Magnesium in PDB 4gp6: Polynucleotide Kinase

All present enzymatic activity of Polynucleotide Kinase:
2.7.1.78;

The structure of Polynucleotide Kinase, PDB code: 4gp6 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)	35.78 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.690, 71.560, 118.610, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.8

The binding sites of Magnesium atom in the Polynucleotide Kinase (pdb code 4gp6). 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: 4gp6:
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:20.9 occ:1.00 O A:HOH1103 2.0 16.1 1.0 O A:HOH1204 2.0 18.9 1.0 OG A:SER22 2.1 18.1 1.0 O A:HOH1101 2.1 18.7 1.0 O1B A:ADP1001 2.1 18.9 1.0 O A:HOH1102 2.2 15.7 1.0 PB A:ADP1001 3.2 19.5 1.0 CB A:SER22 3.3 18.9 1.0 O3B A:ADP1001 3.4 22.9 1.0 O1A A:ADP1001 3.9 25.4 1.0 N A:SER22 4.1 20.6 1.0 O A:HOH1125 4.1 31.1 1.0 OD1 A:ASP78 4.1 20.9 1.0 OD2 A:ASP78 4.2 21.6 1.0 O A:HOH1152 4.2 28.0 1.0 O2B A:ADP1001 4.2 22.1 1.0 O A:HOH1145 4.2 34.3 1.0 CA A:SER22 4.3 21.6 1.0 O3A A:ADP1001 4.3 20.1 1.0 NH2 A:ARG120 4.4 21.3 1.0 O A:HOH1167 4.4 41.7 1.0 OD2 A:ASP38 4.4 33.8 1.0 PA A:ADP1001 4.5 22.6 1.0 CG A:ASP78 4.6 24.8 1.0 O A:HOH1180 4.6 27.8 1.0 O A:HOH1154 4.7 29.4 1.0 NZ A:LYS21 4.9 13.3 1.0 CB A:LYS21 4.9 21.7 1.0 O2A A:ADP1001 5.0 25.6 1.0 CE A:LYS21 5.0 15.2 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:22.8 occ:1.00 O B:HOH1103 2.1 21.3 1.0 O B:HOH1104 2.1 20.1 1.0 O B:HOH1101 2.1 19.9 1.0 O B:HOH1102 2.1 21.4 1.0 OG B:SER22 2.2 19.1 1.0 O1B B:ADP1001 2.2 17.4 1.0 PB B:ADP1001 3.3 18.0 1.0 CB B:SER22 3.4 20.8 1.0 O3B B:ADP1001 3.5 18.3 1.0 O1A B:ADP1001 4.0 19.9 1.0 OD2 B:ASP38 4.1 27.1 1.0 N B:SER22 4.2 13.8 1.0 OD2 B:ASP78 4.2 21.0 1.0 O B:HOH1117 4.2 26.9 1.0 O B:HOH1173 4.3 32.0 1.0 OD1 B:ASP78 4.3 21.9 1.0 O B:HOH1170 4.3 35.5 1.0 O B:HOH1131 4.3 30.0 1.0 O2B B:ADP1001 4.3 16.7 1.0 CA B:SER22 4.4 17.1 1.0 O B:HOH1180 4.4 37.3 1.0 O3A B:ADP1001 4.4 17.0 1.0 NH2 B:ARG120 4.6 31.5 1.0 PA B:ADP1001 4.6 20.1 1.0 CG B:ASP78 4.7 24.3 1.0 NZ B:LYS21 5.0 20.5 1.0 CE B:LYS21 5.0 22.4 1.0 O2A B:ADP1001 5.0 23.2 1.0 CG B:ASP38 5.0 29.4 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