Manganese in PDB 4lr7: Phosphopentomutase S154A Variant

All present enzymatic activity of Phosphopentomutase S154A Variant:
5.4.2.7;

The structure of Phosphopentomutase S154A Variant, PDB code: 4lr7 was solved by W.A.Birmingham, C.A.Starbird, T.D.Panosian, D.P.Nannemann, T.M.Iverson, B.O.Bachmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.245, 76.354, 108.099, 90.00, 108.96, 90.00
R / Rfree (%)	16.5 / 20.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese atom in the Phosphopentomutase S154A Variant (pdb code 4lr7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 14 binding sites of Manganese where determined in the Phosphopentomutase S154A Variant, PDB code: 4lr7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:14.3 occ:1.00 O1P A:TPO85 2.0 26.6 0.3 OD2 A:ASP156 2.1 26.2 1.0 NE2 A:HIS339 2.1 14.0 1.0 OD1 A:ASP286 2.1 15.6 1.0 NE2 A:HIS291 2.2 15.1 1.0 OD2 A:ASP286 2.7 14.4 1.0 CG A:ASP286 2.7 14.8 1.0 CG A:ASP156 2.9 26.9 1.0 CE1 A:HIS339 3.0 14.1 1.0 CD2 A:HIS291 3.1 15.7 1.0 OD1 A:ASP156 3.1 28.9 1.0 CD2 A:HIS339 3.1 14.6 1.0 CE1 A:HIS291 3.1 15.9 1.0 P A:TPO85 3.3 25.6 0.3 O3P A:TPO85 3.9 24.8 0.3 O A:HOH737 3.9 23.6 1.0 O2P A:TPO85 4.0 27.5 0.3 ND1 A:HIS339 4.2 14.4 1.0 CB A:ASP286 4.2 14.2 1.0 ND2 A:ASN330 4.2 14.9 1.0 CG A:HIS339 4.3 14.8 1.0 ND1 A:HIS291 4.3 16.9 1.0 CG A:HIS291 4.3 16.5 1.0 CB A:ASP156 4.4 25.5 1.0 OG1 A:TPO85 4.4 23.9 1.0 O A:HOH504 4.5 25.0 1.0 CE1 A:HIS328 4.6 14.2 1.0 NE2 A:HIS328 4.8 13.9 1.0 CA A:ASP156 4.9 25.7 1.0 MN A:MN402 4.9 13.3 1.0

Manganese binding site 2 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:13.3 occ:1.00 OD2 A:ASP327 2.1 12.7 1.0 OD1 A:ASP13 2.1 13.7 1.0 OG1 A:TPO85 2.1 23.9 1.0 NE2 A:HIS328 2.2 13.9 1.0 OD2 A:ASP13 2.6 13.9 1.0 CG A:ASP13 2.6 13.3 1.0 O2P A:TPO85 2.9 27.5 0.3 CG A:ASP327 2.9 12.6 1.0 P A:TPO85 2.9 25.6 0.3 OD1 A:ASP327 3.0 12.2 1.0 CD2 A:HIS328 3.1 13.6 1.0 CE1 A:HIS328 3.2 14.2 1.0 O1P A:TPO85 3.2 26.6 0.3 CB A:TPO85 3.2 21.6 1.0 CA A:TPO85 3.7 20.0 1.0 CG2 A:TPO85 3.7 21.8 1.0 CB A:ASP13 4.1 12.6 1.0 CG A:HIS328 4.2 13.9 1.0 ND1 A:HIS328 4.2 14.3 1.0 O3P A:TPO85 4.3 24.8 0.3 N A:SER14 4.3 12.6 1.0 N A:TPO85 4.3 19.6 1.0 CB A:ASP327 4.3 12.5 1.0 CE1 A:HIS339 4.4 14.1 1.0 CG A:ASP286 4.5 14.8 1.0 OD2 A:ASP286 4.5 14.4 1.0 CA A:ASP13 4.6 12.5 1.0 O A:HOH667 4.6 39.0 1.0 C A:ASP13 4.7 12.5 1.0 NE2 A:HIS89 4.7 19.2 1.0 OD1 A:ASP286 4.7 15.6 1.0 NE2 A:HIS339 4.8 14.0 1.0 CB A:ASP286 4.9 14.2 1.0 C A:TPO85 4.9 18.8 1.0 CD2 A:HIS89 4.9 17.4 1.0 MN A:MN401 4.9 14.3 1.0 CA A:SER14 5.0 12.8 1.0 CB A:SER14 5.0 13.2 1.0

