Sodium 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:

Potassium

(K)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of the Condensation Domain Tombc From the Tomaymycin Non-Ribosomal Peptide Synthetase, PDB code: 8qnf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 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 Sodium with other atoms in the Na 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:Na614 b:33.7 occ:1.00 HG23 A:VAL190 2.6 27.8 1.0 HG21 A:THR206 2.6 29.9 1.0 OE2 A:GLU173 2.8 30.4 1.0 OG1 A:THR206 2.8 25.7 1.0 HB3 A:LEU186 2.9 30.9 1.0 O A:LEU186 3.1 25.8 1.0 HG1 A:THR206 3.3 31.0 1.0 HD22 A:LEU186 3.3 33.1 1.0 HA A:LEU186 3.3 30.9 1.0 HB A:THR206 3.3 27.4 1.0 CB A:THR206 3.4 22.7 1.0 CG2 A:THR206 3.4 24.8 1.0 CG2 A:VAL190 3.4 23.0 1.0 HE A:ARG189 3.5 33.6 1.0 CD A:GLU173 3.5 24.3 1.0 HB3 A:ARG189 3.5 31.2 1.0 HG21 A:VAL190 3.5 27.8 1.0 HG22 A:VAL190 3.7 27.8 1.0 C A:LEU186 3.7 24.2 1.0 CB A:LEU186 3.7 25.6 1.0 CA A:LEU186 3.8 25.6 1.0 HD12 A:ILE218 3.8 32.4 1.0 HH21 A:ARG189 3.8 33.8 1.0 HG3 A:GLU173 3.9 30.1 1.0 HG2 A:ARG189 3.9 31.2 1.0 H A:VAL190 3.9 29.0 1.0 HG23 A:THR206 4.0 29.9 1.0 NE A:ARG189 4.0 27.9 1.0 HG22 A:THR206 4.0 29.9 1.0 HG2 A:GLU173 4.0 30.1 1.0 CG A:GLU173 4.1 25.0 1.0 CD2 A:LEU186 4.2 27.4 1.0 NH2 A:ARG189 4.2 28.1 1.0 OE1 A:GLU173 4.2 27.6 1.0 O A:HOH760 4.3 30.6 1.0 CZ A:ARG189 4.4 33.1 1.0 CB A:ARG189 4.4 25.9 1.0 HD13 A:ILE218 4.4 32.4 1.0 HB2 A:LEU186 4.4 30.9 1.0 HD23 A:LEU186 4.4 33.1 1.0 N A:VAL190 4.5 24.0 1.0 CG A:ARG189 4.5 25.9 1.0 HB3 A:ALA175 4.5 35.3 1.0 CD1 A:ILE218 4.5 26.9 1.0 CG A:LEU186 4.5 28.5 1.0 HD13 A:LEU186 4.6 32.0 1.0 CB A:VAL190 4.6 23.9 1.0 HB A:VAL190 4.6 28.9 1.0 HB A:ILE218 4.7 27.9 1.0 HH22 A:ARG189 4.8 33.8 1.0 HG21 A:ILE218 4.8 27.0 1.0 CA A:THR206 4.9 24.7 1.0 O A:HOH893 4.9 27.4 1.0 CD A:ARG189 4.9 35.6 1.0 N A:VAL187 4.9 24.8 1.0 HD21 A:LEU186 4.9 33.1 1.0 HB2 A:ARG189 5.0 31.2 1.0

