Magnesium in PDB 4gp7: Polynucleotide Kinase

All present enzymatic activity of Polynucleotide Kinase:
2.7.1.78;

The structure of Polynucleotide Kinase, PDB code: 4gp7 was solved by L.K.Wang, U.Das, 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 / 2.00
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 (%)	17.5 / 23

The structure of Polynucleotide Kinase also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Polynucleotide Kinase (pdb code 4gp7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Polynucleotide Kinase, PDB code: 4gp7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Polynucleotide Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Polynucleotide Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:10.7 occ:1.00 O3G A:ATP1001 2.0 6.3 1.0 O1B A:ATP1001 2.0 6.4 1.0 O A:HOH1129 2.1 15.0 1.0 OG A:SER22 2.1 17.5 1.0 O A:HOH1131 2.1 9.8 1.0 O A:HOH1130 2.1 9.5 1.0 CB A:SER22 3.1 17.5 1.0 PG A:ATP1001 3.2 13.0 1.0 PB A:ATP1001 3.3 12.8 1.0 O3B A:ATP1001 3.5 14.9 1.0 NH2 A:ARG123 3.8 45.6 1.0 N A:SER22 4.0 6.9 1.0 OD2 A:ASP78 4.0 17.6 1.0 O2G A:ATP1001 4.0 16.9 1.0 O1A A:ATP1001 4.0 15.6 1.0 OD2 A:ASP38 4.0 66.0 0.5 CA A:SER22 4.1 11.3 1.0 OD1 A:ASP78 4.1 16.1 1.0 O A:HOH1144 4.1 25.8 1.0 O A:HOH1132 4.2 13.3 1.0 O A:HOH1133 4.3 16.1 1.0 O3A A:ATP1001 4.3 15.1 1.0 O A:HOH1163 4.4 24.0 1.0 O2B A:ATP1001 4.4 9.5 1.0 CG A:ASP78 4.4 21.7 1.0 O1G A:ATP1001 4.5 15.1 1.0 PA A:ATP1001 4.5 14.2 1.0 O2A A:ATP1001 4.6 11.8 1.0 NH2 A:ARG120 4.8 19.2 1.0

Magnesium binding site 2 out of 2 in the Polynucleotide Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Polynucleotide Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:9.1 occ:1.00 O3G B:ATP1001 1.9 13.2 1.0 O B:HOH1119 2.1 10.5 1.0 O1B B:ATP1001 2.1 8.1 1.0 O B:HOH1120 2.1 8.1 1.0 OG B:SER22 2.1 9.3 1.0 O B:HOH1118 2.1 6.6 1.0 CB B:SER22 3.1 13.0 1.0 PG B:ATP1001 3.2 11.8 1.0 PB B:ATP1001 3.3 7.8 1.0 O3B B:ATP1001 3.4 11.9 1.0 O2G B:ATP1001 3.9 7.0 1.0 O B:HOH1138 3.9 28.4 1.0 O1A B:ATP1001 4.0 12.7 1.0 OD2 B:ASP78 4.1 13.7 1.0 O B:HOH1121 4.1 22.6 1.0 N B:SER22 4.1 6.0 1.0 O B:HOH1124 4.1 14.7 1.0 OD1 B:ASP78 4.2 20.0 1.0 CA B:SER22 4.2 6.1 1.0 O B:HOH1133 4.3 18.8 1.0 O3A B:ATP1001 4.3 6.0 1.0 O1G B:ATP1001 4.4 16.4 1.0 O2B B:ATP1001 4.4 4.7 1.0 PA B:ATP1001 4.5 9.3 1.0 CG B:ASP78 4.5 13.3 1.0 NH2 B:ARG120 4.8 19.6 1.0 OD2 B:ASP38 4.8 45.4 1.0 O2A B:ATP1001 4.8 11.7 1.0 O B:HOH1159 4.9 36.5 1.0

L.K.Wang, U.Das, P.Smith, S.Shuman. Structure and Mechanism of the Polynucleotide Kinase Component of the Bacterial Pnkp-HEN1 Rna Repair System. Rna V. 18 2277 2012.
ISSN: ISSN 1355-8382
PubMed: 23118415
DOI: 10.1261/RNA.036061.112