Manganese binding site 3 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:22.2 occ:0.75 O A:HOH519 2.1 27.2 1.0 O A:HOH673 2.1 28.9 1.0 O A:HOH705 2.1 35.9 1.0 OD1 A:ASP28 2.1 23.6 1.0 NE2 A:HIS334 2.2 21.7 1.0 O A:GLY27 2.5 28.6 1.0 CD2 A:HIS334 3.0 21.3 1.0 CE1 A:HIS334 3.3 22.3 1.0 CG A:ASP28 3.4 23.0 1.0 C A:GLY27 3.5 28.9 1.0 CA A:ASP28 4.0 25.4 1.0 OD2 A:ASP338 4.0 21.8 0.5 O A:PHE26 4.0 28.9 1.0 N A:ASP28 4.1 27.3 1.0 OD1 A:ASP338 4.2 21.3 0.5 CG A:HIS334 4.2 21.2 1.0 CB A:ASP28 4.2 23.6 1.0 OD2 A:ASP28 4.3 21.9 1.0 ND1 A:HIS334 4.3 21.8 1.0 NZ A:LYS83 4.3 30.6 1.0 CG A:ASP338 4.4 21.3 0.5 CG2 A:THR340 4.4 17.2 1.0 CA A:GLY27 4.5 30.7 1.0 O A:HIS339 4.6 16.6 1.0 O A:PRO335 4.7 23.8 1.0 C A:PHE26 5.0 29.6 1.0

Manganese binding site 4 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:32.6 occ:0.50 O A:HOH739 1.9 45.4 1.0 O A:HOH738 2.1 33.4 1.0 OD1 A:ASP186 2.1 28.1 1.0 O A:HOH740 2.6 50.0 1.0 CG A:ASP186 3.2 26.8 1.0 CB A:ASP186 3.7 24.7 1.0 NZ A:LYS188 4.1 36.3 1.0 O A:HOH671 4.1 37.8 1.0 OD2 A:ASP186 4.3 27.6 1.0 O A:LEU183 4.4 21.6 1.0 OE1 A:GLU115 4.5 35.5 0.5 CE2 A:TYR189 4.9 30.1 1.0 CA A:ASP186 5.0 24.7 1.0

Manganese binding site 5 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn405 b:33.2 occ:0.50 O A:HOH744 2.0 25.0 1.0 O A:HOH749 2.1 29.3 1.0 O A:HOH748 2.2 41.8 1.0 OD1 A:ASP268 2.5 25.5 1.0 O A:HOH605 3.5 35.5 1.0 CG A:ASP268 3.6 23.7 1.0 OD2 A:ASP268 4.1 24.9 1.0 O A:HOH743 4.3 20.5 1.0 O A:ASP264 4.4 17.6 1.0 O A:HOH751 4.5 60.6 1.0 O A:HOH750 4.8 44.1 1.0 CG1 A:VAL267 4.8 20.1 1.0 CB A:ASP268 4.8 21.9 1.0 N A:ASP268 4.9 19.7 1.0 CA A:ASP268 4.9 21.0 1.0

Manganese binding site 6 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:19.4 occ:1.00 NE2 B:HIS339 2.0 19.5 1.0 OD1 B:ASP286 2.2 21.1 1.0 NE2 B:HIS291 2.2 22.4 1.0 OD2 B:ASP156 2.2 32.4 1.0 O1P B:TPO85 2.5 21.8 0.3 OD2 B:ASP286 2.8 20.4 1.0 CG B:ASP286 2.8 20.1 1.0 CE1 B:HIS339 2.9 19.3 1.0 CG B:ASP156 2.9 31.3 1.0 OD1 B:ASP156 2.9 32.9 1.0 O3P B:TPO85 3.1 22.9 0.3 CD2 B:HIS339 3.1 20.3 1.0 CE1 B:HIS291 3.1 23.4 1.0 CD2 B:HIS291 3.1 22.6 1.0 P B:TPO85 3.2 21.9 0.3 ND1 B:HIS339 4.1 19.7 1.0 O2P B:TPO85 4.1 22.1 0.3 CG B:HIS339 4.2 20.4 1.0 ND1 B:HIS291 4.3 24.3 1.0 CG B:HIS291 4.3 23.9 1.0 CB B:ASP286 4.3 19.0 1.0 ND2 B:ASN330 4.3 20.6 1.0 O B:HOH727 4.4 27.9 1.0 CB B:ASP156 4.4 28.6 1.0 O B:HOH753 4.4 31.1 1.0 OG1 B:TPO85 4.5 21.1 1.0 CE1 B:HIS328 4.5 15.8 1.0 NE2 B:HIS328 4.7 15.5 1.0 MN B:MN402 4.9 16.2 1.0 CA B:ASP156 5.0 28.2 1.0

