Potassium in PDB 8rz6: Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase

The structure of Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase, PDB code: 8rz6 was solved by M.Karanth, S.Schmelz, J.Kirkpatrick, J.Krausze, A.Scrima, T.Carlomagno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.91 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.35, 160.87, 100.15, 90, 125.11, 90
R / Rfree (%)	17.2 / 21.6

The binding sites of Potassium atom in the Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase (pdb code 8rz6). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase, PDB code: 8rz6:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:K603 b:49.4 occ:1.00 O A:ARG214 2.7 15.7 1.0 O A:GLY210 2.8 31.9 1.0 O A:ALA212 2.8 42.6 1.0 OG A:SER128 2.8 61.7 1.0 HB2 A:SER128 2.8 30.6 1.0 H A:ARG214 3.0 32.9 1.0 O A:PRO211 3.2 44.9 1.0 CB A:SER128 3.3 25.5 1.0 H A:GLY210 3.5 28.2 1.0 C A:GLY210 3.5 23.1 1.0 N A:ARG214 3.6 27.4 1.0 C A:PRO211 3.7 35.7 1.0 C A:ALA212 3.8 28.4 1.0 C A:ARG214 3.8 25.6 1.0 O A:HOH748 3.9 53.3 1.0 N A:GLY210 3.9 23.5 1.0 HA A:SER128 3.9 32.4 1.0 HA A:ASN213 4.0 34.5 1.0 HB3 A:SER128 4.0 30.6 1.0 HB3 A:SER215 4.2 24.3 1.0 CA A:SER128 4.2 27.0 1.0 CA A:GLY210 4.3 26.8 1.0 HB3 A:LEU209 4.3 27.1 1.0 N A:ALA212 4.3 34.8 1.0 C A:ASN213 4.3 27.7 1.0 CA A:ARG214 4.3 28.2 1.0 N A:PRO211 4.4 22.8 1.0 CA A:ASN213 4.4 28.8 1.0 N A:ASN213 4.4 29.4 1.0 CA A:PRO211 4.5 40.6 1.0 HA3 A:GLY210 4.5 32.1 1.0 HA A:PRO211 4.5 48.8 1.0 HA A:LEU209 4.6 30.7 1.0 HH12 A:ARG176 4.6 56.5 1.0 HB2 A:ARG214 4.6 35.6 1.0 CA A:ALA212 4.7 45.3 1.0 C A:LEU209 4.7 25.2 1.0 H A:ALA212 4.7 41.8 1.0 HH22 A:ARG176 4.8 67.5 1.0 HD22 A:LEU209 4.9 50.0 1.0 N A:SER215 4.9 18.2 1.0

Potassium binding site 2 out of 4 in the Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:K604 b:59.0 occ:1.00 O B:ARG176 2.7 26.7 1.0 OE1 A:GLU494 2.9 36.2 1.0 O B:HOH826 2.9 41.5 1.0 O A:HOH821 3.0 48.6 1.0 O A:HOH933 3.0 46.7 1.0 OE2 A:GLU494 3.3 33.4 1.0 CD A:GLU494 3.4 38.1 1.0 H B:ARG176 3.7 36.0 1.0 C B:ARG176 3.7 35.9 1.0 HD21 B:LEU186 3.7 31.0 1.0 HB2 B:ARG176 4.0 40.6 1.0 O A:HOH838 4.0 36.9 1.0 HA B:TYR177 4.1 34.0 1.0 HB3 B:GLU182 4.1 35.9 1.0 N B:ARG176 4.4 30.0 1.0 HD11 B:LEU186 4.4 34.4 1.0 CA B:ARG176 4.5 28.1 1.0 HB1 B:ALA175 4.5 37.1 1.0 O B:HOH947 4.5 43.4 1.0 HG B:LEU186 4.6 28.6 1.0 CD2 B:LEU186 4.6 25.9 1.0 N B:TYR177 4.6 28.4 1.0 CB B:ARG176 4.7 33.8 1.0 HD13 A:LEU313 4.7 46.4 1.0 O A:HOH949 4.8 28.6 1.0 CA B:TYR177 4.8 28.3 1.0 CG A:GLU494 4.8 26.1 1.0 HD23 B:LEU186 4.9 31.0 1.0 HG3 A:GLU494 5.0 31.3 1.0 HD12 A:LEU313 5.0 46.4 1.0