Sodium binding site 2 out of 7 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 Sodium with other atoms in the Na 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:Na615 b:36.8 occ:1.00 H A:ARG124 2.1 27.9 0.5 H A:ARG124 2.1 27.9 0.5 O A:ARG457 2.7 31.4 1.0 OE2 A:GLU459 2.8 36.0 1.0 HA A:VAL123 2.8 28.4 0.5 HA A:VAL123 2.8 28.2 0.5 HG3 A:ARG124 2.9 35.0 1.0 N A:ARG124 2.9 23.1 1.0 HG3 A:GLU459 3.1 40.3 1.0 HB2 A:ARG124 3.1 33.0 1.0 HG23 A:VAL123 3.2 31.0 0.5 HB3 A:ARG457 3.4 37.2 1.0 HG13 A:VAL123 3.4 30.4 0.5 H A:ARG457 3.4 32.9 1.0 CG A:ARG124 3.6 29.0 1.0 CB A:ARG124 3.6 27.4 1.0 CA A:VAL123 3.6 23.5 0.5 O A:HOH910 3.6 47.5 1.0 C A:ARG457 3.7 29.3 1.0 CA A:VAL123 3.7 23.4 0.5 CD A:GLU459 3.7 39.8 1.0 C A:VAL123 3.8 22.1 0.5 C A:VAL123 3.8 22.1 0.5 HG2 A:ARG457 3.8 55.0 1.0 HD2 A:ARG124 3.8 35.9 1.0 CG A:GLU459 3.8 33.5 1.0 CA A:ARG124 3.8 24.8 1.0 N A:ARG457 4.0 27.3 1.0 CG2 A:VAL123 4.0 25.7 0.5 CB A:ARG457 4.1 30.9 1.0 HE A:ARG124 4.1 39.1 1.0 CA A:ARG457 4.1 27.3 1.0 CD A:ARG124 4.1 29.8 1.0 CG1 A:VAL123 4.1 25.2 0.5 HG22 A:VAL123 4.2 31.0 0.5 HG12 A:VAL123 4.2 30.4 0.5 O A:ARG124 4.2 28.4 1.0 O A:PHE122 4.3 25.3 1.0 CG A:ARG457 4.4 45.7 1.0 HG2 A:ARG124 4.4 35.0 1.0 CB A:VAL123 4.4 26.0 0.5 HG2 A:GLU459 4.4 40.3 1.0 H A:GLU459 4.5 30.6 0.6 H A:GLU459 4.5 30.6 0.4 NE A:ARG124 4.5 32.4 1.0 HB2 A:GLU459 4.5 35.1 1.0 CB A:VAL123 4.5 26.1 0.5 HB3 A:ARG124 4.5 33.0 1.0 C A:ARG124 4.5 30.3 1.0 HA A:ARG124 4.6 30.0 1.0 HG22 A:VAL123 4.6 32.2 0.5 N A:VAL123 4.7 22.6 0.5 N A:VAL123 4.7 22.6 0.5 HB A:VAL123 4.7 31.4 0.5 HG3 A:ARG457 4.7 55.0 1.0 HA A:ILE458 4.8 33.4 0.6 CB A:GLU459 4.8 29.1 1.0 N A:ILE458 4.8 27.0 0.6 N A:ILE458 4.8 27.2 0.4 HG21 A:VAL123 4.8 31.0 0.5 HA A:ILE458 4.8 33.5 0.4 N A:GLU459 4.8 25.4 1.0 HE2 A:PHE122 4.9 38.0 1.0 OE1 A:GLU459 4.9 36.4 1.0 HD2 A:PHE122 4.9 34.6 1.0 C A:PHE122 4.9 22.4 1.0 HB2 A:ARG457 4.9 37.2 1.0 HG11 A:VAL123 5.0 30.4 0.5 O A:VAL123 5.0 22.8 0.5 O A:VAL123 5.0 23.4 0.5

