Sodium in PDB 7noy: Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One

The structure of Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One, PDB code: 7noy was solved by L.Denkhaus, P.Sartor, O.Einsle, S.Gerhardt, S.Fetzner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.16 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.086, 70.086, 95.048, 90, 90, 120
R / Rfree (%)	18.3 / 21.8

The binding sites of Sodium atom in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One (pdb code 7noy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One, PDB code: 7noy:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One


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 Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:14.2 occ:1.00 O A:HOH552 2.3 12.3 1.0 O A:SER126 2.4 10.5 1.0 O A:HOH432 2.4 12.2 1.0 O A:HOH571 2.5 14.3 1.0 N7 A:SAH301 2.7 13.0 1.0 C8 A:SAH301 3.3 10.6 1.0 C A:SER126 3.5 13.1 1.0 CA A:MET127 3.8 10.6 1.0 C5 A:SAH301 3.9 12.7 1.0 N A:MET127 4.1 11.2 1.0 OD1 A:ASP8 4.1 21.8 1.0 O A:HOH595 4.2 14.2 1.0 CB A:MET127 4.3 13.3 1.0 N6 A:SAH301 4.3 12.4 1.0 CB A:LEU7 4.4 10.9 1.0 N A:LEU7 4.5 12.0 1.0 O A:HOH452 4.6 29.7 1.0 C6 A:SAH301 4.6 12.2 1.0 N9 A:SAH301 4.6 10.8 1.0 CE2 A:PHE11 4.7 13.0 1.0 CD A:PRO128 4.7 13.9 1.0 O A:HOH495 4.7 14.7 1.0 CA A:SER126 4.8 10.7 1.0 CG A:LEU7 4.8 16.0 1.0 CD2 A:LEU78 4.9 19.1 1.0 CB A:SER126 4.9 13.6 1.0 C4 A:SAH301 4.9 12.6 1.0 CA A:LEU7 4.9 11.2 1.0 CD2 A:PHE11 5.0 11.2 1.0 CD1 A:LEU7 5.0 16.4 1.0 C A:MET127 5.0 13.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One


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 Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:38.0 occ:1.00 O A:HOH408 2.3 21.8 1.0 O A:HOH490 2.5 36.2 1.0 O A:HOH472 2.5 27.5 1.0 O A:HOH588 2.6 41.1 1.0 O A:HOH424 2.7 29.8 1.0 O A:PRO187 3.8 15.8 1.0 OE1 A:GLU38 4.1 22.3 1.0 OE2 A:GLU38 4.2 16.5 1.0 NZ A:LYS186 4.4 31.1 1.0 O A:HOH652 4.4 51.4 1.0 CE A:LYS186 4.4 25.7 1.0 O A:HOH640 4.6 24.0 1.0 O A:HOH661 4.6 43.6 1.0 CD A:GLU38 4.6 23.0 1.0 CD A:LYS186 4.7 23.2 1.0 O A:HOH675 4.7 32.0 1.0 C A:PRO187 5.0 15.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One


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 Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis in Complex with Substrate 1- Hydroxyquinolin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:33.0 occ:1.00 O A:GLY162 2.3 16.7 1.0 O A:HOH535 2.4 26.5 1.0 OD1 A:ASN165 2.8 18.8 1.0 C A:GLY162 3.5 17.5 1.0 CG A:ASN165 3.5 18.9 1.0 O A:HOH549 3.5 20.4 1.0 ND2 A:ASN165 3.5 14.5 1.0 O A:HOH544 4.2 19.1 1.0 O A:HOH616 4.2 53.5 1.0 O A:HOH482 4.3 17.8 1.0 N A:GLY162 4.3 16.8 1.0 CA A:GLY162 4.3 16.0 1.0 C A:PRO163 4.4 14.6 1.0 O A:PRO163 4.4 14.5 1.0 N A:PRO163 4.4 13.2 1.0 CA A:PRO163 4.4 12.4 1.0 O A:HOH625 4.4 95.8 1.0 O A:HOH638 4.5 37.0 1.0 O A:ILE164 4.8 15.4 1.0 CB A:ASN165 4.9 10.8 1.0 N A:ILE164 4.9 11.4 1.0 C A:ILE164 4.9 14.3 1.0

P.Sartor, L.Denkhaus, S.Gerhardt, O.Einsle, S.Fetzner. Structural Basis of O-Methylation of (2-Heptyl-)1-Hydroxyquinolin-4(1H)-One and Related Compounds By the Heterocyclic Toxin Methyltransferase RV0560C of Mycobacterium Tuberculosis J.Struct.Biol. 07794 2021.
ISSN: ESSN 1095-8657
DOI: 10.1016/J.JSB.2021.107794