Manganese in PDB 3x0q: Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min

All present enzymatic activity of Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min:
3.6.1.13;

The structure of Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min, PDB code: 3x0q 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 / 1.14
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	49.604, 49.604, 118.830, 90.00, 90.00, 120.00
R / Rfree (%)	15.3 / n/a

The binding sites of Manganese atom in the Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min (pdb code 3x0q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min, PDB code: 3x0q:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:7.7 occ:0.45 O A:HOH301 2.0 13.5 1.0 OE2 A:GLU86 2.1 14.6 1.0 O2B A:AR6201 2.1 10.8 0.7 O1A A:AR6201 2.1 10.7 0.7 O A:HOH302 2.2 18.5 1.0 O A:ALA66 2.3 11.6 1.0 O A:HOH402 2.7 9.0 0.3 CD A:GLU86 3.2 11.2 1.0 PB A:AR6201 3.3 10.1 0.7 PA A:AR6201 3.4 11.2 0.7 MN A:MN203 3.4 29.3 0.3 C A:ALA66 3.5 8.1 1.0 O3A A:AR6201 3.5 10.7 0.7 OE1 A:GLU86 3.6 14.2 1.0 NE2 A:GLN52 3.7 9.0 0.1 O A:HOH386 4.0 40.8 1.0 CA A:GLY67 4.1 11.3 1.0 OE2 A:GLU82 4.1 18.5 0.8 O5' A:AR6201 4.2 15.1 0.7 N A:GLY67 4.3 8.7 1.0 O1B A:AR6201 4.3 12.0 0.7 OE1 A:GLN52 4.3 20.9 0.9 O A:HOH310 4.3 9.9 1.0 NH2 A:ARG54 4.4 9.1 1.0 CG A:GLU86 4.4 9.8 1.0 NE2 A:GLN52 4.5 17.7 0.9 O5D A:AR6201 4.5 10.5 0.7 N A:ALA66 4.5 8.9 1.0 O2A A:AR6201 4.5 11.7 0.7 CA A:ALA66 4.6 8.4 1.0 C5D A:AR6201 4.6 9.6 0.7 CD1 A:ILE131 4.7 16.5 0.5 CD A:GLU82 4.8 18.9 0.8 CD A:GLN52 4.8 14.3 0.9 CD A:GLN52 5.0 11.0 0.1

Manganese binding site 2 out of 3 in the Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:29.3 occ:0.30 O A:HOH303 1.7 26.0 1.0 O1A A:AR6201 2.4 10.7 0.7 OE2 A:GLU82 2.4 18.5 0.8 OE2 A:GLU86 2.7 14.6 1.0 O A:HOH386 3.1 40.8 1.0 CD A:GLU82 3.4 18.9 0.8 MN A:MN202 3.4 7.7 0.5 OE1 A:GLU82 3.4 17.5 0.8 PA A:AR6201 3.5 11.2 0.7 CD A:GLU86 3.6 11.2 1.0 CG A:GLU86 3.7 9.8 1.0 O A:HOH302 3.7 18.5 1.0 O2A A:AR6201 4.0 11.7 0.7 O5' A:AR6201 4.1 15.1 0.7 O A:ALA66 4.4 11.6 1.0 OE1 A:GLU85 4.4 14.8 1.0 CD1 A:ILE131 4.5 16.5 0.5 CB A:GLU82 4.6 9.4 0.2 CG A:GLU82 4.7 16.4 0.8 OE1 A:GLU86 4.7 14.2 1.0 O3A A:AR6201 4.8 10.7 0.7

Manganese binding site 3 out of 3 in the Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 20 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:16.1 occ:0.15 O A:HOH400 1.6 27.0 1.0 O A:ILE131 2.1 14.7 1.0 O A:HOH330 2.5 25.9 1.0 O A:HOH422 3.1 40.9 1.0 CA A:GLU129 3.2 51.0 1.0 C A:ILE131 3.3 11.2 1.0 O A:GLU129 3.3 51.6 1.0 C A:GLU129 3.4 42.5 1.0 N A:ILE131 3.8 16.2 1.0 O A:HOH391 3.8 50.0 1.0 CA A:ILE131 4.0 12.6 0.5 CA A:ILE131 4.0 12.5 0.5 N A:GLU129 4.1 57.7 1.0 CB A:GLU129 4.2 79.1 1.0 N A:GLU132 4.2 10.2 1.0 CB A:ILE131 4.3 14.3 0.5 N A:ALA130 4.4 32.5 1.0 CA A:GLU132 4.5 10.1 1.0 CB A:ILE131 4.6 15.8 0.5 C A:ALA130 4.8 18.9 1.0 N A:VAL133 5.0 10.1 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