Sodium in PDB 4f5p: Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog

All present enzymatic activity of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog:
2.7.7.7;

The structure of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog, PDB code: 4f5p was solved by B.D.Freudenthal, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.11 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.380, 79.240, 54.880, 90.00, 105.49, 90.00
R / Rfree (%)	20.3 / 24.5

The structure of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog (pdb code 4f5p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog, PDB code: 4f5p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:37.8 occ:1.00 O A:HOH501 2.5 22.1 1.0 O P:HOH101 2.5 20.6 1.0 O A:THR101 2.5 19.4 1.0 O A:HOH629 2.5 44.2 1.0 O A:HOH508 2.6 28.0 1.0 NA A:NA403 3.2 17.6 1.0 C A:THR101 3.5 17.7 1.0 CA A:ARG102 4.1 19.0 1.0 N A:ARG102 4.2 19.8 1.0 CB A:THR101 4.4 20.3 1.0 OG1 A:THR101 4.4 20.6 1.0 O A:HOH552 4.4 25.9 1.0 NZ A:LYS27 4.6 42.5 1.0 CA A:THR101 4.6 17.9 1.0 C A:ARG102 4.6 20.6 1.0 OP1 P:DG9 4.8 17.4 1.0 O A:HOH662 4.8 45.8 1.0 O A:ARG102 4.9 20.3 1.0 O A:HOH570 4.9 31.8 1.0

Sodium binding site 2 out of 2 in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:17.6 occ:1.00 O A:THR101 2.3 19.4 1.0 OP1 P:DG9 2.4 17.4 1.0 O A:ILE106 2.4 18.2 1.0 O P:HOH101 2.4 20.6 1.0 O A:VAL103 2.5 19.4 1.0 O A:HOH501 2.5 22.1 1.0 NA A:NA402 3.2 37.8 1.0 C A:THR101 3.3 17.7 1.0 C A:ILE106 3.4 18.2 1.0 C A:VAL103 3.4 21.0 1.0 P P:DG9 3.5 19.2 1.0 OP2 P:DG9 3.8 17.4 1.0 N A:ILE106 3.8 16.8 1.0 CA A:THR101 3.9 17.9 1.0 CA A:SER104 4.0 21.0 1.0 N A:GLY105 4.0 15.6 1.0 N A:SER104 4.1 18.8 1.0 CA A:ILE106 4.2 16.5 1.0 N A:VAL103 4.2 17.1 1.0 C A:SER104 4.3 16.5 1.0 C A:ARG102 4.3 20.6 1.0 CB A:THR101 4.3 20.3 1.0 N A:GLY107 4.4 16.7 1.0 N A:ARG102 4.4 19.8 1.0 CA A:VAL103 4.5 18.2 1.0 O3' P:DC8 4.5 17.8 1.0 CA A:GLY107 4.6 20.6 1.0 CB A:ILE106 4.6 21.2 1.0 CA A:ARG102 4.6 19.0 1.0 O5' P:DG9 4.7 17.7 1.0 C A:GLY105 4.7 14.9 1.0 O A:ARG102 4.8 20.3 1.0 CA A:GLY105 4.9 14.6 1.0 O A:HOH552 4.9 25.9 1.0 O A:LEU100 4.9 20.1 1.0

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Structures of Dntp Intermediate States During Dna Polymerase Active Site Assembly. Structure V. 20 1829 2012.
ISSN: ISSN 0969-2126
PubMed: 22959623
DOI: 10.1016/J.STR.2012.08.008