Sodium in PDB 4u89: 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis

The structure of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis, PDB code: 4u89 was solved by A.Faille, L.Mourey, J.D.Pedelacq, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.32 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.808, 121.263, 48.828, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 16.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis (pdb code 4u89). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis, PDB code: 4u89:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:21.7 occ:1.00 OD2 A:ASP137 2.6 21.2 1.0 O A:HOH513 2.8 15.9 1.0 N A:PHE180 3.0 11.6 1.0 OG1 A:THR141 3.0 19.1 1.0 CG A:ASP137 3.5 15.6 1.0 CA A:THR179 3.7 11.6 0.5 O A:PHE180 3.7 15.1 1.0 CA A:THR179 3.7 11.1 0.5 CG2 A:THR141 3.8 20.2 1.0 CB A:ASP137 3.8 16.6 1.0 CG2 A:THR179 3.8 15.1 0.5 CB A:PHE180 3.8 13.3 1.0 CA A:PHE180 3.8 11.4 1.0 C A:THR179 3.8 10.4 1.0 SD A:MET138 3.8 15.4 0.7 CB A:THR141 3.9 16.6 1.0 O A:ASP137 3.9 16.2 1.0 C A:ASP137 4.0 14.7 1.0 CB A:THR179 4.1 12.5 0.5 CG A:MET138 4.1 21.2 0.3 N A:MET138 4.1 16.9 1.0 C A:PHE180 4.2 12.3 1.0 CA A:MET138 4.2 16.3 0.3 CA A:MET138 4.2 16.0 0.7 CD2 A:PHE180 4.3 15.3 1.0 CB A:THR179 4.4 12.7 0.5 O A:HOH494 4.4 29.4 1.0 CG2 A:THR179 4.4 14.0 0.5 CG A:PHE180 4.5 12.3 1.0 O A:ILE178 4.6 12.9 1.0 OD1 A:ASP137 4.6 18.8 1.0 CA A:ASP137 4.7 17.0 1.0 CG A:MET138 4.7 16.5 0.7 CB A:MET138 4.9 15.7 0.3 N A:THR179 4.9 11.8 1.0

Sodium binding site 2 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:33.8 occ:1.00 OG1 A:THR179 2.7 14.0 0.5 O A:HOH431 2.8 38.8 1.0 O A:HIS177 2.8 12.9 1.0 OG1 A:THR179 3.1 14.4 0.5 O A:HOH430 3.2 41.2 1.0 O A:VAL192 3.4 13.3 1.0 CG2 A:THR179 3.4 14.0 0.5 CB A:THR179 3.6 12.7 0.5 N A:THR179 3.6 11.8 1.0 CB A:ARG194 3.7 14.0 1.0 C A:HIS177 3.7 12.0 1.0 CB A:THR179 3.8 12.5 0.5 NE A:ARG194 3.8 24.9 1.0 NH2 A:ARG194 4.0 32.9 1.0 CG2 A:VAL192 4.0 8.6 0.2 N A:ARG194 4.1 12.1 1.0 C A:ILE178 4.1 11.7 1.0 CD2 A:HIS177 4.2 14.9 1.0 CA A:ILE178 4.2 10.1 1.0 CG A:HIS177 4.2 12.8 1.0 CA A:THR179 4.2 11.1 0.5 N A:ILE178 4.3 11.2 1.0 CZ A:ARG194 4.3 24.6 1.0 CA A:THR179 4.3 11.6 0.5 C A:VAL192 4.4 12.1 1.0 CB A:HIS177 4.4 14.0 1.0 CA A:ARG194 4.5 12.1 1.0 CA A:HIS177 4.7 11.9 1.0 CB A:VAL192 4.7 16.1 0.8 CD A:ARG194 4.7 24.1 1.0 NE2 A:HIS177 4.7 16.8 1.0 ND1 A:HIS177 4.8 18.0 1.0 CG1 A:VAL192 4.8 18.5 0.8 CG A:ARG194 4.8 20.3 1.0 CG2 A:THR179 4.9 15.1 0.5 C A:SER193 4.9 12.0 1.0 CA A:SER193 4.9 11.1 0.2 O A:ILE178 4.9 12.9 1.0 CB A:VAL192 5.0 11.8 0.2

