Manganese in PDB 4lrd: Phosphopentomutase 4H11 Variant

All present enzymatic activity of Phosphopentomutase 4H11 Variant:
5.4.2.7;

The structure of Phosphopentomutase 4H11 Variant, PDB code: 4lrd 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)	39.02 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.293, 60.492, 78.854, 90.00, 98.50, 90.00
R / Rfree (%)	14 / 18

The binding sites of Manganese atom in the Phosphopentomutase 4H11 Variant (pdb code 4lrd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Phosphopentomutase 4H11 Variant, PDB code: 4lrd:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Phosphopentomutase 4H11 Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Phosphopentomutase 4H11 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:10.2 occ:1.00 O3P A:TPO85 2.0 16.8 0.5 OD1 A:ASP286 2.1 12.6 1.0 NE2 A:HIS339 2.2 9.4 1.0 NE2 A:HIS291 2.2 11.0 1.0 O A:HOH502 2.2 17.3 1.0 O A:HOH503 2.3 16.4 1.0 O A:HOH519 2.3 21.2 0.5 O2P A:TPO85 2.7 20.7 0.5 P A:TPO85 2.8 21.6 0.5 CG A:ASP286 3.0 10.0 1.0 CE1 A:HIS339 3.1 10.0 1.0 CD2 A:HIS291 3.2 11.4 1.0 OD2 A:ASP286 3.2 10.0 1.0 CD2 A:HIS339 3.2 8.6 1.0 CE1 A:HIS291 3.2 11.4 1.0 O1P A:TPO85 3.6 21.1 0.5 O A:HOH515 4.1 12.9 1.0 ND1 A:HIS339 4.3 9.2 1.0 OG1 A:TPO85 4.3 11.5 1.0 ND1 A:HIS291 4.3 10.8 1.0 CG A:HIS339 4.3 8.2 1.0 CG A:HIS291 4.3 11.3 1.0 CB A:ASP286 4.4 9.6 1.0 OD2 A:ASP156 4.6 28.4 0.8 O A:HOH685 4.6 27.9 1.0 ND2 A:ASN330 4.6 11.1 1.0 CE1 A:HIS328 4.8 7.2 1.0 NE2 A:HIS328 5.0 7.4 1.0

Manganese binding site 2 out of 3 in the Phosphopentomutase 4H11 Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Phosphopentomutase 4H11 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:7.1 occ:1.00 OG1 A:TPO85 2.1 11.5 1.0 OD2 A:ASP327 2.1 7.0 1.0 OD1 A:ASP13 2.1 8.0 1.0 NE2 A:HIS328 2.2 7.4 1.0 OD2 A:ASP13 2.5 6.8 1.0 CG A:ASP13 2.6 7.2 1.0 O2P A:TPO85 2.7 20.7 0.5 CG A:ASP327 2.9 6.5 1.0 CD2 A:HIS328 3.0 7.5 1.0 OD1 A:ASP327 3.1 6.7 1.0 CB A:TPO85 3.1 9.7 1.0 CE1 A:HIS328 3.2 7.2 1.0 P A:TPO85 3.2 21.6 0.5 CA A:TPO85 3.5 8.8 1.0 CG2 A:TPO85 3.5 9.6 1.0 O A:HOH519 4.0 21.2 0.5 CB A:ASP13 4.1 6.8 1.0 CG A:HIS328 4.2 7.6 1.0 ND1 A:HIS328 4.2 7.5 1.0 CE1 A:HIS339 4.2 10.0 1.0 N A:TPO85 4.3 9.0 1.0 CB A:ASP327 4.3 6.5 1.0 O3P A:TPO85 4.4 16.8 0.5 O1P A:TPO85 4.4 21.1 0.5 N A:SER14 4.4 6.5 1.0 CE1 A:HIS89 4.5 7.2 1.0 CG A:ASP286 4.5 10.0 1.0 OD1 A:ASP286 4.6 12.6 1.0 CA A:ASP13 4.6 6.4 1.0 OD2 A:ASP286 4.7 10.0 1.0 C A:ASP13 4.7 6.8 1.0 C A:TPO85 4.8 8.2 1.0 NE2 A:HIS339 4.8 9.4 1.0 CB A:ASP286 4.9 9.6 1.0 O A:HOH714 4.9 26.8 1.0 ND1 A:HIS89 4.9 6.8 1.0 ND1 A:HIS339 5.0 9.2 1.0

Manganese binding site 3 out of 3 in the Phosphopentomutase 4H11 Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Phosphopentomutase 4H11 Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:28.7 occ:1.00 OD1 A:ASP28 2.2 9.0 1.0 O A:HOH654 2.2 21.9 1.0 O A:HOH568 2.3 14.3 1.0 O A:HOH601 2.3 22.8 1.0 O A:GLY27 2.4 8.8 1.0 NE2 A:HIS334 2.5 11.2 1.0 CD2 A:HIS334 3.1 11.1 1.0 C A:GLY27 3.2 9.8 1.0 CG A:ASP28 3.4 8.8 1.0 CE1 A:HIS334 3.6 11.6 1.0 CA A:ASP28 3.8 8.4 1.0 N A:ASP28 3.9 8.5 1.0 O A:PHE26 3.9 14.7 1.0 CA A:GLY27 4.1 9.4 1.0 O A:HOH571 4.2 15.3 1.0 CB A:ASP28 4.2 8.6 1.0 OD2 A:ASP28 4.2 9.1 1.0 NZ A:LYS83 4.3 9.6 1.0 CG A:HIS334 4.4 10.6 1.0 O A:HOH623 4.6 21.7 1.0 ND1 A:HIS334 4.6 11.6 1.0 CG2 A:THR340 4.6 7.5 1.0 O A:HOH758 4.6 52.4 1.0 O A:HOH680 4.7 29.6 1.0 O A:HIS339 4.7 7.6 1.0 C A:PHE26 4.8 12.1 1.0 N A:GLY27 4.9 10.8 1.0 O A:HOH513 4.9 9.6 1.0 O A:PRO335 4.9 14.8 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