Calcium in PDB 4fj5: RB69 Dna Polymerase Ternary Complex with Datp/Dt

All present enzymatic activity of RB69 Dna Polymerase Ternary Complex with Datp/Dt:
2.7.7.7;

The structure of RB69 Dna Polymerase Ternary Complex with Datp/Dt, PDB code: 4fj5 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)	34.57 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.095, 120.221, 130.778, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 23.8

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Datp/Dt (pdb code 4fj5). 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 Datp/Dt, PDB code: 4fj5:
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 Datp/Dt


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 Datp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:20.6 occ:1.00 OD2 A:ASP411 2.3 21.3 1.0 O1G A:DTP1001 2.3 18.7 1.0 O2B A:DTP1001 2.3 17.9 1.0 O A:LEU412 2.3 18.4 1.0 OD2 A:ASP623 2.3 21.1 1.0 O2A A:DTP1001 2.4 19.5 1.0 PB A:DTP1001 3.4 20.2 1.0 CG A:ASP411 3.4 26.5 1.0 CG A:ASP623 3.4 20.3 1.0 C A:LEU412 3.5 19.6 1.0 PG A:DTP1001 3.6 21.3 1.0 PA A:DTP1001 3.6 22.9 1.0 CA A:CA1003 3.6 47.8 1.0 O3A A:DTP1001 3.7 23.6 1.0 O3B A:DTP1001 3.8 19.3 1.0 OD1 A:ASP623 3.8 19.5 1.0 N A:LEU412 4.0 18.7 1.0 CB A:ASP411 4.0 21.1 1.0 O A:HOH1516 4.0 35.1 1.0 O A:HOH1517 4.2 51.9 1.0 C5' A:DTP1001 4.2 18.1 1.0 CA A:LEU412 4.2 17.5 1.0 O2G A:DTP1001 4.3 21.6 1.0 C A:ASP411 4.3 19.4 1.0 O5' A:DTP1001 4.4 19.8 1.0 OD1 A:ASP411 4.4 22.6 1.0 N A:SER414 4.5 18.9 1.0 N A:THR413 4.5 20.3 1.0 N A:ALA415 4.6 17.8 1.0 CB A:ALA415 4.7 15.9 1.0 CB A:LEU412 4.7 17.6 1.0 CB A:ASP623 4.7 18.5 1.0 O1B A:DTP1001 4.7 20.3 1.0 O3G A:DTP1001 4.7 22.9 1.0 CA A:THR413 4.8 18.4 1.0 O A:ASP411 4.8 21.6 1.0 CA A:ASP411 4.8 20.9 1.0 O1A A:DTP1001 4.8 20.2 1.0 C A:THR413 4.8 19.4 1.0

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


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 Datp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:47.8 occ:1.00 O A:HOH1528 2.5 28.7 1.0 OD1 A:ASP623 2.7 19.5 1.0 O2A A:DTP1001 2.7 19.5 1.0 CG A:ASP623 3.5 20.3 1.0 OD2 A:ASP411 3.5 21.3 1.0 CG A:ASP411 3.6 26.5 1.0 CA A:CA1002 3.6 20.6 1.0 CB A:ASP411 3.6 21.1 1.0 OD2 A:ASP623 3.7 21.1 1.0 C3' P:DT115 3.7 20.3 1.0 PA A:DTP1001 3.9 22.9 1.0 CB A:SER624 4.0 18.6 1.0 O A:HOH1517 4.1 51.9 1.0 O A:HOH1136 4.2 22.1 1.0 OD1 A:ASP411 4.3 22.6 1.0 O1A A:DTP1001 4.4 20.2 1.0 O A:HOH1214 4.4 26.1 1.0 O5' A:DTP1001 4.5 19.8 1.0 OG A:SER624 4.5 22.6 1.0 C5' A:DTP1001 4.6 18.1 1.0 O A:HOH1166 4.6 20.1 1.0 O A:ASP621 4.7 19.3 1.0 C5' P:DT115 4.7 25.9 1.0 C4' P:DT115 4.7 23.7 1.0 O5' P:DT115 4.8 25.3 1.0 N A:SER624 4.8 20.0 1.0 C A:ASP623 4.8 18.9 1.0 C2' P:DT115 4.9 23.0 1.0 CA A:SER624 4.9 19.6 1.0 O1G A:DTP1001 4.9 18.7 1.0 CB A:ASP623 4.9 18.5 1.0

