Sodium in PDB 4f5n: Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog

All present enzymatic activity of Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog:
2.7.7.7;

The structure of Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog, PDB code: 4f5n 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)	22.10 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.322, 79.181, 54.857, 90.00, 105.53, 90.00
R / Rfree (%)	18.7 / 22

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

Fluorine

(F)

2 atoms

The binding sites of Sodium atom in the Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog (pdb code 4f5n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog, PDB code: 4f5n:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp 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 Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:31.8 occ:1.00 O A:THR101 2.5 16.0 1.0 O A:HOH517 2.6 26.7 1.0 O A:HOH502 2.7 22.2 1.0 O P:HOH101 2.9 17.9 1.0 O A:HOH819 2.9 33.8 1.0 NA A:NA402 3.4 14.8 1.0 C A:THR101 3.5 16.1 1.0 CA A:ARG102 4.0 14.9 1.0 N A:ARG102 4.2 15.0 1.0 OG1 A:THR101 4.4 17.7 1.0 O A:HOH725 4.4 33.4 1.0 CB A:THR101 4.4 17.2 1.0 O A:HOH557 4.5 27.4 1.0 C A:ARG102 4.5 15.9 1.0 CA A:THR101 4.6 15.3 1.0 O A:HOH598 4.6 23.3 1.0 NZ A:LYS27 4.7 36.4 1.0 O A:ARG102 4.8 15.8 1.0 O A:HOH894 4.9 31.9 1.0 OP1 P:DG9 4.9 13.6 1.0

Sodium binding site 2 out of 3 in the Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp 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 Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:14.8 occ:1.00 O A:ILE106 2.3 13.7 1.0 O A:THR101 2.4 16.0 1.0 O A:VAL103 2.4 14.6 1.0 OP1 P:DG9 2.4 13.6 1.0 O P:HOH101 2.7 17.9 1.0 O A:HOH502 2.8 22.2 1.0 C A:THR101 3.3 16.1 1.0 C A:ILE106 3.3 14.8 1.0 C A:VAL103 3.4 14.6 1.0 NA A:NA401 3.4 31.8 1.0 P P:DG9 3.5 14.5 1.0 N A:ILE106 3.8 12.5 1.0 CA A:THR101 3.8 15.3 1.0 OP2 P:DG9 3.8 16.8 1.0 CA A:SER104 4.0 13.0 1.0 N A:GLY105 4.0 13.8 1.0 N A:SER104 4.0 13.2 1.0 CA A:ILE106 4.1 12.6 1.0 N A:VAL103 4.1 12.1 1.0 N A:GLY107 4.3 13.1 1.0 CB A:THR101 4.3 17.2 1.0 C A:SER104 4.3 11.8 1.0 C A:ARG102 4.3 15.9 1.0 N A:ARG102 4.4 15.0 1.0 CA A:VAL103 4.4 12.6 1.0 CB A:ILE106 4.4 13.1 1.0 O3' P:DC8 4.5 14.4 1.0 CA A:GLY107 4.6 16.1 1.0 C A:GLY105 4.6 12.9 1.0 CA A:ARG102 4.7 14.9 1.0 O5' P:DG9 4.7 14.8 1.0 O A:ARG102 4.8 15.8 1.0 O A:LEU100 4.8 15.3 1.0 CA A:GLY105 4.9 14.0 1.0 O A:HOH598 5.0 23.3 1.0

Sodium binding site 3 out of 3 in the Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Open Ternary Complex of R283K Dna Polymerase Beta with A Metal Free Dctp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:26.1 occ:1.00 O A:VAL65 2.3 23.1 1.0 O A:LEU62 2.3 26.8 1.0 O A:LYS60 2.4 24.3 1.0 O D:HOH102 2.6 23.8 1.0 O A:HOH570 2.6 30.6 1.0 OP1 D:DC3 2.7 24.5 1.0 C A:LEU62 3.3 28.3 1.0 C A:VAL65 3.4 20.6 1.0 C A:LYS60 3.5 28.8 1.0 P D:DC3 3.7 22.5 1.0 N A:VAL65 3.7 19.3 1.0 OP2 D:DC3 3.9 18.4 1.0 O D:HOH123 3.9 30.8 1.0 CA A:PRO63 4.0 26.9 1.0 N A:GLY64 4.0 23.8 1.0 CA A:VAL65 4.0 20.6 1.0 N A:PRO63 4.0 27.6 1.0 N A:LEU62 4.0 24.9 1.0 C A:LYS61 4.2 29.9 1.0 CA A:LYS60 4.2 24.9 1.0 CB A:VAL65 4.3 18.5 1.0 CA A:LEU62 4.3 23.9 1.0 C A:PRO63 4.4 25.4 1.0 CG A:LYS60 4.4 26.7 1.0 N A:GLY66 4.5 19.1 1.0 N A:LYS61 4.5 29.6 1.0 O A:LYS61 4.5 31.9 1.0 O3' D:DT2 4.5 20.5 1.0 CA A:LYS61 4.7 28.3 1.0 C A:GLY64 4.7 22.7 1.0 CA A:GLY66 4.8 18.9 1.0 O A:ALA59 4.9 22.9 1.0 CB A:LYS60 4.9 26.6 1.0 CA A:GLY64 5.0 21.6 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