Sodium in PDB 4i9q: Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase

All present enzymatic activity of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase:
2.7.7.7;

The structure of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase, PDB code: 4i9q was solved by K.E.Guja, A.Jacewicz, A.Trzemecka, D.Plochocka, E.Yakubovskaya, A.Bebenek, M.Garcia-Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.40 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.781, 119.412, 146.016, 90.00, 90.26, 90.00
R / Rfree (%)	25.2 / 28.7

The structure of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase (pdb code 4i9q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase, PDB code: 4i9q:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:44.1 occ:1.00 N A:LEU415 2.6 24.8 1.0 O2B A:XG41001 2.8 59.9 1.0 N A:SER414 2.8 23.1 1.0 OD2 A:ASP623 2.9 33.9 1.0 CA A:SER414 3.0 23.5 0.1 CA A:SER414 3.0 23.5 0.9 O A:LEU412 3.2 28.4 1.0 N3A A:XG41001 3.3 50.4 1.0 C A:SER414 3.3 22.3 1.0 PB A:XG41001 3.3 36.2 1.0 O1B A:XG41001 3.5 39.7 1.0 C5' A:XG41001 3.7 21.0 1.0 C A:THR413 3.7 26.9 1.0 CA A:LEU415 3.7 24.1 1.0 CB A:LEU415 3.7 21.8 1.0 CG A:ASP623 3.9 29.3 1.0 C A:LEU412 3.9 24.4 1.0 CA A:CA1003 3.9 51.7 1.0 O A:HOH1105 3.9 16.3 1.0 CB A:ASP623 4.0 23.5 1.0 O3' A:XG41001 4.1 27.4 1.0 O A:HOH1314 4.1 36.2 1.0 O5' A:XG41001 4.2 22.4 1.0 CA A:THR413 4.3 28.5 1.0 N A:THR413 4.4 26.9 1.0 C4' A:XG41001 4.4 25.4 1.0 PA A:XG41001 4.5 37.8 1.0 CB A:SER414 4.5 24.4 0.1 CB A:SER414 4.5 24.8 0.9 O A:THR413 4.5 29.8 1.0 O A:SER414 4.5 22.6 1.0 C3' A:XG41001 4.6 24.3 1.0 CB A:LEU412 4.8 23.9 1.0 CA A:LEU412 4.9 25.4 1.0 OG A:SER414 4.9 22.5 0.9 O3B A:XG41001 4.9 58.7 1.0 C A:LEU415 5.0 25.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Ternary Complex of the D714A Mutant of RB69 Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1004 b:59.9 occ:1.00 O B:LEU412 2.5 38.7 1.0 N B:LEU415 2.6 30.3 1.0 N B:SER414 2.8 32.2 1.0 OD2 B:ASP623 2.9 39.7 1.0 CA B:SER414 3.2 29.9 0.9 CA B:SER414 3.2 30.2 0.1 C B:LEU412 3.2 37.4 1.0 O2B B:XG41001 3.3 39.0 1.0 C B:SER414 3.3 30.5 1.0 C B:THR413 3.5 35.7 1.0 CB B:LEU415 3.6 33.3 1.0 CA B:LEU415 3.6 32.9 1.0 CB B:ASP623 3.7 37.7 1.0 CG B:ASP623 3.7 39.3 1.0 N B:THR413 3.9 37.9 1.0 C5' B:XG41001 3.9 29.9 1.0 CB B:LEU412 4.0 27.3 1.0 CA B:THR413 4.0 35.7 1.0 N3A B:XG41001 4.0 27.7 1.0 CA B:LEU412 4.1 37.9 1.0 PB B:XG41001 4.1 37.6 1.0 CA B:CA1003 4.2 78.5 1.0 O B:THR413 4.3 36.4 1.0 O1B B:XG41001 4.3 37.7 1.0 O3' B:XG41001 4.4 33.2 1.0 N B:LEU412 4.5 39.1 1.0 O B:HOH1233 4.5 37.5 1.0 O B:SER414 4.5 27.0 1.0 C4' B:XG41001 4.6 29.7 1.0 CB B:SER414 4.7 29.4 0.9 CB B:SER414 4.7 29.8 0.1 C3' B:XG41001 4.9 30.1 1.0 O5' B:XG41001 4.9 33.6 1.0 O B:HOH1120 4.9 31.4 1.0 OD1 B:ASP623 4.9 39.7 1.0 C B:LEU415 5.0 34.7 1.0

A.Jacewicz, A.Trzemecka, K.E.Guja, D.Plochocka, E.Yakubovskaya, A.Bebenek, M.Garcia-Diaz. A Remote Palm Domain Residue of RB69 Dna Polymerase Is Critical For Enzyme Activity and Influences the Conformation of the Active Site. Plos One V. 8 76700 2013.
ISSN: ESSN 1932-6203
PubMed: 24116139
DOI: 10.1371/JOURNAL.PONE.0076700