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


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 Datp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:36.5 occ:1.00 O A:HOH1392 2.2 36.8 1.0 OD1 A:ASN507 2.2 40.6 1.0 O A:LYS531 2.3 51.1 1.0 O A:ASN505 2.3 44.3 1.0 O A:HOH1114 2.5 43.8 1.0 O A:HOH1518 2.6 35.4 1.0 C A:LYS531 3.3 44.6 1.0 CG A:ASN507 3.4 41.9 1.0 C A:ASN505 3.6 41.9 1.0 CA A:LYS531 4.0 41.8 1.0 ND2 A:ASN507 4.0 45.8 1.0 CB A:ASN505 4.2 45.4 1.0 N A:LYS532 4.2 37.8 1.0 N A:ASN507 4.2 46.1 1.0 C A:PRO506 4.3 44.9 1.0 CA A:PRO506 4.4 38.1 1.0 CA A:LYS532 4.4 40.4 1.0 N A:PRO506 4.5 37.5 1.0 CA A:ASN505 4.5 43.6 1.0 O A:HOH1495 4.5 34.9 1.0 CB A:ASN507 4.6 45.9 1.0 O A:LEU533 4.6 37.9 1.0 O A:ALA502 4.6 40.2 1.0 CB A:LYS531 4.7 43.4 1.0 CA A:ASN507 4.8 44.6 1.0 O A:PRO506 4.8 50.8 1.0 C A:LYS532 4.8 45.3 1.0 N A:LEU533 4.9 42.9 1.0 O A:ILE530 4.9 32.5 1.0

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


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 Datp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:37.5 occ:1.00 O A:HOH1222 2.5 33.8 1.0 O A:HOH1120 2.6 31.3 1.0 O A:HOH1357 2.6 31.4 1.0 O A:HOH1543 2.6 41.8 1.0 O A:HOH1154 2.7 40.3 1.0 O A:HOH1516 2.8 35.1 1.0 O A:HOH1181 2.8 38.6 1.0 OE1 A:GLU716 3.1 47.4 1.0 CD A:GLU716 4.1 42.7 1.0 NZ A:LYS486 4.2 31.9 1.0 CG A:GLU716 4.3 37.0 1.0 OG1 A:THR413 4.4 22.4 1.0 CB A:ASP684 4.4 30.4 1.0 O A:HOH1582 4.5 38.4 1.0 OD1 A:ASP411 4.6 22.6 1.0 O A:ASP411 4.6 21.6 1.0 O A:HOH1569 4.7 48.6 1.0 OD2 A:ASP411 4.8 21.3 1.0 O A:ASP684 4.8 25.9 1.0 O A:HOH1435 4.8 32.0 1.0 OD2 A:ASP684 4.9 40.9 1.0 CG A:ASP411 5.0 26.5 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp/Dt


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 Datp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:62.7 occ:1.00 O A:HOH1600 2.4 44.1 1.0 O A:HOH1526 2.5 31.8 1.0 OE1 A:GLU116 2.5 28.2 1.0 O A:HOH1637 2.5 34.4 1.0 OE2 A:GLU116 3.0 29.5 1.0 CD A:GLU116 3.1 30.1 1.0 O A:HOH1675 4.2 46.1 1.0 OD2 A:ASP114 4.5 40.5 1.0 CD1 A:ILE309 4.6 44.0 1.0 CG A:GLU116 4.6 22.7 1.0 O A:ILE115 4.7 23.8 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