Potassium binding site 3 out of 4 in the Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:K603 b:77.6 occ:1.00 O B:GLY210 2.6 39.1 1.0 OG B:SER128 2.9 55.7 1.0 O B:ARG214 3.2 34.5 1.0 H B:GLY210 3.3 35.7 1.0 HB2 B:SER128 3.4 47.4 1.0 O B:ALA212 3.4 72.8 1.0 HB3 B:LEU209 3.5 41.0 1.0 C B:GLY210 3.5 30.4 1.0 N B:GLY210 3.6 29.7 1.0 H B:ARG214 3.6 66.7 1.0 CB B:SER128 3.7 39.5 1.0 HH12 B:ARG176 3.8 62.7 1.0 O B:HOH881 4.0 51.8 1.0 HA B:LEU209 4.0 42.1 1.0 CA B:GLY210 4.2 36.2 1.0 O B:PRO211 4.2 64.4 1.0 C B:LEU209 4.2 31.6 1.0 HA B:ASN213 4.2 61.3 1.0 HH22 B:ARG176 4.2 88.5 1.0 HD22 B:LEU209 4.2 53.4 1.0 N B:ARG214 4.2 55.6 1.0 C B:ARG214 4.3 45.9 1.0 CB B:LEU209 4.3 34.2 1.0 HA B:SER128 4.3 44.2 1.0 C B:PRO211 4.4 55.6 1.0 HB3 B:SER215 4.4 26.6 1.0 HB3 B:SER128 4.4 47.4 1.0 C B:ALA212 4.4 50.9 1.0 CA B:LEU209 4.4 35.0 1.0 N B:PRO211 4.5 38.8 1.0 HA B:PRO211 4.6 54.4 1.0 HA3 B:GLY210 4.6 43.4 1.0 NH1 B:ARG176 4.7 52.2 1.0 CA B:SER128 4.7 36.8 1.0 CA B:PRO211 4.7 45.4 1.0 O B:HOH717 4.8 34.3 1.0 N B:ALA212 4.8 62.0 1.0 CA B:ASN213 4.9 51.1 1.0 C B:ASN213 4.9 51.0 1.0 HB2 B:LEU209 4.9 41.0 1.0 CA B:ARG214 4.9 54.1 1.0 HA2 B:GLY210 4.9 43.4 1.0 NH2 B:ARG176 5.0 73.7 1.0 CD2 B:LEU209 5.0 44.5 1.0

Potassium binding site 4 out of 4 in the Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Semet Derivative Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:K604 b:49.6 occ:1.00 O A:ARG176 2.7 23.9 1.0 O A:HOH863 2.8 35.0 1.0 OE1 B:GLU494 2.9 33.0 1.0 O B:HOH765 3.0 39.4 1.0 O B:HOH811 3.1 42.3 1.0 OE2 B:GLU494 3.3 29.8 1.0 CD B:GLU494 3.5 37.8 1.0 HD21 A:LEU186 3.6 34.7 1.0 C A:ARG176 3.7 22.3 1.0 H A:ARG176 3.8 32.8 1.0 HA A:TYR177 4.0 30.1 1.0 O B:HOH784 4.0 31.9 1.0 HB2 A:ARG176 4.1 39.7 1.0 HB3 A:GLU182 4.1 26.5 1.0 HD11 A:LEU186 4.4 31.0 1.0 N A:ARG176 4.4 27.3 1.0 HB1 A:ALA175 4.4 32.2 1.0 O A:HOH859 4.5 49.8 1.0 CA A:ARG176 4.5 24.1 1.0 CD2 A:LEU186 4.5 28.9 1.0 N A:TYR177 4.6 21.4 1.0 HG A:LEU186 4.7 32.3 1.0 O A:HOH937 4.8 28.4 1.0 CB A:ARG176 4.8 33.1 1.0 CA A:TYR177 4.8 25.1 1.0 HD23 A:LEU186 4.8 34.7 1.0 HD13 B:LEU313 4.8 42.1 1.0 HD12 B:LEU313 4.9 42.1 1.0 CG B:GLU494 4.9 25.9 1.0

M.N.Karanth, J.P.Kirkpatrick, J.Krausze, S.Schmelz, A.Scrima, T.Carlomagno. The Specificity of Intermodular Recognition in A Prototypical Nonribosomal Peptide Synthetase Depends on An Adaptor Domain Sci Adv V. 10 2024.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADM9404