Sodium in PDB 4ki6: Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position:
2.7.7.7;

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position, PDB code: 4ki6 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)	35.95 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.853, 118.400, 127.970, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.3

The structure of Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Sodium atom in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -2 Position (pdb code 4ki6). 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 Ribonucleotides at -1 and -2 Position, PDB code: 4ki6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -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 Ribonucleotides at -1 and -2 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1008 b:93.1 occ:1.00 O A:ASN505 2.3 0.7 1.0 O A:LYS531 2.4 0.4 1.0 OD1 A:ASN507 2.7 0.1 1.0 C A:LYS531 3.1 0.6 1.0 CB A:ASN505 3.3 0.6 1.0 C A:ASN505 3.4 0.4 1.0 CG A:ASN507 3.5 0.8 1.0 ND2 A:ASN507 3.7 0.6 1.0 CA A:LYS531 3.7 0.1 1.0 CA A:ASN505 4.0 0.5 1.0 CB A:LYS531 4.1 0.9 1.0 N A:LYS532 4.1 0.8 1.0 O A:ALA502 4.5 93.6 1.0 N A:PRO506 4.5 0.5 1.0 CA A:LYS532 4.6 0.6 1.0 CG A:ASN505 4.6 0.6 1.0 ND2 A:ASN505 4.7 0.4 1.0 N A:ASN505 4.8 0.9 1.0 C A:PRO506 4.8 0.7 1.0 N A:ASN507 4.8 0.0 1.0 CA A:PRO506 4.8 0.7 1.0 CB A:ASN507 4.9 0.8 1.0

Sodium binding site 2 out of 2 in the Ternary Complex of RB69 Mutant L415F with Ribonucleotides at -1 and -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 Ribonucleotides at -1 and -2 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1009 b:78.0 occ:1.00 OG A:SER220 3.3 62.8 1.0 OD2 A:ASP275 3.3 49.7 1.0 OD1 A:ASP275 3.4 39.8 1.0 CG A:ASP275 3.8 42.8 1.0 OE1 A:GLU219 4.0 71.8 1.0 OD2 A:ASP272 4.4 49.6 1.0 CB A:SER220 4.6 56.5 1.0 CB A:GLU219 4.8 50.5 1.0 CG A:GLU219 4.8 59.0 1.0 CD A:GLU219 4.9 66.8 1.0 CG2 A:ILE274 4.9 41.4 1.0 ND2 A:ASN217 4.9 61.4 1.0 N A:SER220 5.0 50.9 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