Sodium binding site 3 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:28.7 occ:1.00 O A:HOH540 2.7 26.4 1.0 O A:HOH616 2.8 38.3 1.0 N A:LEU74 2.9 13.7 1.0 O A:CYS82 3.5 17.6 1.0 CG A:LEU74 3.5 20.0 1.0 O A:PRO72 3.6 16.0 1.0 CB A:LEU74 3.6 17.6 1.0 CB A:CYS82 3.7 17.0 1.0 CA A:ILE73 3.8 14.0 1.0 C A:ILE73 3.8 12.1 1.0 CA A:LEU74 3.8 13.3 1.0 O A:HOH630 3.9 43.2 1.0 CD1 A:LEU74 4.2 26.6 1.0 O A:HOH671 4.2 30.7 1.0 C A:PRO72 4.3 13.1 1.0 O A:HOH584 4.3 44.7 1.0 N A:ILE73 4.4 13.5 1.0 C A:CYS82 4.4 15.2 1.0 CD2 A:LEU74 4.6 22.7 1.0 CA A:CYS82 4.6 16.1 1.0 C A:LEU74 4.7 13.1 1.0 SG A:CYS82 4.9 24.5 1.0 O A:LEU74 4.9 13.9 1.0

Sodium binding site 4 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:27.9 occ:1.00 O A:HOH666 2.7 37.6 1.0 O A:HOH650 2.8 28.9 1.0 O A:HOH543 2.9 26.6 1.0 N A:TYR25 2.9 14.0 1.0 CD2 A:TYR25 3.7 16.6 1.0 CA A:LEU24 3.8 13.2 1.0 CD2 A:LEU24 3.8 14.7 1.0 CA A:TYR25 3.8 14.4 1.0 C A:LEU24 3.8 14.0 1.0 CB A:LEU24 3.9 14.1 1.0 N A:SER26 3.9 16.3 1.0 CB A:TYR25 3.9 15.9 1.0 OG A:SER26 4.0 23.1 1.0 CG A:TYR25 4.1 14.0 1.0 C A:TYR25 4.2 14.6 1.0 CG A:LEU24 4.5 13.9 1.0 O A:HOH652 4.6 44.3 1.0 O A:SER26 4.6 21.2 1.0 CE2 A:TYR25 4.6 20.1 1.0 O A:HOH611 4.7 40.5 1.0 O A:HOH538 4.9 26.0 1.0 CB A:SER26 4.9 19.6 1.0 CA A:SER26 4.9 16.4 1.0

Sodium binding site 5 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:22.2 occ:1.00 O A:HOH486 2.7 17.2 1.0 O A:HOH487 2.8 23.8 1.0 N A:ALA95 2.9 13.1 1.0 CB A:ALA95 3.5 16.8 1.0 CB A:CYS94 3.7 10.7 1.0 CD A:PRO117 3.8 12.1 1.0 CA A:ALA95 3.8 15.0 1.0 C A:CYS94 3.8 11.8 1.0 CG A:PRO117 3.9 14.5 1.0 CA A:CYS94 3.9 11.1 1.0 O A:HOH490 4.2 35.9 1.0 O A:HOH437 4.3 16.5 1.0 CB A:PRO117 4.7 13.4 1.0 O A:HOH455 4.8 32.8 1.0 SG A:CYS94 4.8 13.1 1.0 O A:HOH439 4.9 19.9 1.0 O A:HOH480 4.9 32.5 1.0 C A:ALA95 5.0 12.4 1.0 N A:PRO117 5.0 11.3 1.0

Sodium binding site 6 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:40.5 occ:1.00 O A:HOH556 2.6 27.6 1.0 O A:HOH571 2.7 34.4 1.0 O A:HOH417 2.8 23.6 1.0 CD1 A:LEU196 4.2 17.6 1.0 O A:HOH525 4.4 25.1 1.0 ND1 A:HIS177 4.6 18.0 1.0 O A:HOH496 4.7 20.0 1.0 CD2 A:LEU196 4.8 16.8 1.0 O A:HOH534 5.0 25.7 1.0 CD1 A:LEU131 5.0 23.9 1.0