Sodium binding site 3 out of 7 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 Sodium with other atoms in the Na binding site number 3 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:Na616 b:33.2 occ:1.00 HE A:ARG366 2.4 30.1 1.0 HD2 A:ARG366 2.7 31.7 1.0 OD2 A:ASP227 2.8 29.6 1.0 O A:HOH966 2.8 26.3 1.0 OG A:SER364 2.9 29.3 1.0 HG12 A:VAL379 3.0 37.7 0.3 O A:PHE378 3.1 27.0 1.0 HG A:SER364 3.1 35.4 1.0 NE A:ARG366 3.1 25.0 1.0 HG3 A:ARG366 3.1 32.1 1.0 HG13 A:VAL379 3.2 37.7 0.3 HG13 A:VAL379 3.2 33.5 0.1 CD A:ARG366 3.2 26.3 1.0 HB2 A:PHE378 3.3 30.1 1.0 HG23 A:VAL379 3.3 36.1 0.5 HG22 A:VAL379 3.3 36.1 0.5 HA A:SER364 3.4 29.3 1.0 HB2 A:SER364 3.4 38.1 1.0 CG A:ASP227 3.4 29.5 1.0 HB3 A:ALA229 3.5 28.6 1.0 CG1 A:VAL379 3.5 31.2 0.3 CB A:SER364 3.6 31.6 1.0 CG A:ARG366 3.7 26.6 1.0 CG2 A:VAL379 3.8 30.0 0.5 HG11 A:VAL379 3.9 37.7 0.3 HB2 A:ALA229 3.9 28.6 1.0 HB2 A:ASP227 3.9 30.0 1.0 HG22 A:VAL379 3.9 33.0 0.1 C A:PHE378 3.9 26.4 1.0 H A:LEU365 4.0 35.6 1.0 CA A:SER364 4.0 24.2 1.0 OD1 A:ASP227 4.0 25.5 1.0 CB A:PHE378 4.1 25.0 1.0 H A:ALA229 4.1 29.2 1.0 O A:HOH794 4.1 44.8 1.0 CG1 A:VAL379 4.1 27.8 0.1 CB A:ALA229 4.1 23.7 1.0 HD3 A:ARG366 4.1 31.7 1.0 HB3 A:PHE378 4.2 30.1 1.0 HG21 A:VAL379 4.2 36.1 0.5 CB A:ASP227 4.3 24.9 1.0 HG11 A:VAL379 4.3 33.5 0.1 O A:HOH1032 4.3 38.5 1.0 CZ A:ARG366 4.3 26.1 1.0 HB2 A:ARG366 4.3 35.1 1.0 HH21 A:ARG366 4.3 32.9 1.0 H A:PHE378 4.4 29.1 1.0 HG2 A:ARG366 4.4 32.1 1.0 H A:ARG366 4.4 31.0 1.0 HB3 A:SER364 4.5 38.1 1.0 CA A:PHE378 4.6 22.9 1.0 N A:LEU365 4.6 29.5 1.0 HB3 A:ASP227 4.6 30.0 1.0 CB A:ARG366 4.6 29.1 1.0 HG12 A:VAL379 4.7 33.5 0.1 HB1 A:ALA229 4.7 28.6 1.0 HA A:VAL379 4.7 33.2 0.5 HA A:VAL379 4.7 33.2 0.3 NH2 A:ARG366 4.7 27.3 1.0 HA A:VAL379 4.7 33.3 0.1 CG2 A:VAL379 4.8 27.4 0.1 N A:VAL379 4.8 27.9 0.3 N A:VAL379 4.8 28.0 0.1 N A:VAL379 4.8 27.9 0.5 C A:SER364 4.8 27.5 1.0 CB A:VAL379 4.8 27.4 0.3 CB A:VAL379 4.9 26.9 0.1 N A:ALA229 4.9 24.2 1.0 N A:PHE378 4.9 24.1 1.0 N A:ARG366 5.0 25.7 1.0

Sodium binding site 4 out of 7 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 Sodium with other atoms in the Na binding site number 4 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:Na617 b:40.7 occ:1.00 HH22 A:ARG355 2.1 34.9 0.6 OD2 A:ASP389 2.7 39.9 1.0 NH2 A:ARG355 2.9 28.9 0.6 HH12 A:ARG355 3.0 40.5 0.6 HE3 A:MET392 3.4 43.5 1.0 HE2 A:MET392 3.4 43.5 1.0 HH21 A:ARG355 3.4 34.9 0.6 NH1 A:ARG355 3.6 33.6 0.6 CZ A:ARG355 3.7 32.8 0.6 CG A:ASP389 3.8 36.0 1.0 CE A:MET392 3.8 36.1 1.0 O A:HOH832 4.3 43.3 1.0 HE1 A:MET392 4.3 43.5 1.0 HH21 A:ARG355 4.4 44.1 0.4 HH11 A:ARG355 4.4 40.5 0.6 OD1 A:ASP389 4.4 36.0 1.0 HG2 A:MET392 4.5 37.8 1.0 HE A:ARG355 4.7 41.9 0.4 HB3 A:ASP389 4.7 38.1 1.0 NE A:ARG355 4.9 30.9 0.6 CB A:ASP389 4.9 31.6 1.0 HG3 A:MET392 5.0 37.8 1.0