Manganese binding site 7 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:16.2 occ:1.00 NE2 B:HIS328 2.1 15.5 1.0 OD2 B:ASP327 2.1 14.7 1.0 OD1 B:ASP13 2.1 19.3 1.0 OG1 B:TPO85 2.1 21.1 1.0 O1P B:TPO85 2.5 21.8 0.3 OD2 B:ASP13 2.6 18.6 1.0 CG B:ASP13 2.7 18.8 1.0 P B:TPO85 2.9 21.9 0.3 CG B:ASP327 3.0 13.8 1.0 CD2 B:HIS328 3.0 15.3 1.0 CE1 B:HIS328 3.1 15.8 1.0 OD1 B:ASP327 3.1 13.4 1.0 CB B:TPO85 3.3 19.7 1.0 O2P B:TPO85 3.6 22.1 0.3 CG2 B:TPO85 3.6 19.4 1.0 CA B:TPO85 3.7 18.1 1.0 CB B:ASP13 4.1 18.2 1.0 CG B:HIS328 4.2 15.7 1.0 O3P B:TPO85 4.2 22.9 0.3 ND1 B:HIS328 4.2 15.9 1.0 N B:TPO85 4.3 18.1 1.0 O B:HOH703 4.3 27.7 1.0 N B:SER14 4.4 18.1 1.0 CB B:ASP327 4.4 13.6 1.0 CE1 B:HIS339 4.4 19.3 1.0 CG B:ASP286 4.5 20.1 1.0 OD2 B:ASP286 4.5 20.4 1.0 CA B:ASP13 4.7 17.3 1.0 NE2 B:HIS89 4.7 14.8 1.0 OD1 B:ASP286 4.7 21.1 1.0 C B:ASP13 4.8 18.4 1.0 NE2 B:HIS339 4.8 19.5 1.0 MN B:MN401 4.9 19.4 1.0 C B:TPO85 4.9 17.4 1.0 CB B:ASP286 4.9 19.0 1.0 CD2 B:HIS89 4.9 14.2 1.0

Manganese binding site 8 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:37.9 occ:0.50 O B:HOH712 2.1 44.4 1.0 O B:HOH709 2.1 43.7 1.0 NE2 B:HIS36 2.4 31.6 1.0 O B:HOH610 2.4 42.4 1.0 CD2 B:HIS36 3.3 30.7 1.0 CE1 B:HIS36 3.4 30.4 1.0 O B:GLY30 4.4 32.9 1.0 ND1 B:HIS36 4.5 28.9 1.0 CG B:HIS36 4.5 29.0 1.0 OE2 B:GLU39 4.6 39.8 0.5 OE1 B:GLU39 4.9 40.7 0.5

Manganese binding site 9 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn404 b:46.8 occ:1.00 OD1 B:ASP28 2.2 32.6 1.0 NE2 B:HIS334 2.3 31.4 1.0 O B:HOH766 2.4 35.6 1.0 O B:GLY27 2.7 38.4 1.0 OD2 B:ASP338 2.7 27.5 0.5 CD2 B:HIS334 3.1 30.4 1.0 CG B:ASP28 3.4 31.2 1.0 CE1 B:HIS334 3.4 31.7 1.0 C B:GLY27 3.4 37.6 1.0 O B:PHE26 3.7 39.0 1.0 CG B:ASP338 3.8 27.7 0.5 CA B:ASP28 3.9 33.0 1.0 N B:ASP28 4.0 35.2 1.0 OD2 B:ASP28 4.2 30.3 1.0 CB B:ASP28 4.2 30.9 1.0 NZ B:LYS83 4.2 25.2 1.0 OD1 B:ASP338 4.3 28.5 0.5 CA B:GLY27 4.3 39.9 1.0 CG B:HIS334 4.3 30.1 1.0 ND1 B:HIS334 4.4 31.0 1.0 C B:PHE26 4.7 39.0 1.0 O B:HIS339 4.7 23.3 1.0 O B:HOH636 4.7 41.3 1.0 CG2 B:THR340 4.7 23.0 1.0 CB B:ASP338 5.0 26.8 0.5

Manganese binding site 10 out of 14 in the Phosphopentomutase S154A Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Phosphopentomutase S154A Variant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn405 b:46.2 occ:1.00 OD1 B:ASP186 2.2 28.5 1.0 O B:HOH774 2.3 30.6 1.0 O B:HOH776 2.3 42.0 1.0 O B:HOH775 2.4 49.9 1.0 O B:HOH773 2.4 38.3 1.0 CG B:ASP186 3.4 27.2 1.0 CB B:ASP186 3.9 25.1 1.0 NZ B:LYS188 4.2 36.9 1.0 OE1 B:GLU115 4.3 31.0 0.5 OE2 B:GLU115 4.4 35.3 0.5 OD2 B:ASP186 4.4 27.9 1.0 O B:LEU183 4.6 22.2 1.0 OH B:TYR189 4.6 37.0 1.0 CD B:GLU115 4.7 33.2 0.5 CE2 B:TYR189 4.7 30.8 1.0 CE B:LYS188 4.9 36.8 1.0

W.R.Birmingham, C.A.Starbird, T.D.Panosian, D.P.Nannemann, T.M.Iverson, B.O.Bachmann. Bioretrosynthetic Construction of A Didanosine Biosynthetic Pathway. Nat.Chem.Biol. V. 10 392 2014.
ISSN: ISSN 1552-4450
PubMed: 24657930
DOI: 10.1038/NCHEMBIO.1494