Manganese in PDB 3x0p: Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 15 Min

All present enzymatic activity of Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 15 Min:
3.6.1.13;

The structure of Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 15 Min, PDB code: 3x0p 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 / 1.22
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	49.738, 49.738, 119.235, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / n/a

The binding sites of Manganese atom in the Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 15 Min (pdb code 3x0p). 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 15 Min, PDB code: 3x0p:
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 15 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 15 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:12.8 occ:0.35 O A:HOH301 1.9 19.7 1.0 OE2 A:GLU86 2.1 18.9 1.0 O2B A:AR6201 2.1 17.1 0.7 O2A A:AR6201 2.1 18.4 0.7 O A:HOH302 2.2 28.1 1.0 O A:ALA66 2.5 17.5 1.0 O A:HOH394 2.8 13.9 0.3 CD A:GLU86 3.2 15.7 1.0 PB A:AR6201 3.3 17.0 0.7 MN A:MN203 3.4 38.3 0.1 PA A:AR6201 3.4 19.9 0.7 O3A A:AR6201 3.6 18.7 0.7 C A:ALA66 3.6 12.8 1.0 OE1 A:GLU86 3.6 20.1 1.0 NE2 A:GLN52 3.6 19.9 0.1 OE2 A:GLU82 4.2 28.3 0.9 CA A:GLY67 4.2 16.3 1.0 OE1 A:GLN52 4.3 29.0 0.9 O A:HOH309 4.3 14.7 1.0 O5' A:AR6201 4.3 24.0 0.7 O1B A:AR6201 4.3 20.4 0.7 N A:GLY67 4.4 13.8 1.0 NH2 A:ARG54 4.4 14.8 1.0 NE2 A:GLN52 4.4 22.6 0.9 CG A:GLU86 4.4 15.3 1.0 O5D A:AR6201 4.5 17.7 0.7 N A:ALA66 4.5 13.8 1.0 O1A A:AR6201 4.6 20.4 0.7 C5D A:AR6201 4.6 17.0 0.7 CA A:ALA66 4.6 12.7 1.0 CD A:GLN52 4.8 19.7 0.9 CD1 A:ILE131 4.8 23.5 0.5 CD A:GLU82 4.8 27.4 0.9 CD A:GLN52 4.8 18.2 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 15 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 15 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:38.3 occ:0.15 O A:HOH303 1.9 29.0 1.0 O2A A:AR6201 2.7 18.4 0.7 OE2 A:GLU86 2.7 18.9 1.0 OE2 A:GLU82 2.9 28.3 0.9 MN A:MN202 3.4 12.8 0.3 CG A:GLU86 3.5 15.3 1.0 CD A:GLU86 3.5 15.7 1.0 O A:HOH302 3.6 28.1 1.0 PA A:AR6201 3.8 19.9 0.7 CD A:GLU82 3.9 27.4 0.9 OE1 A:GLU82 4.0 30.8 0.9 CD1 A:ILE131 4.1 23.5 0.5 O5' A:AR6201 4.3 24.0 0.7 O1A A:AR6201 4.4 20.4 0.7 O A:ALA66 4.6 17.5 1.0 OE1 A:GLU85 4.6 21.6 1.0 OE1 A:GLU86 4.7 20.1 1.0 O A:HOH301 4.9 19.7 1.0 CB A:GLU85 5.0 15.7 1.0 CB A:GLU86 5.0 15.0 1.0

Manganese binding site 3 out of 3 in the Adp Ribose Pyrophosphatase From Thermus Thermophilus HB8 in Esmm-State at Reaction Time of 15 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 15 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:13.6 occ:0.10 O A:HOH377 1.6 36.5 1.0 O A:ILE131 2.1 21.1 1.0 O A:HOH390 2.2 83.4 1.0 O A:HOH376 2.4 32.5 1.0 C A:ILE131 3.3 17.1 1.0 N A:ILE131 3.8 21.1 1.0 CA A:ILE131 4.0 18.1 0.5 CA A:ILE131 4.1 17.8 0.5 N A:GLU132 4.2 15.9 1.0 CB A:ILE131 4.3 20.8 0.5 CA A:GLU132 4.5 15.8 1.0 CB A:ILE131 4.5 21.2 0.5 N A:ALA130 4.6 40.7 1.0 C A:ALA130 4.9 24.8 1.0 N A:VAL133 5.0 14.8 1.0 O A:GLU86 5.0 17.7 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