Sodium binding site 5 out of 7 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 Sodium with other atoms in the Na binding site number 5 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:Na618 b:47.1 occ:1.00 OD2 A:ASP417 2.1 64.3 0.7 H A:ASP417 2.1 39.0 0.3 H A:ASP417 2.1 38.6 0.7 HB3 A:ASP417 2.6 44.7 0.3 O A:HOH849 2.7 45.7 1.0 N A:ASP417 3.0 32.4 0.3 N A:ASP417 3.0 32.0 0.7 CG A:ASP417 3.0 49.1 0.7 HB2 A:ASP417 3.1 45.2 0.7 HB3 A:PRO415 3.1 41.3 1.0 OD1 A:ASP417 3.1 42.1 0.3 O A:HOH710 3.2 56.1 1.0 CB A:ASP417 3.3 37.1 0.3 H A:PHE416 3.4 36.7 1.0 HB3 A:PHE416 3.4 39.8 1.0 CB A:ASP417 3.4 37.5 0.7 CG A:ASP417 3.5 38.2 0.3 N A:PHE416 3.6 30.5 1.0 CA A:ASP417 3.7 33.4 0.3 HA2 A:GLY100 3.7 52.1 1.0 CA A:ASP417 3.8 33.1 0.7 CB A:PRO415 3.8 34.3 1.0 HA3 A:GLY103 3.9 64.1 1.0 O A:PHE99 3.9 35.5 1.0 HB2 A:PRO415 3.9 41.3 1.0 C A:PRO415 3.9 32.6 1.0 C A:PHE416 3.9 29.3 1.0 OD1 A:ASP417 4.0 44.0 0.7 CA A:PHE416 4.1 29.4 1.0 HA A:PRO415 4.1 39.8 1.0 HB2 A:ASP417 4.2 44.7 0.3 CB A:PHE416 4.2 33.0 1.0 CA A:PRO415 4.2 33.0 1.0 HB3 A:PHE99 4.2 42.2 1.0 H A:LYS418 4.2 41.2 0.7 H A:LYS418 4.3 41.2 0.3 O A:HOH896 4.3 51.0 1.0 HB3 A:ASP417 4.4 45.2 0.7 HA A:ASP417 4.4 40.2 0.3 OD1 A:ASN380 4.4 29.2 1.0 C A:PHE99 4.4 35.7 1.0 H A:GLY103 4.5 60.4 1.0 HA A:ASP417 4.5 39.8 0.7 O A:HOH868 4.5 34.4 1.0 OD2 A:ASP417 4.5 43.1 0.3 HD2 A:PHE416 4.5 42.7 1.0 O A:PRO415 4.6 32.2 1.0 CA A:GLY100 4.6 43.3 1.0 HB2 A:PHE416 4.7 39.8 1.0 CA A:GLY103 4.7 53.3 1.0 N A:GLY100 4.8 31.7 1.0 C A:ASP417 4.8 34.3 0.3 N A:LYS418 4.8 34.2 1.0 C A:ASP417 4.8 34.1 0.7 HA2 A:GLY103 5.0 64.1 1.0

Sodium binding site 6 out of 7 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 Sodium with other atoms in the Na binding site number 6 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:Na619 b:43.4 occ:1.00 O A:HOH861 2.5 44.7 1.0 OD2 A:ASP295 2.7 42.4 1.0 O A:ASP295 2.8 31.0 1.0 O A:THR352 2.8 35.8 1.0 CG A:ASP295 3.2 44.0 1.0 O A:HOH720 3.3 53.6 1.0 HA A:THR352 3.4 34.6 1.0 HB3 A:ASP295 3.4 47.0 1.0 C A:THR352 3.6 29.5 1.0 OD1 A:ASP295 3.8 39.1 1.0 CB A:ASP295 3.9 39.0 1.0 C A:ASP295 3.9 30.1 1.0 CA A:THR352 4.0 28.7 1.0 HD3 A:PRO297 4.1 49.4 1.0 HB A:THR352 4.3 33.0 1.0 O A:HIS351 4.4 35.9 1.0 CA A:ASP295 4.6 37.5 1.0 O2 A:GOL613 4.6 59.0 1.0 HB2 A:ASP295 4.7 47.0 1.0 HG3 A:PRO297 4.7 47.3 1.0 HA3 A:GLY353 4.7 42.9 1.0 CB A:THR352 4.7 27.4 1.0 N A:GLY353 4.8 34.4 1.0 HA A:LEU296 4.8 37.0 1.0 CD A:PRO297 4.9 41.0 1.0 N A:PRO297 4.9 33.0 1.0

Sodium binding site 7 out of 7 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 Sodium with other atoms in the Na binding site number 7 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:Na620 b:29.0 occ:1.00 OE1 A:GLU494 2.7 36.3 1.0 O A:HOH942 2.9 46.1 1.0 CD A:GLU494 3.4 31.1 1.0 OE2 A:GLU494 3.6 39.4 1.0 O A:HOH841 3.8 31.8 1.0 HD13 A:LEU313 4.4 55.6 1.0 HD12 A:LEU313 4.6 55.6 1.0 CG A:GLU494 4.7 31.9 1.0 HG3 A:GLU494 4.8 38.4 1.0 CD1 A:LEU313 4.8 46.2 1.0 HD11 A:LEU313 4.9 55.6 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