Calcium in PDB 4khs: Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at 0 Position

All present enzymatic activity of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at 0 Position:
2.7.7.7;

The structure of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at 0 Position, PDB code: 4khs 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)	27.08 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.699, 119.572, 127.800, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.6

The structure of Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at 0 Position also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	4 atoms

The binding sites of Calcium atom in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at 0 Position (pdb code 4khs). 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 0 Position, PDB code: 4khs:
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 0 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 0 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:31.8 occ:1.00 O2B A:TTP1002 2.1 30.1 1.0 O1G A:TTP1002 2.2 26.7 1.0 O2A A:TTP1002 2.2 27.6 1.0 OD2 A:ASP623 2.3 36.2 1.0 O A:LEU412 2.4 33.6 1.0 OD1 A:ASP411 2.4 46.7 1.0 OD2 A:ASP411 2.4 55.1 1.0 CG A:ASP411 2.8 48.5 1.0 PB A:TTP1002 3.3 28.8 1.0 CG A:ASP623 3.4 37.3 1.0 PG A:TTP1002 3.4 28.9 1.0 PA A:TTP1002 3.5 30.3 1.0 C A:LEU412 3.5 33.4 1.0 O A:HOH1363 3.7 38.6 1.0 O A:HOH1654 3.8 57.5 1.0 O3A A:TTP1002 3.8 37.7 1.0 O3B A:TTP1002 3.9 31.9 1.0 OD1 A:ASP623 3.9 37.0 1.0 N A:LEU412 4.0 33.6 1.0 O2G A:TTP1002 4.1 32.0 1.0 C5' A:TTP1002 4.2 23.1 1.0 CB A:ASP411 4.3 44.6 1.0 CA A:LEU412 4.3 34.3 1.0 N A:SER414 4.4 32.3 0.5 N A:SER414 4.4 32.3 0.5 O5' A:TTP1002 4.5 30.4 1.0 O A:HOH1468 4.5 60.6 1.0 O1B A:TTP1002 4.5 29.6 1.0 O1A A:TTP1002 4.6 31.6 1.0 N A:THR413 4.6 33.1 1.0 CB A:ASP623 4.7 33.2 1.0 C A:ASP411 4.7 35.7 1.0 N A:PHE415 4.7 28.1 1.0 O3G A:TTP1002 4.7 36.3 1.0 CA A:THR413 4.7 34.5 1.0 CB A:PHE415 4.7 23.8 1.0 C A:THR413 4.9 34.3 1.0 CB A:LEU412 4.9 36.0 1.0 CA A:ASP411 4.9 39.3 1.0

Calcium binding site 2 out of 3 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at 0 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 0 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:49.4 occ:1.00 O A:HOH1499 2.4 42.5 1.0 O A:HOH1500 2.4 46.7 1.0 OE2 A:GLU196 2.4 45.2 1.0 OD2 A:ASP192 2.5 55.5 1.0 OE1 A:GLU196 2.5 45.8 1.0 OD1 A:ASP192 2.5 52.5 1.0 CD A:GLU196 2.8 45.4 1.0 CG A:ASP192 2.8 53.1 1.0 O A:HOH1188 4.0 45.3 1.0 ND2 A:ASN193 4.0 62.5 1.0 CG A:GLU196 4.3 45.2 1.0 CB A:ASP192 4.3 48.5 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of RB69 Mutant L415F with A Ribonucleotide at 0 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 0 Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1007 b:73.9 occ:1.00 O A:LYS531 2.0 71.9 1.0 O A:ASN505 2.3 81.0 1.0 O A:HOH1504 2.4 55.2 1.0 O A:HOH1505 2.4 74.6 1.0 O A:HOH1646 2.4 45.2 1.0 O A:HOH1506 2.4 49.1 1.0 OD1 A:ASN507 2.4 77.5 1.0 C A:LYS531 3.0 73.4 1.0 C A:ASN505 3.5 81.2 1.0 CG A:ASN507 3.6 83.1 1.0 CA A:LYS531 3.8 73.8 1.0 N A:LYS532 3.9 73.3 1.0 CA A:LYS532 4.1 77.3 1.0 N A:ASN507 4.1 82.0 1.0 ND2 A:ASN507 4.1 86.0 1.0 CA A:PRO506 4.2 76.8 1.0 CB A:ASN505 4.3 84.8 1.0 N A:PRO506 4.3 76.7 1.0 C A:PRO506 4.4 81.0 1.0 CB A:LYS531 4.5 76.2 1.0 CA A:ASN505 4.5 85.3 1.0 O A:LEU533 4.6 68.9 1.0 N A:LEU533 4.6 71.3 1.0 C A:LYS532 4.6 75.3 1.0 O A:ILE530 4.7 69.0 1.0 CB A:ASN507 4.8 85.2 1.0 O A:HOH1566 4.8 52.5 1.0 O A:ALA502 4.8 77.4 1.0 CA A:ASN507 4.9 85.2 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