Calcium in PDB 4khu: Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position:
2.7.7.7;

The structure of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position, PDB code: 4khu 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)	21.62 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.977, 119.350, 127.860, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.7

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

Sodium

(Na)

4 atoms

The binding sites of Calcium atom in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position (pdb code 4khu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position, PDB code: 4khu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:29.6 occ:1.00 O1B A:TTP1001 2.1 25.5 1.0 O1A A:TTP1001 2.2 23.0 1.0 O2G A:TTP1001 2.2 24.4 1.0 OD1 A:ASP623 2.3 28.3 1.0 O A:LEU412 2.4 27.8 1.0 OD2 A:ASP411 2.5 40.5 1.0 OD1 A:ASP411 2.6 47.5 1.0 CG A:ASP411 2.9 42.8 1.0 PB A:TTP1001 3.3 28.8 1.0 CG A:ASP623 3.4 30.3 1.0 PG A:TTP1001 3.5 28.2 1.0 PA A:TTP1001 3.5 32.1 1.0 NA A:NA1008 3.5 46.2 1.0 C A:LEU412 3.6 30.1 1.0 O3A A:TTP1001 3.8 29.8 1.0 OD2 A:ASP623 3.8 31.6 1.0 O3B A:TTP1001 3.9 33.0 1.0 N A:LEU412 4.0 32.0 1.0 C5' A:TTP1001 4.2 26.2 1.0 O1G A:TTP1001 4.2 27.3 1.0 CA A:LEU412 4.3 29.4 1.0 CB A:ASP411 4.3 40.5 1.0 O5' A:TTP1001 4.5 34.1 1.0 O2A A:TTP1001 4.5 34.6 1.0 N A:SER414 4.6 31.5 1.0 O2B A:TTP1001 4.6 28.7 1.0 N A:THR413 4.6 29.9 1.0 C A:ASP411 4.6 34.0 1.0 N A:PHE415 4.6 24.6 1.0 CB A:PHE415 4.7 24.8 1.0 CB A:ASP623 4.7 28.5 1.0 O3G A:TTP1001 4.7 37.4 1.0 CB A:LEU412 4.8 27.3 1.0 CA A:THR413 4.8 30.9 1.0 O A:HOH1556 4.9 62.5 1.0 C A:THR413 4.9 33.8 1.0 CA A:ASP411 4.9 36.4 1.0 O A:ASP623 5.0 30.2 1.0

Calcium binding site 2 out of 3 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:66.0 occ:1.00 O A:HOH1516 2.4 45.7 1.0 O A:HOH1542 2.4 67.4 1.0 O A:ASN505 2.4 65.1 1.0 O A:LYS531 2.6 55.1 1.0 OD1 A:ASN507 3.0 62.7 1.0 O A:HOH1548 3.2 72.3 1.0 C A:LYS531 3.5 57.8 1.0 CG A:ASN507 3.6 65.1 1.0 C A:ASN505 3.6 66.3 1.0 ND2 A:ASN507 3.8 65.1 1.0 N A:ASN507 4.0 68.6 1.0 CA A:LYS531 4.1 56.0 1.0 CA A:PRO506 4.3 61.9 1.0 C A:PRO506 4.4 66.7 1.0 N A:LYS532 4.4 59.1 1.0 CB A:ASN505 4.4 78.1 1.0 N A:PRO506 4.4 61.5 1.0 CB A:LYS531 4.6 56.4 1.0 O A:ALA502 4.6 61.1 1.0 CA A:LYS532 4.6 60.3 1.0 O A:HOH1585 4.6 48.5 1.0 CA A:ASN505 4.7 73.1 1.0 CB A:ASN507 4.8 67.4 1.0 CA A:ASN507 4.8 69.2 1.0 O A:LEU533 4.9 56.1 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at -1 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:58.2 occ:1.00 O A:HOH1101 2.4 39.9 1.0 O A:HOH1472 2.4 43.3 1.0 O A:HOH1248 2.4 37.4 1.0 OE2 A:GLU196 2.7 41.5 1.0 OD1 A:ASP192 2.7 52.4 1.0 OD2 A:ASP192 2.7 54.4 1.0 OE1 A:GLU196 2.8 41.9 1.0 CG A:ASP192 3.1 53.0 1.0 CD A:GLU196 3.1 41.2 1.0 O A:HOH1205 4.1 41.5 1.0 ND2 A:ASN193 4.2 55.1 1.0 O A:HOH1465 4.2 55.0 1.0 CB A:ASP192 4.6 47.8 1.0 CG A:GLU196 4.6 38.1 1.0 CG A:ASN193 4.9 52.0 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