Sodium in PDB 3cq8: Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase

All present enzymatic activity of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase:
2.7.7.7;

The structure of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase, PDB code: 3cq8 was solved by X.Zhong, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.70 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.840, 117.006, 127.823, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 28.1

The structure of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase (pdb code 3cq8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase, PDB code: 3cq8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1007 b:45.8 occ:1.00 OE2 A:GLU177 2.4 53.5 1.0 OE1 A:GLU172 2.6 50.4 1.0 OE1 A:GLU177 2.9 57.1 1.0 CD A:GLU177 3.0 54.6 1.0 OE2 A:GLU172 3.3 52.2 1.0 CD A:GLU172 3.4 50.5 1.0 O A:HOH1433 3.4 42.2 1.0 CG A:GLN171 4.2 50.1 1.0 CB A:GLN171 4.3 47.4 1.0 CG A:GLU177 4.5 51.3 1.0 CG A:GLU172 4.8 48.9 1.0 N A:GLN171 5.0 44.1 1.0

Sodium binding site 2 out of 3 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1008 b:67.1 occ:1.00 OD1 A:ASN507 2.0 89.1 1.0 O A:LYS531 2.1 74.9 1.0 O A:ASN505 2.2 75.3 1.0 CB A:ASN505 2.6 79.4 1.0 CG A:ASN507 2.8 88.3 1.0 C A:ASN505 3.0 77.1 1.0 ND2 A:ASN507 3.1 88.2 1.0 C A:LYS531 3.3 75.8 1.0 CA A:ASN505 3.3 77.5 1.0 CG A:ASN505 3.8 80.5 1.0 N A:ASN507 4.0 82.7 1.0 CA A:LYS532 4.1 76.0 1.0 N A:LYS532 4.1 76.1 1.0 N A:PRO506 4.2 78.3 1.0 CB A:ASN507 4.2 85.8 1.0 CA A:LYS531 4.3 75.6 1.0 ND2 A:ASN505 4.4 81.2 1.0 OD1 A:ASN505 4.5 80.2 1.0 N A:ASN505 4.6 77.3 1.0 C A:LYS532 4.6 75.8 1.0 CA A:ASN507 4.6 84.0 1.0 O A:LYS532 4.7 75.8 1.0 CB A:LYS531 4.8 76.6 1.0 CA A:PRO506 4.8 79.5 1.0 C A:PRO506 4.9 81.3 1.0

Sodium binding site 3 out of 3 in the Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of the L415F Mutant RB69 Exo(-)Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:56.1 occ:1.00 O A:ASN606 1.9 64.8 1.0 O A:GLY610 2.4 78.9 1.0 CB A:GLU612 2.5 80.6 1.0 CA A:GLU612 2.7 78.5 1.0 N A:GLU612 2.8 79.3 1.0 C A:ASN606 3.0 65.9 1.0 C A:THR611 3.2 79.9 1.0 CG A:GLU612 3.4 84.1 1.0 O A:THR611 3.5 80.7 1.0 C A:GLY610 3.6 78.9 1.0 CB A:ASN606 3.7 61.7 1.0 CA A:ASN606 3.7 64.1 1.0 OE1 A:GLU612 3.9 88.2 1.0 N A:GLU607 4.0 67.7 1.0 CD A:GLU612 4.2 87.2 1.0 C A:GLU612 4.2 76.7 1.0 CA A:THR611 4.2 79.5 1.0 N A:THR611 4.3 79.8 1.0 CA A:GLU607 4.4 69.9 1.0 CA A:GLY610 4.6 78.0 1.0 OD1 A:ASN606 4.6 60.2 1.0 CG A:ASN606 4.7 60.2 1.0 N A:GLY613 4.8 75.7 1.0 N A:GLY610 5.0 76.8 1.0

X.Zhong, L.C.Pedersen, T.A.Kunkel. Characterization of A Replicative Dna Polymerase Mutant with Reduced Fidelity and Increased Translesion Synthesis Capacity. Nucleic Acids Res. V. 36 3892 2008.
ISSN: ISSN 0305-1048
PubMed: 18503083
DOI: 10.1093/NAR/GKN312