Sodium in PDB 7nmk: Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Methylation Product 1- Methoxyquinolin-4(1H)-One

The structure of Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Methylation Product 1- Methoxyquinolin-4(1H)-One, PDB code: 7nmk 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)	17.47 / 1.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.866, 69.866, 95.644, 90, 90, 120
R / Rfree (%)	16.9 / 18.7

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

Sodium binding site 1 out of 2 in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Methylation Product 1- Methoxyquinolin-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 with Bound Methylation Product 1- Methoxyquinolin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:14.5 occ:1.00 O A:SER126 2.5 11.8 1.0 O A:HOH581 2.5 15.8 1.0 O A:HOH452 2.5 14.6 1.0 O A:HOH577 2.5 14.9 1.0 N7 A:SAH301 2.6 11.4 1.0 C8 A:SAH301 3.3 11.5 1.0 C A:SER126 3.6 10.4 1.0 CA A:MET127 3.8 10.1 0.7 CA A:MET127 3.8 9.6 0.3 C5 A:SAH301 3.9 11.1 1.0 N A:MET127 4.1 9.6 1.0 CG A:MET127 4.2 13.1 0.3 O A:HOH425 4.2 25.9 1.0 O A:HOH631 4.2 13.7 1.0 OD1 A:ASP8 4.3 16.9 1.0 CB A:MET127 4.3 11.1 0.7 N6 A:SAH301 4.4 13.6 1.0 CB A:MET127 4.5 11.3 0.3 CB A:LEU7 4.5 12.1 1.0 O A:HOH607 4.5 19.0 0.5 N9 A:SAH301 4.6 10.3 1.0 C6 A:SAH301 4.6 12.1 1.0 CE2 A:PHE11 4.6 11.2 1.0 CD A:PRO128 4.6 13.3 1.0 N A:LEU7 4.7 12.8 1.0 O A:HOH549 4.8 12.8 1.0 CA A:SER126 4.8 9.2 1.0 C4 A:SAH301 4.9 10.3 1.0 CD2 A:PHE11 4.9 10.8 1.0 CD1 A:LEU7 4.9 15.6 1.0 C A:MET127 4.9 12.2 1.0 CD2 A:LEU78 4.9 17.1 1.0 CG A:LEU7 4.9 15.0 1.0 CB A:SER126 5.0 12.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Methylation Product 1- Methoxyquinolin-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 with Bound Methylation Product 1- Methoxyquinolin-4(1H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:28.5 occ:1.00 O A:HOH443 2.4 18.6 1.0 O A:HOH653 2.4 36.5 1.0 O A:HOH515 2.4 31.0 1.0 O A:HOH727 2.4 38.7 1.0 O A:HOH521 2.5 20.4 1.0 O A:HOH446 2.6 23.9 1.0 O A:PRO187 3.9 14.1 1.0 O A:HOH686 4.2 33.2 1.0 OE1 A:GLU38 4.3 15.7 1.0 NZ A:LYS186 4.3 22.9 1.0 OE2 A:GLU38 4.4 14.7 1.0 CE A:LYS186 4.5 19.8 1.0 CD A:LYS186 4.5 18.0 1.0 O A:HOH717 4.6 35.8 1.0 O A:HOH671 4.6 21.7 1.0 CD A:GLU38 4.8 14.7 1.0 O A:HOH641 4.8 30.2 1.0 C A:PRO187 5.0 14.8 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