Calcium in PDB 4fji: RB69 Dna Polymerase Ternary Complex with Dctp/Dc

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dctp/Dc:
2.7.7.7;

The structure of RB69 Dna Polymerase Ternary Complex with Dctp/Dc, PDB code: 4fji was solved by S.Xia, J.Wang, W.H.Konigsberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.18 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.310, 119.565, 130.228, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26.4

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dctp/Dc (pdb code 4fji). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the RB69 Dna Polymerase Ternary Complex with Dctp/Dc, PDB code: 4fji:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dc


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/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:27.4 occ:1.00 OD1 A:ASP623 2.2 24.6 1.0 OD2 A:ASP411 2.2 26.5 1.0 O1G A:DCP1001 2.3 24.8 1.0 O A:LEU412 2.3 29.0 1.0 O2A A:DCP1001 2.3 27.1 1.0 O2B A:DCP1001 2.4 28.8 1.0 CG A:ASP623 3.3 28.0 1.0 CG A:ASP411 3.4 30.4 1.0 CA A:CA1003 3.4 70.8 1.0 PB A:DCP1001 3.5 29.5 1.0 C A:LEU412 3.5 30.0 1.0 PG A:DCP1001 3.6 31.1 1.0 PA A:DCP1001 3.6 26.2 1.0 O A:HOH1208 3.8 25.1 1.0 OD2 A:ASP623 3.8 26.7 1.0 N A:LEU412 3.9 29.8 1.0 O3B A:DCP1001 3.9 34.0 1.0 O3A A:DCP1001 3.9 30.9 1.0 CB A:ASP411 4.0 29.4 1.0 C5' A:DCP1001 4.1 27.4 1.0 CA A:LEU412 4.2 27.4 1.0 O2G A:DCP1001 4.3 25.9 1.0 O5' A:DCP1001 4.3 26.4 1.0 OD1 A:ASP411 4.4 32.2 1.0 C A:ASP411 4.4 29.6 1.0 CB A:ASP623 4.5 27.1 1.0 N A:THR413 4.5 29.1 1.0 CB A:ALA415 4.6 22.3 1.0 N A:ALA415 4.6 25.1 1.0 N A:SER414 4.6 29.4 1.0 CB A:LEU412 4.7 28.4 1.0 O3G A:DCP1001 4.7 29.4 1.0 O1A A:DCP1001 4.8 28.9 1.0 CA A:THR413 4.8 31.7 1.0 O1B A:DCP1001 4.8 31.3 1.0 CA A:ASP411 4.9 29.3 1.0 C A:THR413 4.9 29.1 1.0 O A:ASP411 4.9 28.6 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dc


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/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:70.8 occ:1.00 O2A A:DCP1001 2.6 27.1 1.0 O A:HOH1246 2.7 23.6 1.0 OD2 A:ASP623 2.8 26.7 1.0 OD2 A:ASP411 3.1 26.5 1.0 CA A:CA1002 3.4 27.4 1.0 CG A:ASP411 3.4 30.4 1.0 OD1 A:ASP623 3.5 24.6 1.0 CG A:ASP623 3.6 28.0 1.0 PA A:DCP1001 3.7 26.2 1.0 CB A:ASP411 3.8 29.4 1.0 C3' P:DOC115 4.0 22.7 1.0 C5' P:DOC115 4.1 27.6 1.0 OD1 A:ASP411 4.1 32.2 1.0 O1A A:DCP1001 4.1 28.9 1.0 O5' A:DCP1001 4.2 26.4 1.0 CB A:SER624 4.3 27.2 1.0 O A:HOH1127 4.4 24.4 1.0 C4' P:DOC115 4.5 30.1 1.0 C5' A:DCP1001 4.6 27.4 1.0 O1G A:DCP1001 4.6 24.8 1.0 O A:HOH1173 4.6 29.5 1.0 OG A:SER624 4.9 25.8 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dc


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/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:52.4 occ:1.00 O A:LYS531 2.2 44.6 1.0 OD1 A:ASN507 2.3 58.1 1.0 O A:HOH1117 2.4 32.5 1.0 O A:ASN505 2.4 54.8 1.0 O A:HOH1239 2.5 34.1 1.0 O A:HOH1116 2.5 28.3 1.0 O A:HOH1189 2.8 43.3 1.0 C A:LYS531 3.2 48.0 1.0 CG A:ASN507 3.4 54.2 1.0 C A:ASN505 3.6 56.0 1.0 ND2 A:ASN507 4.0 54.5 1.0 CA A:LYS531 4.0 47.9 1.0 N A:ASN507 4.0 54.3 1.0 N A:LYS532 4.1 50.5 1.0 CA A:PRO506 4.3 55.9 1.0 C A:PRO506 4.3 55.1 1.0 CA A:LYS532 4.4 52.0 1.0 O A:LEU533 4.4 47.4 1.0 N A:PRO506 4.4 55.5 1.0 CB A:ASN505 4.4 57.5 1.0 CB A:ASN507 4.5 54.7 1.0 O A:ALA502 4.6 48.7 1.0 C A:LYS532 4.6 51.5 1.0 CA A:ASN505 4.6 57.9 1.0 CB A:LYS531 4.7 48.5 1.0 CA A:ASN507 4.7 55.9 1.0 O A:ILE530 4.7 49.1 1.0 N A:LEU533 4.8 49.8 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of RB69 Dna Polymerase Ternary Complex with Dctp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:59.9 occ:1.00 O A:HOH1208 2.6 25.1 1.0 OE1 A:GLU716 3.4 46.5 1.0 NZ A:LYS486 4.0 32.2 1.0 CD A:GLU716 4.3 48.0 1.0 CG A:GLU716 4.4 40.9 1.0 CB A:ASP684 4.5 37.6 1.0 OG1 A:THR413 4.5 30.9 1.0 OD1 A:ASP411 4.6 32.2 1.0 O A:ASP684 4.6 27.4 1.0 O A:ASP411 4.7 28.6 1.0 OD2 A:ASP411 4.9 26.5 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/Dc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of RB69 Dna Polymerase Ternary Complex with Dctp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:69.3 occ:1.00 O A:HOH1170 2.4 35.4 1.0 OE1 A:GLU116 2.8 45.4 1.0 OE2 A:GLU116 2.8 49.4 1.0 CD A:GLU116 3.2 44.5 1.0 OD2 A:ASP114 3.9 53.4 1.0 O A:ILE115 4.5 38.4 1.0 CG A:GLU116 4.7 40.5 1.0 O A:HOH1248 4.7 41.5 1.0 CG A:ASP114 5.0 46.2 1.0

S.Xia, J.Wang, W.H.Konigsberg. Dna Mismatch Synthesis Complexes Provide Insights Into Base Selectivity of A B Family Dna Polymerase. J.Am.Chem.Soc. V. 135 193 2013.
ISSN: ISSN 0002-7863
PubMed: 23214497
DOI: 10.1021/JA3079048