Sodium in PDB 6wm5: Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii

The structure of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii, PDB code: 6wm5 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, New York Consortium Onmembrane Protein Structure (Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.338, 60.241, 85.377, 90.00, 90.91, 90.00
R / Rfree (%)	23.5 / 27.7

The binding sites of Sodium atom in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii (pdb code 6wm5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii, PDB code: 6wm5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:41.4 occ:1.00 OG1 A:THR82 2.4 24.4 1.0 OD1 A:ASP31 2.4 28.4 1.0 CG A:ASP31 3.3 19.1 1.0 CB A:THR82 3.5 30.6 1.0 OD2 A:ASP31 3.5 21.5 1.0 CG2 A:THR82 3.5 28.6 1.0 OG1 A:FLC301 3.7 38.4 1.0 N A:GLY85 3.8 18.8 1.0 O A:HOH435 3.9 24.9 1.0 CA A:GLY85 3.9 21.3 1.0 CD2 A:PHE84 4.2 19.2 1.0 N A:THR82 4.4 28.2 1.0 CA A:THR82 4.5 31.5 1.0 CB A:ASP31 4.7 18.8 1.0 CGC A:FLC301 4.7 38.3 1.0 C A:PHE84 4.8 15.7 1.0 CB A:PHE84 5.0 20.7 1.0

Sodium binding site 2 out of 7 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:21.8 occ:1.00 OD1 A:ASP89 2.4 30.9 1.0 OD1 A:ASP71 2.4 29.7 1.0 O A:ASP68 2.5 30.1 1.0 OG1 A:THR34 2.5 19.8 1.0 OD2 A:ASP68 2.5 30.7 1.0 CG A:ASP68 2.8 29.8 1.0 OD1 A:ASP68 3.0 36.4 1.0 CG A:ASP71 3.2 27.5 1.0 CG A:ASP89 3.3 25.9 1.0 CB A:THR34 3.3 18.4 1.0 NA A:NA304 3.4 24.9 1.0 C A:ASP68 3.4 23.7 1.0 CG2 A:THR34 3.5 15.0 1.0 CA A:THR34 3.6 15.2 1.0 CB A:ASP71 3.9 24.6 1.0 CB A:ASP68 4.0 22.3 1.0 CB A:ASP89 4.0 18.6 1.0 CA A:ASP68 4.0 23.2 1.0 OD2 A:ASP71 4.0 27.6 1.0 OD2 A:ASP89 4.1 31.9 1.0 CA A:ASP89 4.4 17.5 1.0 N A:THR34 4.5 15.9 1.0 N A:MET69 4.5 30.1 1.0 C A:THR34 4.7 20.0 1.0 CA A:MET69 4.7 29.0 1.0 N A:ASP71 4.8 22.5 1.0 O A:THR34 4.9 22.6 1.0 O A:HOH415 4.9 22.5 1.0 O A:HOH413 4.9 20.8 1.0

Sodium binding site 3 out of 7 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:24.9 occ:1.00 OD1 A:ASP89 2.4 30.9 1.0 OD1 A:ASP93 2.4 25.7 1.0 OD1 A:ASP68 2.5 36.4 1.0 O A:HOH415 2.6 22.5 1.0 O A:ASP89 2.6 16.2 1.0 OD2 A:ASP68 2.7 30.7 1.0 CG A:ASP68 2.9 29.8 1.0 CG A:ASP93 3.3 19.4 1.0 NA A:NA303 3.4 21.8 1.0 CG A:ASP89 3.4 25.9 1.0 C A:ASP89 3.5 15.8 1.0 N A:ASP93 3.7 14.3 1.0 CA A:ASP89 3.8 17.5 1.0 O A:HOH412 3.9 23.8 1.0 OD2 A:ASP93 3.9 26.2 1.0 O A:HOH401 4.0 21.7 1.0 CB A:CYS92 4.0 19.6 1.0 CA A:ASP93 4.2 13.8 1.0 CB A:ASP89 4.2 18.6 1.0 OD2 A:ASP89 4.2 31.9 1.0 C A:CYS92 4.2 17.1 1.0 CB A:ASP93 4.3 15.2 1.0 CB A:ASP68 4.3 22.3 1.0 CG2 A:THR34 4.4 15.0 1.0 OG1 A:THR38 4.5 17.0 1.0 CA A:CYS92 4.7 17.5 1.0 N A:ALA90 4.8 16.2 1.0 O A:ASP68 4.9 30.1 1.0 O A:CYS92 4.9 14.3 1.0

Sodium binding site 4 out of 7 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:38.5 occ:1.00 O A:ARG113 2.4 25.4 1.0 C A:ARG113 3.4 24.3 1.0 CG A:ARG115 3.6 25.5 1.0 N A:ARG115 3.7 23.3 1.0 CA A:ASP114 3.9 23.0 1.0 N A:ASP114 4.0 24.8 1.0 C A:ASP114 4.3 21.9 1.0 CB A:ARG115 4.3 25.3 1.0 CD A:ARG115 4.4 21.9 1.0 NE A:ARG115 4.5 28.3 1.0 CA A:ARG115 4.6 23.1 1.0 CA A:ARG113 4.6 21.9 1.0 CB A:ARG113 4.7 23.3 1.0

