Manganese in PDB 4j6o: Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp

All present enzymatic activity of Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp:
3.1.3.16;

The structure of Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp, PDB code: 4j6o was solved by L.Wang, P.Smith, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.69 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.700, 38.660, 92.950, 90.00, 91.80, 90.00
R / Rfree (%)	16.4 / 20.6

The binding sites of Manganese atom in the Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp (pdb code 4j6o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp, PDB code: 4j6o:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn508 b:18.9 occ:1.00 OD2 A:ASP233 2.2 18.6 1.0 OD2 A:ASP187 2.2 18.7 1.0 O5 A:CIT509 2.2 26.8 1.0 NE2 A:HIS189 2.3 17.3 1.0 O1 A:CIT509 2.3 25.6 1.0 O A:HOH602 2.3 20.7 1.0 C6 A:CIT509 3.0 27.1 1.0 CG A:ASP233 3.1 23.9 1.0 CE1 A:HIS189 3.2 18.6 1.0 CD2 A:HIS189 3.3 18.6 1.0 CG A:ASP187 3.4 19.8 1.0 C1 A:CIT509 3.4 27.8 1.0 O A:HOH614 3.5 12.7 1.0 CB A:ASP233 3.6 18.8 1.0 O6 A:CIT509 3.6 27.5 1.0 CB A:ASP187 3.9 15.1 1.0 C3 A:CIT509 3.9 27.5 1.0 O7 A:CIT509 4.0 27.8 1.0 OD2 A:ASP392 4.1 19.7 1.0 C2 A:CIT509 4.2 27.1 1.0 O2 A:CIT509 4.2 26.2 1.0 NH1 A:ARG237 4.2 23.5 1.0 CD2 A:HIS264 4.2 22.5 1.0 OD1 A:ASP233 4.3 19.2 1.0 CE1 A:HIS323 4.3 20.4 1.0 ND1 A:HIS189 4.3 18.9 1.0 OD1 A:ASP187 4.3 18.5 1.0 NE2 A:HIS264 4.4 24.2 1.0 CG A:HIS189 4.4 19.5 1.0 NE2 A:HIS323 4.5 19.5 1.0 O A:HOH605 4.6 18.5 1.0 OD1 A:ASN263 4.7 18.8 0.6 O A:HIS376 5.0 22.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Phosphatase Domain of C. Thermocellum (Bacterial) Pnkp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:26.6 occ:1.00 O B:HOH603 2.1 26.9 1.0 OD2 B:ASP233 2.1 28.5 1.0 O5 B:CIT502 2.1 32.6 1.0 OD2 B:ASP187 2.2 24.7 1.0 O2 B:CIT502 2.2 30.7 1.0 NE2 B:HIS189 2.3 31.1 1.0 C6 B:CIT502 3.0 33.0 1.0 CG B:ASP233 3.1 29.1 1.0 CE1 B:HIS189 3.2 27.9 1.0 C1 B:CIT502 3.3 28.6 1.0 CD2 B:HIS189 3.3 27.6 1.0 CG B:ASP187 3.3 23.8 1.0 CB B:ASP233 3.5 28.1 1.0 O B:HOH602 3.5 18.5 1.0 O6 B:CIT502 3.6 35.2 1.0 CB B:ASP187 3.9 22.5 1.0 C3 B:CIT502 3.9 29.3 1.0 C2 B:CIT502 4.0 28.5 1.0 NH1 B:ARG237 4.1 33.6 1.0 OD2 B:ASP392 4.1 28.3 1.0 O7 B:CIT502 4.1 30.5 1.0 O1 B:CIT502 4.2 29.6 1.0 CD2 B:HIS264 4.2 30.1 1.0 OD1 B:ASP233 4.2 27.4 1.0 ND1 B:HIS189 4.3 31.8 1.0 CE1 B:HIS323 4.3 30.3 1.0 OD1 B:ASP187 4.4 25.6 1.0 CG B:HIS189 4.4 29.3 1.0 NE2 B:HIS323 4.5 28.6 1.0 NE2 B:HIS264 4.6 32.2 1.0 O B:HOH614 4.6 27.4 1.0 OD1 B:ASN263 4.8 39.0 1.0 O B:HIS376 5.0 27.4 1.0

L.K.Wang, P.Smith, S.Shuman. Structure and Mechanism of the 2',3' Phosphatase Component of the Bacterial Pnkp-HEN1 Rna Repair System. Nucleic Acids Res. V. 41 5864 2013.
ISSN: ISSN 0305-1048
PubMed: 23595150
DOI: 10.1093/NAR/GKT221