Calcium in PDB 4fk4: RB69 Dna Polymerase Ternary Complex with Dgtp/Dg

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Dgtp/Dg:
2.7.7.7;

The structure of RB69 Dna Polymerase Ternary Complex with Dgtp/Dg, PDB code: 4fk4 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)	46.90 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.799, 120.407, 130.727, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.2

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dgtp/Dg (pdb code 4fk4). 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 Dgtp/Dg, PDB code: 4fk4:
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 Dgtp/Dg


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 Dgtp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:23.9 occ:1.00 OD1 A:ASP623 2.3 27.5 1.0 O2B A:DGT1001 2.3 21.4 1.0 OD2 A:ASP411 2.3 25.6 1.0 O1G A:DGT1001 2.3 21.9 1.0 O A:LEU412 2.3 21.4 1.0 O2A A:DGT1001 2.4 22.3 1.0 PB A:DGT1001 3.4 22.7 1.0 CG A:ASP623 3.4 26.8 1.0 CG A:ASP411 3.5 27.6 1.0 C A:LEU412 3.5 23.5 1.0 PG A:DGT1001 3.6 25.4 1.0 PA A:DGT1001 3.6 25.5 1.0 CA A:CA1003 3.6 47.4 1.0 O3A A:DGT1001 3.8 25.4 1.0 OD2 A:ASP623 3.8 24.8 1.0 O A:HOH1119 3.9 30.5 1.0 O3B A:DGT1001 3.9 26.5 1.0 O A:HOH1402 3.9 31.2 1.0 N A:LEU412 4.0 22.3 1.0 CB A:ASP411 4.0 24.7 1.0 CA A:LEU412 4.2 23.7 1.0 O2G A:DGT1001 4.3 27.7 1.0 C5' A:DGT1001 4.3 21.0 1.0 C A:ASP411 4.4 22.8 1.0 O5' A:DGT1001 4.5 22.1 1.0 OD1 A:ASP411 4.5 25.9 1.0 N A:THR413 4.5 24.0 1.0 N A:SER414 4.6 23.2 1.0 N A:ALA415 4.6 22.4 1.0 CB A:ALA415 4.6 21.6 1.0 CB A:ASP623 4.7 24.3 1.0 CB A:LEU412 4.7 22.2 1.0 O1B A:DGT1001 4.7 23.6 1.0 O3G A:DGT1001 4.7 24.3 1.0 O1A A:DGT1001 4.7 20.8 1.0 CA A:THR413 4.8 23.9 1.0 O A:ASP411 4.8 24.6 1.0 CA A:ASP411 4.8 24.7 1.0 C A:THR413 4.9 23.2 1.0

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


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 Dgtp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:47.4 occ:1.00 O A:HOH1363 2.5 27.4 1.0 O2A A:DGT1001 2.6 22.3 1.0 OD2 A:ASP623 2.7 24.8 1.0 CG A:ASP623 3.5 26.8 1.0 OD2 A:ASP411 3.6 25.6 1.0 CA A:CA1002 3.6 23.9 1.0 OD1 A:ASP623 3.6 27.5 1.0 CG A:ASP411 3.7 27.6 1.0 CB A:ASP411 3.7 24.7 1.0 C3' P:DOC115 3.7 26.3 1.0 O A:HOH1119 3.8 30.5 1.0 PA A:DGT1001 3.9 25.5 1.0 C5' P:DOC115 3.9 29.4 1.0 CB A:SER624 4.0 25.1 1.0 C4' P:DOC115 4.3 23.6 1.0 O A:HOH1204 4.3 23.2 1.0 O1A A:DGT1001 4.3 20.8 1.0 OD1 A:ASP411 4.4 25.9 1.0 O A:HOH1175 4.4 26.4 1.0 O5' A:DGT1001 4.4 22.1 1.0 OG A:SER624 4.6 25.6 1.0 O P:HOH204 4.6 22.7 1.0 O A:ASP621 4.6 24.2 1.0 C5' A:DGT1001 4.6 21.0 1.0 N A:SER624 4.8 24.2 1.0 O1G A:DGT1001 4.9 21.9 1.0 C A:ASP623 4.9 24.8 1.0 CA A:SER624 4.9 24.7 1.0 CB A:ASP623 5.0 24.3 1.0

