Calcium in PDB 3nci: RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution:
2.7.7.7;

The structure of RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution, PDB code: 3nci was solved by M.Wang, G.Blaha, T.A.Steitz, W.H.Konigsberg, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.504, 119.404, 129.763, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.1

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution (pdb code 3nci). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution, PDB code: 3nci:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca905 b:19.5 occ:1.00 OD1 A:ASP623 2.2 24.5 1.0 O1G A:DCP904 2.2 20.7 1.0 O2B A:DCP904 2.3 14.3 1.0 O A:LEU412 2.3 16.9 1.0 OD2 A:ASP411 2.5 30.2 1.0 O2A A:DCP904 2.6 22.2 1.0 OD1 A:ASP411 2.7 31.4 1.0 CG A:ASP411 2.9 27.6 1.0 CG A:ASP623 3.3 21.6 1.0 PB A:DCP904 3.3 18.0 1.0 C A:LEU412 3.5 18.5 1.0 PG A:DCP904 3.5 21.6 1.0 O A:HOH2044 3.6 44.6 1.0 PA A:DCP904 3.7 20.5 1.0 O3A A:DCP904 3.7 19.5 1.0 CA A:CA906 3.8 42.3 1.0 OD2 A:ASP623 3.8 23.9 1.0 O3B A:DCP904 3.8 19.8 1.0 N A:LEU412 4.1 18.4 1.0 O A:HOH1911 4.2 35.4 1.0 O2G A:DCP904 4.3 20.5 1.0 N A:SER414 4.3 16.1 1.0 CA A:LEU412 4.3 18.1 1.0 C5' A:DCP904 4.3 16.7 1.0 CB A:ASP411 4.4 24.7 1.0 N A:THR413 4.5 17.2 1.0 CB A:ASP623 4.5 20.3 1.0 O5' A:DCP904 4.5 19.8 1.0 C A:ASP411 4.6 21.0 1.0 CA A:THR413 4.6 18.2 1.0 O3G A:DCP904 4.6 21.2 1.0 N A:LEU415 4.6 13.6 1.0 O1B A:DCP904 4.7 18.8 1.0 C A:THR413 4.7 16.9 1.0 CB A:LEU412 4.9 17.3 1.0 O1A A:DCP904 4.9 19.8 1.0 CA A:ASP411 5.0 21.9 1.0

Calcium binding site 2 out of 3 in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca906 b:42.3 occ:1.00 O A:HOH1696 2.3 38.3 1.0 O2A A:DCP904 2.5 22.2 1.0 OD2 A:ASP411 2.6 30.2 1.0 OD2 A:ASP623 2.7 23.9 1.0 O A:HOH1992 2.9 30.6 1.0 O A:HOH1888 3.1 29.9 1.0 CG A:ASP623 3.6 21.6 1.0 OD1 A:ASP623 3.7 24.5 1.0 CG A:ASP411 3.7 27.6 1.0 C3' P:DOC115 3.7 12.9 1.0 CA A:CA905 3.8 19.5 1.0 O A:HOH2044 3.8 44.6 1.0 PA A:DCP904 3.8 20.5 1.0 CB A:SER624 4.1 22.5 1.0 O1A A:DCP904 4.1 19.8 1.0 O A:HOH1424 4.3 17.9 1.0 OD1 A:ASP411 4.5 31.4 1.0 OG A:SER624 4.5 25.7 1.0 O5' A:DCP904 4.5 19.8 1.0 C5' P:DOC115 4.6 15.9 1.0 CB A:ASP411 4.6 24.7 1.0 O5' P:DOC115 4.7 16.2 1.0 C5' A:DCP904 4.7 16.7 1.0 C4' P:DOC115 4.7 11.3 1.0 O A:HOH2045 4.8 42.9 1.0 O P:HOH249 4.8 28.9 1.0 N A:SER624 4.8 19.9 1.0 O A:ASP621 4.8 15.7 1.0 C A:ASP623 4.9 19.6 1.0 C2' P:DOC115 4.9 10.6 1.0 O1G A:DCP904 4.9 20.7 1.0 OE2 A:GLU686 4.9 37.2 1.0 CB A:ASP623 5.0 20.3 1.0 CA A:SER624 5.0 21.4 1.0

Calcium binding site 3 out of 3 in the RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of RB69 Dna Polymerase Ternary Complex with Dctp Opposite Dg at 1.8 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca907 b:30.1 occ:1.00 O A:LYS531 2.3 33.9 1.0 OD1 A:ASN507 2.3 36.5 1.0 O A:ASN505 2.3 33.2 1.0 O A:HOH929 2.3 30.1 1.0 O A:HOH928 2.4 19.4 1.0 O A:HOH931 2.5 33.4 1.0 O A:HOH927 2.5 19.5 1.0 C A:LYS531 3.3 33.8 1.0 CG A:ASN507 3.5 36.5 1.0 C A:ASN505 3.6 33.9 1.0 CA A:LYS531 4.0 33.1 1.0 N A:ASN507 4.1 34.7 1.0 ND2 A:ASN507 4.2 35.2 1.0 N A:LYS532 4.2 33.3 1.0 CB A:ASN505 4.2 35.5 0.5 CB A:ASN505 4.2 34.7 0.5 C A:PRO506 4.3 34.6 1.0 CA A:PRO506 4.3 33.8 1.0 CA A:LYS532 4.4 33.7 1.0 N A:PRO506 4.5 33.7 1.0 CA A:ASN505 4.5 34.6 0.5 CA A:ASN505 4.5 34.3 0.5 O A:HOH932 4.5 20.2 1.0 O A:LEU533 4.5 30.0 1.0 CB A:ASN507 4.6 36.0 1.0 O A:ALA502 4.6 29.4 1.0 CB A:LYS531 4.7 34.8 1.0 CA A:ASN507 4.7 35.9 1.0 C A:LYS532 4.8 33.1 1.0 N A:LEU533 4.8 31.8 1.0 O A:ILE530 4.9 28.6 1.0

M.Wang, S.Xia, G.Blaha, T.A.Steitz, W.H.Konigsberg, J.Wang. Insights Into Base Selectivity From the 1.8 A Resolution Structure of An RB69 Dna Polymerase Ternary Complex. Biochemistry V. 50 581 2011.
ISSN: ISSN 0006-2960
PubMed: 21158418
DOI: 10.1021/BI101192F