Magnesium in PDB 4jt4: Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp

All present enzymatic activity of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp:
2.7.1.78;

The structure of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp, PDB code: 4jt4 was solved by U.Das, L.K.Wang, P.Smith, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.54 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.306, 66.781, 119.546, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 21.8

The structure of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp (pdb code 4jt4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp, PDB code: 4jt4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:21.0 occ:1.00 O3G A:DTP202 1.9 13.8 1.0 O A:HOH303 2.0 15.5 1.0 O2B A:DTP202 2.0 15.8 1.0 OG A:SER22 2.1 14.0 1.0 O A:HOH301 2.1 14.7 1.0 O A:HOH304 2.2 18.8 1.0 CB A:SER22 3.2 22.5 1.0 PG A:DTP202 3.2 18.6 1.0 PB A:DTP202 3.3 20.4 1.0 O3B A:DTP202 3.5 16.1 1.0 NH2 A:ARG123 3.9 35.4 1.0 O2G A:DTP202 3.9 15.1 1.0 O2A A:DTP202 4.0 21.6 1.0 OD2 A:ASP78 4.0 17.6 1.0 N A:SER22 4.1 13.2 1.0 O A:HOH343 4.1 23.3 1.0 O A:HOH348 4.1 22.9 1.0 O A:HOH379 4.1 32.5 1.0 OD1 A:ASP78 4.1 21.8 1.0 O A:HOH414 4.1 32.6 1.0 CA A:SER22 4.2 16.1 1.0 O3A A:DTP202 4.4 20.1 1.0 O1G A:DTP202 4.4 18.1 1.0 O1B A:DTP202 4.4 15.6 1.0 CG A:ASP78 4.5 23.8 1.0 PA A:DTP202 4.5 18.6 1.0 NH2 A:ARG120 4.7 16.7 1.0 O1A A:DTP202 4.8 18.8 1.0 OD2 A:ASP38 4.9 44.2 0.5

Magnesium binding site 2 out of 2 in the Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Clostridium Thermocellum Polynucleotide Kinase Bound to Datp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:17.4 occ:1.00 O3G B:DTP202 2.0 17.7 1.0 O1B B:DTP202 2.0 14.7 1.0 O B:HOH305 2.1 16.9 1.0 O B:HOH303 2.1 15.1 1.0 OG B:SER22 2.2 15.0 1.0 O B:HOH306 2.3 13.9 1.0 CB B:SER22 3.1 13.8 1.0 PB B:DTP202 3.2 16.7 1.0 PG B:DTP202 3.2 21.4 1.0 O3B B:DTP202 3.4 21.3 1.0 O2G B:DTP202 3.9 13.5 1.0 O2A B:DTP202 3.9 16.1 1.0 N B:SER22 4.0 13.1 1.0 O B:HOH344 4.0 30.6 1.0 O B:HOH328 4.0 22.3 1.0 OD2 B:ASP78 4.1 20.6 1.0 O B:HOH338 4.1 22.6 1.0 OD1 B:ASP78 4.1 19.6 1.0 O B:HOH313 4.1 20.5 1.0 CA B:SER22 4.1 10.6 1.0 O3A B:DTP202 4.2 12.6 1.0 O B:HOH383 4.2 33.0 1.0 O2B B:DTP202 4.3 15.1 1.0 O1G B:DTP202 4.4 16.6 1.0 PA B:DTP202 4.4 17.9 1.0 CG B:ASP78 4.5 25.7 1.0 O1A B:DTP202 4.7 17.9 1.0 OD2 B:ASP38 4.9 69.7 1.0 NH2 B:ARG120 4.9 22.0 1.0

U.Das, L.K.Wang, P.Smith, S.Shuman. Structural and Biochemical Analysis of the Phosphate Donor Specificity of the Polynucleotide Kinase Component of the Bacterial PNKPHEN1 Rna Repair System. Biochemistry V. 52 4734 2013.
ISSN: ISSN 0006-2960
PubMed: 23721485
DOI: 10.1021/BI400412X