Sodium in PDB 3ogu: Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna

All present enzymatic activity of Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna:
2.7.7.7;

The structure of Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna, PDB code: 3ogu was solved by A.Marx, K.Diederichs, K.Bergen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	175.474, 56.782, 47.602, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.3

The binding sites of Sodium atom in the Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna (pdb code 3ogu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna, PDB code: 3ogu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na336 b:27.6 occ:1.00 OP1 P:DG6 2.6 30.7 1.0 O A:THR101 2.8 34.0 1.0 O A:ILE106 2.8 28.8 1.0 O A:VAL103 2.8 27.8 1.0 O A:HOH618 2.9 40.5 1.0 O P:HOH20 3.0 44.0 1.0 C A:THR101 3.4 32.5 1.0 C A:VAL103 3.5 27.6 1.0 O A:HOH366 3.5 38.3 1.0 C A:ILE106 3.6 29.8 1.0 P P:DG6 3.6 30.5 1.0 N A:ILE106 3.8 25.9 1.0 OP2 P:DG6 3.8 27.1 1.0 CA A:SER104 3.9 22.7 1.0 CA A:THR101 4.0 29.2 1.0 N A:SER104 4.0 24.6 1.0 N A:GLY105 4.0 21.8 1.0 N A:VAL103 4.1 25.9 1.0 CA A:ILE106 4.2 27.6 1.0 C A:ARG102 4.3 28.6 1.0 N A:ARG102 4.3 26.2 1.0 C A:SER104 4.4 24.5 1.0 CA A:VAL103 4.4 25.0 1.0 N A:GLY107 4.5 27.9 1.0 CB A:THR101 4.5 29.0 1.0 CA A:ARG102 4.6 27.5 1.0 O3' P:DT5 4.6 25.7 1.0 CB A:ILE106 4.6 27.3 1.0 C A:GLY105 4.7 24.5 1.0 O A:HOH614 4.8 56.5 1.0 O A:ARG102 4.8 28.9 1.0 O A:LEU100 4.8 25.9 1.0 O5' P:DG6 4.8 29.2 1.0 CA A:GLY107 4.8 28.6 1.0 CA A:GLY105 5.0 21.5 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na338 b:94.5 occ:1.00 O A:HOH405 3.3 41.8 1.0 O2S A:MES339 3.4 0.1 1.0 O1S A:MES339 3.6 0.1 1.0 OE2 A:GLU154 3.7 35.5 1.0 O A:HOH519 3.8 59.4 1.0 CG A:PRO151 3.8 30.5 1.0 S A:MES339 4.1 0.2 1.0 CD A:PRO151 4.4 29.9 1.0 O A:HOH423 4.5 42.0 1.0 O3S A:MES339 4.6 0.1 1.0 NH2 A:ARG253 4.7 30.4 1.0 CD A:GLU154 4.7 34.2 1.0 O A:HOH560 4.8 47.5 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta Mutant 5P20 Complexed with 6BP of Dna within 5.0Å range: probe atom residue distance (Å) B Occ P:Na337 b:0.5 occ:1.00 O P:HOH176 3.3 35.6 1.0 OP2 P:DG3 3.6 42.9 1.0 O P:HOH215 3.8 62.8 1.0 P P:DG3 4.8 41.0 1.0

S.Gieseking, K.Bergen, F.Di Pasquale, K.Diederichs, W.Welte, A.Marx. Human Dna Polymerase Beta Mutations Allowing Efficient Abasic Site Bypass. J.Biol.Chem. V. 286 4011 2011.
ISSN: ISSN 0021-9258
PubMed: 21107011
DOI: 10.1074/JBC.M110.176826