Potassium in PDB 8qnf: Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase

The structure of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase, PDB code: 8qnf 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)	19.94 / 1.65
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.65, 160.06, 163.9, 90, 90, 90
R / Rfree (%)	17.7 / 19.7

The structure of Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

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

Potassium binding site 1 out of 2 in the Crystal 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 Crystal 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:K621 b:84.9 occ:1.00 OD2 A:ASP445 2.6 35.6 1.0 O A:HIS372 2.9 31.9 1.0 HA A:HIS372 3.2 33.6 1.0 HB2 A:ASP445 3.2 37.0 1.0 HB1 A:ALA229 3.3 28.6 1.0 HG23 A:VAL233 3.3 29.4 1.0 HD3 A:ARG366 3.3 31.7 1.0 HG22 A:VAL233 3.5 29.4 1.0 CG A:ASP445 3.5 40.7 1.0 HH11 A:ARG366 3.6 31.5 1.0 HG21 A:VAL233 3.6 29.4 1.0 CG2 A:VAL233 3.7 24.4 1.0 HB3 A:HIS372 3.7 33.6 1.0 C A:HIS372 3.7 27.5 1.0 HH22 A:ARG236 3.7 47.6 0.4 O A:HOH908 3.8 46.1 1.0 HH21 A:ARG236 3.8 47.7 0.4 CB A:ASP445 3.8 30.7 1.0 NH1 A:ARG366 3.9 26.1 1.0 CA A:HIS372 3.9 27.9 1.0 HH22 A:ARG236 3.9 48.8 0.2 HB3 A:ASP445 4.1 37.0 1.0 HH12 A:ARG366 4.1 31.5 1.0 CD A:ARG366 4.2 26.3 1.0 O A:HOH898 4.2 42.4 1.0 CB A:ALA229 4.2 23.7 1.0 CB A:HIS372 4.2 27.9 1.0 HH22 A:ARG236 4.3 47.7 0.4 CZ A:ARG366 4.3 26.1 1.0 NH2 A:ARG236 4.4 39.6 0.4 HD2 A:ARG366 4.4 31.7 1.0 HB3 A:ALA229 4.4 28.6 1.0 NE A:ARG366 4.5 25.0 1.0 NH2 A:ARG236 4.5 39.5 0.4 O A:HOH1012 4.5 52.1 1.0 NH2 A:ARG236 4.5 40.5 0.2 HH21 A:ARG236 4.5 48.8 0.2 HH21 A:ARG236 4.6 47.6 0.4 OD1 A:ASP445 4.6 38.4 1.0 O A:ALA229 4.7 24.9 1.0 HB2 A:ALA229 4.7 28.6 1.0 CG A:HIS372 4.8 31.4 1.0 H A:ASP445 4.8 34.2 1.0 HD2 A:HIS372 4.9 35.2 1.0 O A:THR371 5.0 26.9 1.0 N A:GLU373 5.0 24.7 1.0 HA A:GLU373 5.0 34.8 1.0

Potassium binding site 2 out of 2 in the Crystal 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 Crystal 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:K622 b:50.3 occ:1.00 O A:LYS306 2.7 32.8 1.0 HG13 A:VAL305 3.0 46.2 1.0 HG12 A:VAL305 3.5 46.2 1.0 HD2 A:HIS308 3.5 43.0 1.0 HE2 A:HIS308 3.5 43.6 1.0 CG1 A:VAL305 3.6 38.4 1.0 HG11 A:VAL305 3.7 46.2 1.0 HA A:GLN307 3.9 38.4 1.0 C A:LYS306 3.9 30.1 1.0 CD2 A:HIS308 4.1 35.7 1.0 NE2 A:HIS308 4.1 36.2 1.0 O A:HOH879 4.5 49.3 1.0 H A:LYS306 4.6 42.5 1.0 N A:LYS306 4.7 35.3 1.0 CA A:GLN307 4.7 31.9 1.0 OE1 A:GLN307 4.8 30.4 1.0 N A:GLN307 4.8 29.6 1.0 O A:HOH843 4.9 31.3 1.0 CA A:LYS306 4.9 35.2 1.0 HB3 A:LYS306 4.9 40.4 1.0 CB A:VAL305 5.0 37.8 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