Manganese in PDB 3x0r: Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min

All present enzymatic activity of Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min:
3.6.1.13;

The structure of Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min, PDB code: 3x0r was solved by Y.Furuike, Y.Akita, I.Miyahara, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.15
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	49.648, 49.648, 118.828, 90.00, 90.00, 120.00
R / Rfree (%)	14.3 / n/a

The binding sites of Manganese atom in the Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min (pdb code 3x0r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min, PDB code: 3x0r:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn205 b:9.8 occ:0.15 O A:HOH301 1.7 14.8 1.0 O A:HOH341 2.0 19.6 1.0 OE2 A:GLU86 2.0 13.9 1.0 O A:HOH401 2.4 46.4 0.5 O A:ALA66 2.5 13.6 1.0 O3 A:SO4203 2.7 18.9 0.5 O A:HOH377 2.8 13.6 0.5 CD A:GLU86 3.2 11.7 1.0 O2 A:SO4203 3.2 29.8 0.5 S A:SO4203 3.4 16.8 0.5 C A:ALA66 3.6 9.7 1.0 OE1 A:GLU86 3.7 13.6 1.0 NE2 A:GLN52 3.9 20.2 1.0 O1 A:SO4203 4.1 27.5 0.5 CA A:GLY67 4.2 13.3 1.0 OE2 A:GLU82 4.2 19.3 1.0 O A:HOH302 4.3 10.9 1.0 O A:HOH407 4.3 26.5 0.5 CG A:GLU86 4.3 11.5 1.0 N A:GLY67 4.4 10.3 1.0 NH2 A:ARG54 4.5 11.9 1.0 O A:HOH340 4.5 32.1 1.0 N A:ALA66 4.5 9.9 1.0 CA A:ALA66 4.6 9.8 1.0 CD A:GLU82 4.7 18.8 1.0 O4 A:SO4203 4.7 27.1 0.5 CD A:GLN52 4.9 18.3 1.0 CD1 A:ILE131 5.0 31.0 0.5 O A:HOH303 5.0 21.9 1.0 OE1 A:GLU82 5.0 21.7 1.0 CB A:ALA66 5.0 10.4 1.0

Manganese binding site 2 out of 2 in the Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in E'-State at Reaction Time of 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn206 b:18.6 occ:0.20 O A:HOH369 1.6 26.7 1.0 O A:ILE131 2.1 17.3 1.0 O A:HOH370 2.5 19.7 0.5 C A:ILE131 3.2 13.6 1.0 O A:HOH371 3.4 40.9 1.0 N A:ILE131 4.0 17.9 1.0 CA A:ILE131 4.1 14.8 0.5 CA A:ILE131 4.1 14.2 0.5 N A:GLU132 4.2 11.6 1.0 CB A:ILE131 4.4 18.6 0.5 CA A:GLU132 4.4 11.3 1.0 CB A:ILE131 4.6 20.0 0.5 N A:ALA130 4.7 43.7 1.0 N A:VAL133 4.9 10.7 1.0 C A:ALA130 5.0 23.0 1.0

Y.Furuike, Y.Akita, I.Miyahara, N.Kamiya. Adp-Ribose Pyrophosphatase Reaction in Crystalline State Conducted By Consecutive Binding of Two Manganese(II) Ions As Cofactors Biochemistry V. 55 1801 2016.
ISSN: ISSN 0006-2960
PubMed: 26979298
DOI: 10.1021/ACS.BIOCHEM.5B00886