Sodium binding site 7 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:29.4 occ:1.00 O A:HOH507 2.5 23.6 1.0 O A:HOH663 2.7 33.5 1.0 O A:HOH500 2.8 13.3 1.0 NE1 A:TRP83 2.9 13.2 1.0 O A:GLY89 3.2 11.3 1.0 CG A:PRO165 3.4 18.0 1.0 CD1 A:TRP83 3.5 12.8 1.0 O A:HOH664 3.5 32.6 1.0 CG A:PRO81 4.0 17.5 1.0 CE2 A:TRP83 4.1 12.1 1.0 CD A:PRO81 4.1 14.0 1.0 CB A:PRO165 4.2 16.6 1.0 O A:PRO81 4.2 17.5 1.0 O A:HOH503 4.2 13.3 1.0 C A:GLY89 4.3 9.9 1.0 N A:GLY89 4.6 10.6 1.0 C2A A:COA301 4.7 13.2 1.0 CZ2 A:TRP83 4.7 14.1 1.0 OE2 A:GLU80 4.8 40.4 1.0 CD A:PRO165 4.8 14.5 1.0 CG A:TRP83 4.8 12.6 1.0 N A:PRO81 4.8 13.0 1.0 N3A A:COA301 4.9 11.6 1.0 CB A:GLU80 5.0 16.5 1.0 O A:LYS161 5.0 12.1 1.0

Sodium binding site 8 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:46.0 occ:1.00 C2 A:PG4314 2.9 38.6 1.0 O4 A:PG4314 3.2 43.5 1.0 O3 A:PG4314 3.2 48.9 1.0 O A:HOH577 3.5 50.3 1.0 O1 A:PG4314 3.5 54.0 1.0 C1 A:PG4314 3.6 41.8 1.0 CA A:PRO143 3.7 19.7 1.0 O2 A:PG4314 3.7 61.5 1.0 C6 A:PG4314 3.7 34.3 1.0 C5 A:PG4314 3.8 43.6 1.0 CB A:PRO143 3.8 22.6 1.0 C3 A:PG4314 3.9 54.2 1.0 CG A:PRO143 3.9 25.7 1.0 C7 A:PG4314 3.9 54.1 1.0 C4 A:PG4314 4.0 55.8 1.0 O5 A:PG4314 4.2 62.6 1.0 N A:PRO143 4.2 18.6 1.0 CD A:PRO143 4.5 24.4 1.0 C8 A:PG4314 4.7 92.7 1.0 C A:MET142 4.8 15.7 1.0 C A:PRO143 5.0 17.4 1.0 O A:MET142 5.0 20.3 1.0

Sodium binding site 9 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:37.6 occ:1.00 O A:HOH473 3.1 40.3 1.0 NH2 A:ARG190 3.7 28.2 1.0 O A:HOH407 4.6 30.3 1.0 CZ A:ARG190 4.8 24.7 1.0

Sodium binding site 10 out of 11 in the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na311 b:37.3 occ:1.00 O A:GLU17 2.7 14.8 1.0 O A:HOH435 2.7 27.9 1.0 O A:HOH444 2.9 27.4 1.0 C A:GLU17 3.6 12.3 1.0 CA A:GLU17 3.9 17.8 1.0 CB A:GLU17 4.3 24.0 1.0 NH1 A:ARG104 4.4 18.8 1.0 CD2 A:LEU66 4.5 22.0 1.0 NH2 A:ARG104 4.6 20.8 1.0 O A:LEU19 4.8 11.9 1.0 N A:ASP18 4.8 12.1 1.0 O A:HOH453 4.9 38.8 1.0 CZ A:ARG104 5.0 18.6 1.0

A.Faille, S.Gavalda, K.Rottier, L.Mourey, J.D.Pedelacq. X-Ray Structure of the 4'-Phosphopantetheinyl Transferase Pptt From Mycobacterium Tuberculosis To Be Published.