Sodium in PDB 1mq2: Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp:
2.7.7.7;

The structure of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp, PDB code: 1mq2 was solved by J.M.Krahn, W.A.Beard, H.Miller, A.P.Grollman, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.200, 81.000, 55.600, 90.00, 106.10, 90.00
R / Rfree (%)	25.7 / 31.7

The binding sites of Sodium atom in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp (pdb code 1mq2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp, PDB code: 1mq2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:22.6 occ:1.00 O A:THR101 2.0 22.0 1.0 O A:HOH344 2.2 23.2 1.0 O A:ILE106 2.3 21.1 1.0 OP1 P:DG9 2.4 21.8 1.0 O A:VAL103 2.5 21.1 1.0 O A:HOH345 2.7 21.9 1.0 C A:THR101 3.1 23.7 1.0 C A:VAL103 3.4 19.4 1.0 C A:ILE106 3.5 18.2 1.0 P P:DG9 3.5 21.7 1.0 OP2 P:DG9 3.8 21.8 1.0 CA A:THR101 3.8 24.6 1.0 N A:ILE106 3.9 14.7 1.0 N A:GLY105 3.9 16.7 1.0 CA A:SER104 4.1 17.8 1.0 N A:VAL103 4.1 20.5 1.0 N A:SER104 4.1 19.6 1.0 C A:ARG102 4.1 21.1 1.0 N A:ARG102 4.2 20.8 1.0 CA A:ILE106 4.2 16.1 1.0 CB A:THR101 4.4 24.3 1.0 O3' P:DC8 4.4 20.9 1.0 CA A:VAL103 4.4 19.4 1.0 N A:GLY107 4.4 18.3 1.0 O A:ARG102 4.4 21.9 1.0 C A:SER104 4.5 17.2 1.0 CA A:ARG102 4.5 21.6 1.0 CA A:GLY107 4.6 18.4 1.0 C A:GLY105 4.6 15.6 1.0 CB A:ILE106 4.7 17.2 1.0 O5' P:DG9 4.7 25.5 1.0 O A:LEU100 4.8 26.2 1.0 CA A:GLY105 4.9 15.9 1.0

Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Complexed with Gapped Dna Containing An 8-Oxo-7,8-Dihydro-Guanine and Damp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:37.6 occ:1.00 O A:LYS60 2.3 37.2 1.0 O D:HOH346 2.4 37.1 1.0 O A:VAL65 2.4 36.2 1.0 OP1 D:DC3 2.4 36.1 1.0 O A:HOH347 2.5 37.3 1.0 O A:LEU62 2.6 37.2 1.0 C A:VAL65 3.5 35.2 1.0 C A:LYS60 3.5 38.9 1.0 C A:LEU62 3.6 36.7 1.0 P D:DC3 3.7 34.0 1.0 N A:VAL65 3.8 34.6 1.0 OP2 D:DC3 4.0 34.0 1.0 CA A:VAL65 4.1 34.5 1.0 N A:GLY64 4.1 37.3 1.0 CA A:PRO63 4.2 36.9 1.0 C A:LYS61 4.2 39.0 1.0 CA A:LYS60 4.3 39.2 1.0 CG A:LYS60 4.3 38.8 1.0 N A:PRO63 4.3 36.2 1.0 O A:LYS61 4.3 38.6 1.0 N A:LEU62 4.3 37.6 1.0 CB A:VAL65 4.4 33.1 1.0 N A:LYS61 4.5 39.4 1.0 N A:GLY66 4.6 35.8 1.0 O3' D:DT2 4.6 32.2 1.0 C A:PRO63 4.6 37.3 1.0 CA A:LEU62 4.6 37.5 1.0 CA A:LYS61 4.7 39.9 1.0 O5' D:DC3 4.8 33.3 1.0 C A:GLY64 4.8 35.5 1.0 CA A:GLY66 4.9 36.0 1.0 CB A:LYS60 4.9 39.4 1.0

J.M.Krahn, W.A.Beard, H.Miller, A.P.Grollman, S.H.Wilson. Structure of Dna Polymerase Beta with the Mutagenic Dna Lesion 8-Oxodeoxyguanine Reveals Structural Insights Into Its Coding Potential Structure V. 11 121 2003.
ISSN: ISSN 0969-2126
PubMed: 12517346
DOI: 10.1016/S0969-2126(02)00930-9