Sodium in PDB 4khw: Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position:
2.7.7.7;

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position, PDB code: 4khw was solved by A.R.Clausen, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.355, 118.630, 126.310, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.4

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Sodium atom in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position (pdb code 4khw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position, PDB code: 4khw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position


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 RB69 Mutant L415F with Ribonucleotide at -2 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:55.7 occ:1.00 O A:HOH1543 2.4 58.9 1.0 O A:HOH1544 2.4 53.7 1.0 O A:HOH1542 2.4 77.7 1.0 O A:ALA721 2.8 59.9 1.0 O A:HOH1462 2.9 45.4 1.0 C A:ALA721 3.9 57.1 1.0 OE2 A:GLU501 4.1 76.2 1.0 CA A:ALA721 4.3 54.7 1.0 O A:TYR720 4.6 53.9 1.0 OE2 A:GLU722 4.8 77.2 1.0 OE1 A:GLU501 4.9 81.1 1.0 CD A:GLU501 4.9 77.6 1.0

Sodium binding site 2 out of 2 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotide at -2 Position


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 RB69 Mutant L415F with Ribonucleotide at -2 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1011 b:72.8 occ:1.00 O A:HOH1538 2.3 56.8 1.0 O A:HOH1541 2.4 43.8 1.0 OD1 A:ASN232 2.4 50.8 1.0 O A:HOH1540 2.4 47.2 1.0 O A:HOH1539 2.4 49.9 1.0 CG A:ASN232 3.5 48.5 1.0 CD A:LYS231 4.0 49.9 1.0 ND2 A:ASN232 4.0 50.0 1.0 OD1 A:ASN228 4.0 39.6 1.0 CE A:LYS231 4.3 56.8 1.0 CG A:LYS231 4.5 46.6 1.0 NZ A:LYS231 4.5 59.9 1.0 O A:ASN228 4.6 39.0 1.0 O A:SER127 4.7 51.0 1.0 CB A:ASN232 4.7 44.3 1.0 N A:ASN232 4.8 41.5 1.0 CG A:ASN228 4.8 35.2 1.0 CA A:ASN232 4.9 42.6 1.0 CB A:LYS231 4.9 42.6 1.0 O A:HOH1327 5.0 44.4 1.0

A.R.Clausen, M.S.Murray, A.R.Passer, L.C.Pedersen, T.A.Kunkel. Structure-Function Analysis of Ribonucleotide Bypass By B Family Dna Replicases. Proc.Natl.Acad.Sci.Usa V. 110 16802 2013.
ISSN: ISSN 0027-8424
PubMed: 24082122
DOI: 10.1073/PNAS.1309119110