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


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 Dgtp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:43.6 occ:1.00 O A:ASN505 2.2 43.0 1.0 OD1 A:ASN507 2.3 49.2 1.0 O A:HOH1203 2.3 28.9 1.0 O A:LYS531 2.3 47.0 1.0 O A:HOH1393 2.5 28.6 1.0 O A:HOH1476 2.6 28.9 1.0 C A:LYS531 3.3 46.6 1.0 CG A:ASN507 3.4 51.3 1.0 C A:ASN505 3.5 46.2 1.0 ND2 A:ASN507 4.0 47.9 1.0 N A:ASN507 4.1 50.5 1.0 CB A:ASN505 4.1 49.0 1.0 CA A:LYS531 4.1 45.3 1.0 C A:PRO506 4.2 48.8 1.0 CA A:PRO506 4.2 46.8 1.0 N A:LYS532 4.2 46.2 1.0 N A:PRO506 4.3 45.6 1.0 CA A:LYS532 4.4 46.5 1.0 CA A:ASN505 4.4 48.3 1.0 O A:LEU533 4.5 41.1 1.0 CB A:ASN507 4.5 52.0 1.0 O A:HOH1523 4.6 30.3 1.0 O A:HOH1559 4.6 28.4 1.0 O A:ALA502 4.7 41.4 1.0 CA A:ASN507 4.7 51.9 1.0 O A:PRO506 4.7 49.4 1.0 C A:LYS532 4.8 45.5 1.0 N A:LEU533 4.8 43.2 1.0 CB A:LYS531 4.9 47.6 1.0 O A:ILE530 4.9 38.0 1.0

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


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 Dgtp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:41.3 occ:1.00 O A:HOH1561 2.5 27.2 1.0 O A:HOH1127 2.5 30.1 1.0 O A:HOH1563 2.7 37.9 1.0 O A:HOH1562 2.7 31.6 1.0 O A:HOH1402 3.1 31.2 1.0 O A:HOH1564 3.3 34.9 1.0 OE1 A:GLU716 4.0 36.5 1.0 NZ A:LYS486 4.3 31.7 1.0 OG1 A:THR413 4.4 26.3 1.0 O A:ASP411 4.5 24.6 1.0 CB A:ASP684 4.5 34.6 1.0 OD1 A:ASP411 4.5 25.9 1.0 O A:ASP684 4.6 26.5 1.0 O A:HOH1379 4.7 31.0 1.0 OD2 A:ASP411 4.7 25.6 1.0 O A:HOH1537 4.7 31.0 1.0 CG A:ASP411 4.9 27.6 1.0 CD A:GLU716 4.9 39.0 1.0 O2G A:DGT1001 5.0 27.7 1.0 CG A:GLU716 5.0 34.8 1.0 O A:ARG685 5.0 25.7 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp/Dg


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 Dgtp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:50.8 occ:1.00 O A:HOH1545 2.3 37.1 1.0 O A:HOH1405 2.4 29.1 1.0 O A:HOH1123 2.5 21.0 1.0 OE1 A:GLU116 2.6 31.0 1.0 OE2 A:GLU116 2.7 33.1 1.0 CD A:GLU116 3.0 30.2 1.0 CD1 A:ILE309 4.1 51.6 1.0 OD2 A:ASP114 4.2 43.2 1.0 O A:HOH1658 4.2 32.5 1.0 O A:HOH1263 4.4 32.0 1.0 CG A:GLU116 4.5 25.6 1.0 O A:ILE115 4.6 25.5 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