Sodium in PDB 5vyq: Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid

The structure of Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid, PDB code: 5vyq was solved by M.M.Dunsirn, J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.486, 73.018, 173.265, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20

The structure of Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid (pdb code 5vyq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid, PDB code: 5vyq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid


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 N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:14.7 occ:1.00 O A:HOH615 2.2 24.6 1.0 O A:HOH480 2.2 16.4 1.0 O A:TYR56 2.3 13.5 1.0 O A:VAL53 2.4 15.4 1.0 O A:HOH434 2.4 21.0 1.0 C A:TYR56 3.5 12.4 1.0 C A:VAL53 3.5 15.7 1.0 O A:HOH672 3.9 22.8 1.0 O A:GLU54 4.0 20.7 1.0 CG2 A:VAL76 4.1 14.3 1.0 N A:TYR56 4.3 12.2 1.0 C A:GLU54 4.3 18.4 1.0 N A:ASP57 4.3 12.1 1.0 CA A:ASP57 4.4 11.2 1.0 CA A:VAL53 4.4 13.8 1.0 CA A:TYR56 4.5 11.3 1.0 CB A:VAL76 4.5 11.3 1.0 N A:GLU54 4.5 16.1 1.0 OD1 A:ASP57 4.5 15.3 1.0 CA A:GLU54 4.6 19.7 1.0 O A:GLY75 4.6 14.2 1.0 O A:ILE52 4.7 12.1 1.0 CG1 A:VAL53 4.8 15.8 1.0 N A:ARG55 4.9 16.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid


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 N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:25.3 occ:1.00 O A:HOH614 2.1 36.0 1.0 O A:HOH625 2.4 31.2 1.0 O A:MET1 2.5 26.9 1.0 OD2 A:ASP57 2.6 15.2 1.0 OG1 A:THR3 2.6 15.6 1.0 O A:HOH630 2.6 33.4 1.0 O A:HOH626 3.5 34.7 1.0 CB A:THR3 3.6 15.1 1.0 CG A:ASP57 3.6 13.3 1.0 C A:MET1 3.6 25.6 1.0 N A:THR3 3.7 14.3 1.0 O A:HOH645 4.0 39.9 1.0 OD1 A:ASP57 4.0 15.3 1.0 CA A:THR3 4.3 13.4 1.0 O A:HOH643 4.3 39.4 1.0 C A:VAL2 4.4 15.0 1.0 O A:HOH428 4.4 25.0 1.0 CA A:VAL2 4.4 18.4 1.0 N A:VAL2 4.5 20.6 1.0 OD2 A:ASP26 4.5 22.9 1.0 CA A:MET1 4.5 33.5 1.0 CG2 A:THR3 4.8 15.7 1.0 CB A:MET1 4.9 39.3 1.0 CB A:ASP57 4.9 12.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid


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 N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:32.9 occ:1.00 OH A:TYR30 2.6 20.8 1.0 CZ A:TYR30 3.6 17.8 1.0 CE2 A:TYR30 3.7 19.4 1.0 O A:HOH508 3.8 29.6 1.0 O A:HOH402 4.2 27.5 1.0 CE1 A:TYR30 4.9 17.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid


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 N-Formyltransferase RV3404C From Mycobacterium Tuberculosis in Complex with Ydp-QUI4N and Folinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:22.9 occ:1.00 O B:HOH535 2.1 25.8 1.0 O B:HOH586 2.3 27.9 1.0 O B:HOH422 2.4 32.8 1.0 O B:VAL53 2.4 20.6 1.0 O B:TYR56 2.5 13.7 1.0 O B:HOH619 2.5 30.6 1.0 C B:TYR56 3.5 13.9 1.0 C B:VAL53 3.6 18.1 1.0 OD1 B:ASP57 4.1 16.5 1.0 O B:HOH705 4.1 37.4 1.0 O B:HOH701 4.2 43.0 1.0 N B:ASP57 4.3 11.8 1.0 N B:TYR56 4.3 15.1 1.0 O B:GLU54 4.3 22.3 1.0 CA B:ASP57 4.3 12.4 1.0 CA B:VAL53 4.4 17.9 1.0 C B:GLU54 4.5 20.5 1.0 CA B:TYR56 4.6 14.1 1.0 N B:GLU54 4.6 21.4 1.0 O B:HOH446 4.6 29.0 1.0 CG1 B:VAL53 4.6 20.8 1.0 O B:GLY75 4.6 14.1 1.0 CA B:GLU54 4.7 22.2 1.0 CG2 B:VAL76 4.7 16.1 1.0 O B:HOH443 4.7 31.6 1.0 O B:ILE52 4.9 14.9 1.0 CG B:ASP57 4.9 15.6 1.0 C B:ARG55 4.9 17.7 1.0 CB B:VAL76 5.0 14.1 1.0

M.M.Dunsirn, J.B.Thoden, M.Gilbert, H.M.Holden. Biochemical Investigation of RV3404C From Mycobacterium Tuberculosis. Biochemistry V. 56 3818 2017.
ISSN: ISSN 1520-4995
PubMed: 28665588
DOI: 10.1021/ACS.BIOCHEM.7B00506