Magnesium in PDB 3ty9: Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate

All present enzymatic activity of Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate:
6.5.1.3;

The structure of Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate, PDB code: 3ty9 was solved by P.Smith, L.Wang, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.19 / 3.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.500, 132.760, 162.770, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 26.6

The binding sites of Magnesium atom in the Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate (pdb code 3ty9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate, PDB code: 3ty9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1000 b:75.7 occ:1.00 O A:THR731 2.8 80.9 1.0 O A:ILE737 2.9 83.5 1.0 O A:ASP734 3.0 73.7 1.0 CG2 A:THR731 3.3 75.0 1.0 O A:HOH38 3.4 51.3 1.0 C A:THR731 3.9 83.6 1.0 CA A:MET738 3.9 72.4 1.0 C A:ILE737 3.9 74.4 1.0 C A:ASP734 4.1 76.3 1.0 CB A:THR731 4.3 77.7 1.0 CA A:THR731 4.4 80.9 1.0 N A:MET738 4.4 68.2 1.0 N A:ALA739 4.5 69.8 1.0 CB A:MET738 4.5 67.6 1.0 OG1 A:THR731 4.7 71.3 1.0 C A:MET738 4.7 70.1 1.0 CA A:SER735 4.8 80.5 1.0 N A:SER735 4.9 78.9 1.0 N A:ASP734 4.9 87.3 1.0 N A:GLN732 5.0 85.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1000 b:73.0 occ:1.00 O B:THR731 2.7 83.3 1.0 O B:ILE737 2.9 76.1 1.0 O B:ASP734 2.9 76.0 1.0 C B:THR731 3.7 88.9 1.0 CB B:THR731 3.8 80.0 1.0 CA B:MET738 4.0 74.5 1.0 C B:ILE737 4.0 75.9 1.0 C B:ASP734 4.1 79.7 1.0 CA B:THR731 4.1 87.0 1.0 OG1 B:THR731 4.3 78.2 1.0 N B:MET738 4.5 73.9 1.0 N B:ALA739 4.5 79.3 1.0 CB B:MET738 4.7 68.6 1.0 CA B:SER735 4.7 78.6 1.0 C B:MET738 4.8 78.0 1.0 N B:SER735 4.8 80.7 1.0 N B:ASP734 4.8 89.9 1.0 N B:GLN732 4.9 89.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1000 b:75.4 occ:1.00 O C:ASP734 2.6 85.8 1.0 O C:ILE737 2.8 76.0 1.0 O C:THR731 2.8 0.1 1.0 C C:ASP734 3.8 83.0 1.0 C C:THR731 3.8 96.8 1.0 C C:ILE737 3.9 77.3 1.0 CA C:SER735 4.1 82.1 1.0 CA C:MET738 4.2 81.9 1.0 CB C:THR731 4.2 90.9 1.0 CA C:THR731 4.2 95.1 1.0 O C:SER735 4.3 83.3 1.0 N C:SER735 4.4 75.1 1.0 C C:SER735 4.5 80.2 1.0 N C:MET738 4.5 82.2 1.0 OG1 C:THR731 4.6 86.5 1.0 N C:ALA739 4.9 82.8 1.0 CB C:MET738 4.9 81.1 1.0 N C:GLN732 4.9 95.8 1.0 N C:ASP734 4.9 94.5 1.0 CA C:ASP734 4.9 87.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of C. Thermocellum Pnkp Ligase Domain Amp-Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1000 b:90.4 occ:1.00 O D:ASP734 2.4 93.5 1.0 O D:THR731 2.7 0.8 1.0 C D:ASP734 3.1 95.2 1.0 O D:ILE737 3.4 92.8 1.0 N D:ASP734 3.5 0.9 1.0 CA D:ASP734 3.9 93.7 1.0 C D:THR731 3.9 0.8 1.0 N D:SER735 4.0 91.1 1.0 CG2 D:THR731 4.1 0.4 1.0 CA D:SER735 4.2 92.9 1.0 N D:ASP733 4.4 0.9 1.0 C D:ASP733 4.4 0.3 1.0 C D:ILE737 4.6 94.0 1.0 CA D:THR731 4.7 0.3 1.0 CA D:ASP733 4.8 0.4 1.0 C D:GLN732 4.8 0.9 1.0 N D:GLN732 4.9 0.6 1.0 C D:SER735 5.0 93.5 1.0 CA D:MET738 5.0 0.8 1.0

P.Smith, L.K.Wang, P.A.Nair, S.Shuman. The Adenylyltransferase Domain of Bacterial Pnkp Defines A Unique Rna Ligase Family. Proc.Natl.Acad.Sci.Usa V. 109 2296 2012.
ISSN: ISSN 0027-8424
PubMed: 22308407
DOI: 10.1073/PNAS.1116827109