Sodium binding site 5 out of 7 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:43.0 occ:1.00 OG1 C:THR34 2.4 29.8 1.0 OD1 C:ASP89 2.4 37.9 1.0 O C:ASP68 2.5 45.2 1.0 OD2 C:ASP68 2.5 46.0 1.0 OD2 C:ASP71 2.6 40.4 1.0 CG C:ASP68 2.8 46.8 1.0 CG C:ASP71 2.8 46.2 1.0 OD1 C:ASP68 3.0 49.6 1.0 CB C:THR34 3.2 24.1 1.0 CG C:ASP89 3.3 32.2 1.0 CG2 C:THR34 3.3 21.5 1.0 OD1 C:ASP71 3.4 48.5 1.0 C C:ASP68 3.4 43.8 1.0 CA C:THR34 3.5 23.9 1.0 NA C:NA303 3.6 33.7 1.0 CB C:ASP71 3.6 39.9 1.0 CB C:ASP68 3.9 35.6 1.0 CA C:ASP68 3.9 43.3 1.0 CB C:ASP89 4.0 27.6 1.0 OD2 C:ASP89 4.2 39.3 1.0 O C:HOH412 4.4 34.8 1.0 N C:THR34 4.4 22.4 1.0 CA C:ASP89 4.4 26.2 1.0 N C:MET69 4.5 42.3 1.0 O C:HOH408 4.5 37.5 1.0 C C:THR34 4.6 22.6 1.0 O C:THR34 4.7 22.6 1.0 CA C:ASP71 4.8 30.0 1.0 CA C:MET69 4.8 35.2 1.0 N C:ASP71 4.9 32.2 1.0

Sodium binding site 6 out of 7 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:33.7 occ:1.00 OD1 C:ASP93 2.3 33.5 1.0 OD1 C:ASP89 2.4 37.9 1.0 OD2 C:ASP68 2.5 46.0 1.0 OD1 C:ASP68 2.6 49.6 1.0 O C:ASP89 2.7 19.1 1.0 CG C:ASP68 2.8 46.8 1.0 CG C:ASP93 3.2 30.3 1.0 O C:HOH424 3.3 34.3 1.0 CG C:ASP89 3.5 32.2 1.0 N C:ASP93 3.5 16.8 1.0 NA C:NA302 3.6 43.0 1.0 C C:ASP89 3.6 23.1 1.0 OD2 C:ASP93 3.8 26.3 1.0 CA C:ASP89 3.9 26.2 1.0 CB C:CYS92 3.9 14.4 1.0 CA C:ASP93 4.0 21.7 1.0 C C:CYS92 4.1 16.9 1.0 OG1 C:THR38 4.1 22.9 1.0 CB C:ASP93 4.1 22.1 1.0 OD2 C:ASP89 4.2 39.3 1.0 CB C:ASP89 4.3 27.6 1.0 CB C:ASP68 4.3 35.6 1.0 CG2 C:THR34 4.5 21.5 1.0 CA C:CYS92 4.5 18.9 1.0 O C:HOH416 4.6 32.0 1.0 O C:CYS92 4.7 19.6 1.0 N C:ALA90 4.8 22.2 1.0 N C:CYS92 5.0 13.0 1.0

Sodium binding site 7 out of 7 in the Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of A Phosphatidylinositol-Phosphate Synthase (Pips) From Mycobacterium Kansasii within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:37.4 occ:1.00 OG1 C:THR82 2.4 29.5 1.0 OG1 C:FLC301 2.7 38.6 1.0 N C:THR82 3.1 28.8 1.0 OD2 C:ASP31 3.2 33.5 1.0 CB C:THR82 3.4 29.3 1.0 CGC C:FLC301 3.5 45.2 1.0 CA C:GLY85 3.5 24.6 1.0 OG2 C:FLC301 3.5 51.0 1.0 OD1 C:ASP31 3.6 35.4 1.0 CG2 C:THR82 3.7 28.8 1.0 CG C:ASP31 3.8 28.9 1.0 CA C:THR82 3.8 32.8 1.0 N C:GLY85 3.9 29.3 1.0 C C:GLY81 3.9 36.1 1.0 CA C:GLY81 4.0 41.9 1.0 O C:HOH420 4.2 33.0 1.0 O C:THR82 4.2 32.7 1.0 C C:THR82 4.4 30.1 1.0 O C:HOH436 4.5 35.4 1.0 C C:GLY85 4.7 29.2 1.0 CG C:FLC301 4.9 49.2 1.0 O C:GLY81 4.9 46.7 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