Magnesium in PDB 4mde: Structure of Bacterial Polynucleotide Kinase Product Complex Bound to Gdp and Dna

The structure of Structure of Bacterial Polynucleotide Kinase Product Complex Bound to Gdp and Dna, PDB code: 4mde was solved by S.Shuman, U.Das, L.K.Wang, P.Smith, A.Jacewicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.99 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.440, 73.120, 119.040, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.6

The binding sites of Magnesium atom in the Structure of Bacterial Polynucleotide Kinase Product Complex Bound to Gdp and Dna (pdb code 4mde). 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 Bacterial Polynucleotide Kinase Product Complex Bound to Gdp and Dna, PDB code: 4mde:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Bacterial Polynucleotide Kinase Product Complex Bound to Gdp and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Bacterial Polynucleotide Kinase Product Complex Bound to Gdp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:13.8 occ:1.00 O1B A:GDP1001 2.0 15.3 1.0 OP3 C:DC1 2.1 13.7 1.0 O A:HOH1103 2.1 11.8 1.0 OG A:SER22 2.1 11.3 1.0 O A:HOH1101 2.2 14.4 1.0 O A:HOH1102 2.2 14.1 1.0 NH2 A:ARG123 3.0 35.0 1.0 CB A:SER22 3.2 11.7 1.0 PB A:GDP1001 3.4 14.1 1.0 P C:DC1 3.4 14.4 1.0 O3B A:GDP1001 3.7 15.4 1.0 OP2 C:DC1 3.9 13.1 1.0 N A:SER22 4.0 10.9 1.0 O1A A:GDP1001 4.0 15.3 1.0 OD2 A:ASP78 4.1 14.5 1.0 ND2 A:ASN38 4.1 13.1 1.0 OP1 C:DC1 4.1 15.8 1.0 O A:HOH1110 4.1 14.0 1.0 OD1 A:ASP78 4.1 14.3 1.0 O A:HOH1163 4.1 29.8 1.0 CA A:SER22 4.2 12.0 1.0 CZ A:ARG123 4.2 20.4 1.0 O2B A:GDP1001 4.2 12.9 1.0 O A:HOH1143 4.4 17.5 1.0 O3A A:GDP1001 4.5 16.1 1.0 O5' C:DC1 4.5 15.0 1.0 CG A:ASP78 4.5 13.3 1.0 NH1 A:ARG123 4.6 41.9 1.0 O C:HOH104 4.6 14.9 1.0 PA A:GDP1001 4.6 16.0 1.0 NZ A:LYS21 4.8 12.1 1.0 CE A:LYS21 4.9 11.0 1.0 O2A A:GDP1001 5.0 15.1 1.0 CB A:LYS21 5.0 12.7 1.0

Magnesium binding site 2 out of 2 in the Structure of Bacterial Polynucleotide Kinase Product Complex Bound to Gdp and Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Bacterial Polynucleotide Kinase Product Complex Bound to Gdp and Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:15.0 occ:1.00 OP1 D:DC1 2.1 15.4 1.0 O1B B:GDP1001 2.1 14.8 1.0 OG B:SER22 2.1 14.6 1.0 O B:HOH1101 2.1 18.2 1.0 O B:HOH1103 2.1 13.3 1.0 O B:HOH1102 2.2 11.9 1.0 CB B:SER22 3.2 15.5 1.0 P D:DC1 3.4 16.4 1.0 PB B:GDP1001 3.4 16.1 1.0 NH2 B:ARG123 3.5 43.2 1.0 O3B B:GDP1001 3.7 17.7 1.0 OP2 D:DC1 3.9 15.2 1.0 NH1 B:ARG123 4.0 19.5 1.0 N B:SER22 4.0 14.1 1.0 OD2 B:ASP78 4.1 16.9 1.0 OD1 B:ASP78 4.1 14.7 1.0 OP3 D:DC1 4.1 16.2 1.0 O1A B:GDP1001 4.1 18.0 1.0 O B:HOH1111 4.1 14.9 1.0 O B:HOH1184 4.2 34.7 1.0 CA B:SER22 4.2 14.0 1.0 CZ B:ARG123 4.2 41.3 1.0 ND2 B:ASN38 4.2 14.8 1.0 O D:HOH103 4.3 17.6 1.0 O2B B:GDP1001 4.3 13.6 1.0 CG B:ASP78 4.5 17.3 1.0 O5' D:DC1 4.5 18.1 1.0 O3A B:GDP1001 4.5 18.3 1.0 O B:HOH1142 4.5 23.8 1.0 PA B:GDP1001 4.7 18.8 1.0 NZ B:LYS21 4.7 12.5 1.0 CE B:LYS21 4.8 13.1 1.0 CB B:LYS21 5.0 16.0 1.0

U.Das, L.K.Wang, P.Smith, A.Jacewicz, S.Shuman. Structures of Bacterial Polynucleotide Kinase in A Michaelis Complex with Gtp*MG2+ and 5'-Oh Oligonucleotide and A Product Complex with Gdp*MG2+ and 5'-PO4 Oligonucleotide Reveal A Mechanism of General Acid-Base Catalysis and the Determinants of Phosphoacceptor Recognition. Nucleic Acids Res. V. 42 1152 2014.
ISSN: ISSN 0305-1048
PubMed: 24150947
DOI: 10.1093/NAR/GKT936