.0 HB A:VAL1539 4.1 20.9 1.0 HB2 A:TYR1361 4.1 35.1 1.0 HE A:ARG1536 4.1 61.9 1.0 HD2 A:ARG1543 4.1 44.7 1.0 CA A:ALA1540 4.1 26.4 1.0 N A:ALA1540 4.2 23.3 1.0 CB A:ALA1540 4.2 23.8 1.0 H A:ALA1540 4.2 27.8 1.0 CD A:ARG1543 4.2 37.4 1.0 HG2 A:ARG1536 4.4 41.7 1.0 CG A:PRO1362 4.4 32.0 1.0 HG3 A:ARG1536 4.6 41.7 1.0 HB1 A:ALA1540 4.6 28.4 1.0 CB A:VAL1539 4.6 17.5 1.0 O A:ARG1536 4.7 24.5 1.0 C A:VAL1539 4.7 23.8 1.0 HG13 A:VAL1539 4.8 26.5 1.0 HB3 A:TYR1361 4.8 35.1 1.0 HE A:ARG1543 4.8 41.8 1.0 CB A:TYR1361 4.9 29.4 1.0 NE A:ARG1543 4.9 35.0 1.0 HB3 A:ALA1540 4.9 28.4 1.0 NE A:ARG1536 4.9 51.6 1.0 CG A:ARG1536 5.0 34.8 1.0 HH21 A:ARG1536 5.0 85.2 1.0

Iodine binding site 3 out of 5 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis


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 A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:I1803 b:156.7 occ:1.00 HB3 A:GLU1672 3.3 29.5 1.0 HD13 A:LEU1676 3.8 35.9 1.0 OE2 A:GLU1672 4.0 37.1 1.0 HE1 A:PHE1669 4.1 35.1 1.0 CB A:GLU1672 4.3 24.7 1.0 HG2 A:ARG1673 4.3 44.5 1.0 HA A:ARG1673 4.4 30.9 1.0 HB2 A:GLU1672 4.5 29.5 1.0 HH12 A:ARG1605 4.6 55.0 1.0 HG3 A:ARG1673 4.6 44.5 1.0 O A:GLU1672 4.6 22.5 1.0 HB2 A:LEU1676 4.7 28.7 1.0 C A:GLU1672 4.7 19.6 1.0 HD22 A:LEU1676 4.7 45.8 1.0 CD1 A:LEU1676 4.8 30.0 1.0 CD A:GLU1672 4.8 37.5 1.0 CE1 A:PHE1669 4.9 29.4 1.0 HG2 A:GLU1672 4.9 35.0 1.0 O A:HOH2199 4.9 51.3 1.0 N A:ARG1673 4.9 21.2 1.0 CG A:ARG1673 4.9 37.2 1.0 NH1 A:ARG1605 4.9 45.9 1.0 CG A:GLU1672 5.0 29.3 1.0

Iodine binding site 4 out of 5 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis


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 A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:I1801 b:111.2 occ:1.00 HB2 B:ALA1764 3.2 52.7 1.0 HA B:PHE1619 3.2 50.3 1.0 HB3 B:ARG1618 3.8 40.3 1.0 HD2 B:PHE1619 3.9 64.4 1.0 CA B:PHE1619 4.0 42.0 1.0 O B:HOH2069 4.0 47.8 1.0 HB2 B:PHE1619 4.1 55.0 1.0 N B:PHE1619 4.1 41.4 1.0 CB B:ALA1764 4.1 44.0 1.0 H B:PHE1619 4.3 49.6 1.0 HB1 B:ALA1764 4.3 52.7 1.0 O B:ALA1760 4.3 54.0 1.0 HB2 B:ARG1618 4.4 40.3 1.0 HB1 B:ALA1760 4.4 71.3 1.0 C B:ARG1618 4.5 41.2 1.0 CB B:PHE1619 4.5 46.0 1.0 CB B:ARG1618 4.5 33.7 1.0 HB3 B:ALA1764 4.5 52.7 1.0 CD2 B:PHE1619 4.6 53.8 1.0 O B:ARG1618 4.7 48.0 1.0 HA B:ALA1764 4.9 48.9 1.0

Iodine binding site 5 out of 5 in the Crystal Structure of A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis


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 A Dehydrating Condensation Domain, Ambe-Cmodaa, Involved in Nonribosomal Peptide Synthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:I1802 b:159.9 occ:1.00 HD21 B:LEU1662 2.9 62.8 1.0 HB3 B:SER1600 3.1 45.2 1.0 HA B:SER1600 3.5 49.7 1.0 HD23 B:LEU1662 3.5 62.8 1.0 CD2 B:LEU1662 3.6 52.4 1.0 CB B:SER1600 3.8 37.7 1.0 HD12 B:LEU1596 3.8 41.5 1.0 HB2 B:SER1600 3.8 45.2 1.0 HD22 B:LEU1662 4.0 62.8 1.0 CA B:SER1600 4.0 41.5 1.0 HB3 B:ARG1599 4.1 56.4 1.0 HB2 B:ARG1599 4.1 56.4 1.0 N B:SER1600 4.1 45.4 1.0 C B:ARG1599 4.3 47.4 1.0 O B:ARG1599 4.4 42.6 1.0 HD11 B:LEU1596 4.5 41.5 1.0 H B:SER1600 4.5 54.4 1.0 CD1 B:LEU1596 4.5 34.7 1.0 CB B:ARG1599 4.5 47.1 1.0 HE B:ARG1599 4.6 63.7 1.0 HD13 B:LEU1596 4.7 41.5 1.0 HD11 B:LEU1662 4.9 51.7 1.0 CG B:LEU1662 4.9 41.0 1.0 HG B:LEU1662 5.0 49.1 1.0

J.B.Patteson, C.M.Fortinez, A.T.Putz, J.Rodriguez-Rivas, L.H.Bryant 3Rd, K.Adhikari, M.Weigt, T.M.Schmeing, B.Li. Structure and Function of A Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis. J.Am.Chem.Soc. V. 144 14057 2022.
ISSN: ESSN 1520-5126
PubMed: 35895935
DOI: 10.1021/JACS.1C13404