Sodium in PDB 6wmv: Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding

The structure of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding, PDB code: 6wmv was solved by M.Belcher Dufrisne, C.D.Jorge, C.G.Timoteo, V.I.Petrou, K.U.Ashraf, S.Banerjee, O.B.Clarke, H.Santos, F.Mancia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.08 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.089, 60.857, 85.417, 90.00, 90.74, 90.00
R / Rfree (%)	22.3 / 27

The binding sites of Sodium atom in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding (pdb code 6wmv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding, PDB code: 6wmv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:53.3 occ:1.00 OG1 A:THR82 2.4 35.6 1.0 OD1 A:ASP31 2.4 41.7 1.0 O16 A:TCE305 2.8 58.7 1.0 CG A:ASP31 3.1 34.0 1.0 OD2 A:ASP31 3.1 33.7 1.0 CB A:THR82 3.6 38.6 1.0 CG2 A:THR82 3.7 34.9 1.0 CA A:GLY85 3.7 24.6 1.0 N A:GLY85 3.8 31.4 1.0 C14 A:TCE305 3.8 58.3 1.0 O15 A:TCE305 4.2 54.2 1.0 N A:THR82 4.4 37.9 1.0 CA A:THR82 4.5 37.4 1.0 CB A:ASP31 4.6 31.1 1.0 CD2 A:PHE84 4.6 27.9 1.0 C A:PHE84 4.9 27.3 1.0

Sodium binding site 2 out of 4 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:43.6 occ:1.00 OD1 A:ASP68 2.4 42.8 1.0 CG A:ASP71 2.4 52.1 1.0 O A:ASP68 2.4 42.5 1.0 OD1 A:ASP89 2.5 48.2 1.0 OD1 A:ASP71 2.5 59.5 1.0 OD2 A:ASP71 2.5 45.6 1.0 OG1 A:THR34 2.6 36.9 1.0 CG A:ASP89 3.0 43.9 1.0 CB A:ASP71 3.4 41.4 1.0 C A:ASP68 3.5 39.7 1.0 CG A:ASP68 3.5 41.5 1.0 OD2 A:ASP89 3.5 53.7 1.0 CB A:THR34 3.5 25.8 1.0 CG2 A:THR34 3.8 30.9 1.0 CB A:ASP89 3.8 31.3 1.0 CA A:THR34 3.9 26.5 1.0 NA A:NA304 4.0 45.6 1.0 CA A:ASP68 4.2 30.4 1.0 OD2 A:ASP68 4.2 45.0 1.0 N A:ASP71 4.3 43.1 1.0 N A:MET69 4.4 45.4 1.0 CA A:ASP71 4.4 39.0 1.0 CA A:ASP89 4.4 28.8 1.0 CB A:ASP68 4.4 33.3 1.0 N A:THR34 4.5 21.8 1.0 CA A:MET69 4.5 40.2 1.0 C A:MET69 4.9 35.7 1.0

Sodium binding site 3 out of 4 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:45.6 occ:1.00 OD1 A:ASP93 2.3 39.3 1.0 OD1 A:ASP89 2.4 48.2 1.0 OD1 A:ASP68 2.5 42.8 1.0 OD2 A:ASP68 2.5 45.0 1.0 O A:ASP89 2.7 38.2 1.0 CG A:ASP68 2.8 41.5 1.0 CG A:ASP93 3.4 36.4 1.0 N A:ASP93 3.5 29.7 1.0 CG A:ASP89 3.5 43.9 1.0 C A:ASP89 3.6 32.8 1.0 CB A:CYS92 3.6 33.8 1.0 CA A:ASP89 3.8 28.8 1.0 C A:CYS92 3.9 27.5 1.0 OG1 A:THR38 4.0 29.2 1.0 NA A:NA303 4.0 43.6 1.0 CA A:ASP93 4.0 31.6 1.0 CG2 A:THR34 4.1 30.9 1.0 CB A:ASP68 4.1 33.3 1.0 OD2 A:ASP93 4.2 43.8 1.0 CB A:ASP89 4.3 31.3 1.0 CB A:ASP93 4.3 33.8 1.0 CA A:CYS92 4.3 26.6 1.0 OD2 A:ASP89 4.4 53.7 1.0 O A:HOH401 4.5 39.4 1.0 O A:CYS92 4.6 33.4 1.0 N A:CYS92 4.8 32.4 1.0 N A:ALA90 4.8 30.4 1.0 NH1 A:ARG152 4.9 43.3 1.0 O A:LEU88 4.9 36.6 1.0

Sodium binding site 4 out of 4 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii with Evidence of Substrate Binding within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:54.6 occ:1.00 OD2 C:ASP68 2.4 62.3 1.0 OD1 C:ASP68 2.4 66.0 1.0 OD1 C:ASP93 2.5 45.9 1.0 OD1 C:ASP89 2.5 66.5 1.0 CG C:ASP68 2.6 60.6 1.0 O C:ASP89 3.3 40.4 1.0 CG C:ASP93 3.6 39.7 1.0 CG C:ASP89 3.7 47.8 1.0 OG1 C:THR38 3.8 39.6 1.0 N C:ASP93 3.9 29.8 1.0 CB C:CYS92 3.9 34.0 1.0 CB C:ASP68 4.0 54.9 1.0 C C:ASP89 4.1 32.9 1.0 CA C:ASP89 4.1 35.3 1.0 CG2 C:THR34 4.1 36.1 1.0 C C:CYS92 4.3 29.7 1.0 OD2 C:ASP93 4.4 44.4 1.0 CA C:ASP93 4.4 31.1 1.0 CB C:ASP89 4.5 39.4 1.0 OD2 C:ASP89 4.6 50.6 1.0 CB C:ASP93 4.6 37.1 1.0 CA C:CYS92 4.7 33.0 1.0 O C:CYS92 4.9 37.8 1.0

M.Belcher Dufrisne, C.D.Jorge, C.G.Timoteo, V.I.Petrou, K.U.Ashraf, S.Banerjee, O.B.Clarke, H.Santos, F.Mancia. Structural and Functional Characterization of Phosphatidylinositol-Phosphate Biosynthesis in Mycobacteria. J.Mol.Biol. 2020.
ISSN: ESSN 1089-8638
PubMed: 32389689
DOI: 10.1016/J.JMB.2020.04.028