Sodium in PDB 7ndm: Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Substrate 4-Hydroxyisoquinolin- 1(2H)-One

The structure of Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Substrate 4-Hydroxyisoquinolin- 1(2H)-One, PDB code: 7ndm 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)	19.08 / 1.35
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.337, 70.337, 97.885, 90, 90, 120
R / Rfree (%)	16.6 / 18.7

The binding sites of Sodium atom in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Substrate 4-Hydroxyisoquinolin- 1(2H)-One (pdb code 7ndm). 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 with Bound Substrate 4-Hydroxyisoquinolin- 1(2H)-One, PDB code: 7ndm:
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 with Bound Substrate 4-Hydroxyisoquinolin- 1(2H)-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 Substrate 4-Hydroxyisoquinolin- 1(2H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:13.6 occ:1.00 O A:SER126 2.4 11.6 1.0 O A:HOH536 2.5 12.3 1.0 O A:HOH603 2.5 12.0 1.0 O A:HOH595 2.6 15.7 1.0 N7 A:SAH301 2.6 11.2 1.0 C8 A:SAH301 3.2 9.2 1.0 C A:SER126 3.5 11.2 1.0 CA A:MET127 3.7 9.1 1.0 C5 A:SAH301 3.8 10.9 1.0 N A:MET127 4.1 9.5 1.0 O A:HOH421 4.1 16.7 1.0 CB A:MET127 4.2 11.9 1.0 O A:HOH626 4.2 11.3 1.0 OD1 A:ASP8 4.3 13.4 1.0 N6 A:SAH301 4.4 11.3 1.0 CB A:LEU7 4.5 8.8 1.0 N9 A:SAH301 4.5 9.4 1.0 C6 A:SAH301 4.6 10.6 1.0 CE2 A:PHE11 4.6 9.4 1.0 O A:HOH538 4.6 19.2 1.0 CD A:PRO128 4.7 12.3 1.0 N A:LEU7 4.7 10.3 1.0 CA A:SER126 4.8 9.3 1.0 O A:HOH540 4.8 12.4 1.0 C4 A:SAH301 4.8 9.5 1.0 CB A:SER126 4.9 11.5 1.0 C A:MET127 4.9 11.8 1.0 CD2 A:PHE11 4.9 9.3 1.0 CG A:LEU7 5.0 13.0 1.0 CD2 A:LEU78 5.0 15.7 1.0 CD1 A:LEU7 5.0 12.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Substrate 4-Hydroxyisoquinolin- 1(2H)-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 Substrate 4-Hydroxyisoquinolin- 1(2H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:26.1 occ:1.00 O A:HOH727 2.3 35.0 1.0 O A:HOH505 2.4 17.4 1.0 O A:HOH545 2.4 32.2 1.0 O A:HOH646 2.4 26.5 1.0 O A:HOH444 2.5 22.9 1.0 O A:HOH487 2.7 19.5 1.0 O A:PRO187 4.0 12.3 1.0 OE1 A:GLU38 4.2 14.2 1.0 O A:HOH697 4.3 31.1 1.0 NZ A:LYS186 4.3 18.7 1.0 OE2 A:GLU38 4.3 12.2 1.0 CE A:LYS186 4.5 16.4 1.0 O A:HOH660 4.6 21.5 1.0 CD A:LYS186 4.7 16.8 1.0 CD A:GLU38 4.7 15.8 1.0 O A:HOH715 4.9 29.8 1.0 O A:HOH643 4.9 22.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Heterocyclic Toxin Methyltransferase From Mycobacterium Tuberculosis with Bound Substrate 4-Hydroxyisoquinolin- 1(2H)-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 with Bound Substrate 4-Hydroxyisoquinolin- 1(2H)-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:9.4 occ:1.00 O A:HOH680 2.9 43.6 1.0 CE1 A:HIS71 3.0 12.1 1.0 O A:HOH477 3.2 10.8 1.0 NE A:ARG69 3.2 13.6 1.0 NH2 A:ARG69 3.3 14.8 1.0 O A:HOH642 3.3 24.0 1.0 O A:HOH629 3.6 40.6 1.0 CZ A:ARG69 3.7 20.2 1.0 ND1 A:HIS71 3.9 15.0 1.0 CG2 A:ILE43 4.0 11.9 1.0 NE2 A:HIS71 4.0 13.8 1.0 O A:PHE48 4.1 14.0 1.0 CB A:ARG69 4.2 10.6 1.0 O A:HOH640 4.2 49.3 1.0 CD A:ARG69 4.4 11.6 1.0 CD2 A:LEU66 4.4 10.3 1.0 O A:ILE43 4.4 10.8 1.0 O A:HOH512 4.6 18.8 1.0 O A:ARG69 4.6 19.9 1.0 CB A:PHE48 4.9 10.7 1.0 CG A:ARG69 4.9 12.7 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