Calcium in PDB 4fj9: RB69 Dna Polymerase Ternary Complex with Dttp/Dt

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

The structure of RB69 Dna Polymerase Ternary Complex with Dttp/Dt, PDB code: 4fj9 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)	38.18 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.143, 119.782, 130.448, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.5

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dttp/Dt (pdb code 4fj9). 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 Dttp/Dt, PDB code: 4fj9:
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 Dttp/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 Dttp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:24.9 occ:1.00 O1G A:TTP1001 2.2 22.9 1.0 O A:LEU412 2.3 22.1 1.0 OD2 A:ASP623 2.3 24.0 1.0 O2A A:TTP1001 2.3 23.6 1.0 OD2 A:ASP411 2.3 26.3 1.0 O2B A:TTP1001 2.3 22.5 1.0 PB A:TTP1001 3.4 22.9 1.0 CG A:ASP623 3.4 24.0 1.0 C A:LEU412 3.5 23.6 1.0 CG A:ASP411 3.5 26.6 1.0 PG A:TTP1001 3.5 23.8 1.0 PA A:TTP1001 3.6 23.5 1.0 CA A:CA1003 3.6 51.2 1.0 O3A A:TTP1001 3.8 24.6 1.0 O3B A:TTP1001 3.8 24.3 1.0 OD1 A:ASP623 3.9 23.4 1.0 N A:LEU412 4.0 24.0 1.0 O A:HOH1652 4.0 31.9 1.0 CB A:ASP411 4.0 25.8 1.0 O2G A:TTP1001 4.1 23.8 1.0 CA A:LEU412 4.2 23.4 1.0 C A:ASP411 4.3 24.6 1.0 C5' A:TTP1001 4.4 22.4 1.0 O5' A:TTP1001 4.5 23.1 1.0 OD1 A:ASP411 4.5 27.3 1.0 N A:THR413 4.5 23.9 1.0 N A:ALA415 4.5 22.6 1.0 N A:SER414 4.6 24.2 1.0 CB A:ALA415 4.6 21.3 1.0 CB A:LEU412 4.7 23.0 1.0 O3G A:TTP1001 4.7 24.5 1.0 CB A:ASP623 4.7 23.6 1.0 CA A:THR413 4.7 24.6 1.0 O1A A:TTP1001 4.8 22.7 1.0 O A:ASP411 4.8 25.6 1.0 O1B A:TTP1001 4.8 25.9 1.0 CA A:ASP411 4.8 25.6 1.0 C A:THR413 4.9 23.9 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:51.2 occ:1.00 OD1 A:ASP623 2.7 23.4 1.0 O2A A:TTP1001 2.7 23.6 1.0 OD2 A:ASP411 3.3 26.3 1.0 CG A:ASP623 3.5 24.0 1.0 CG A:ASP411 3.6 26.6 1.0 CA A:CA1002 3.6 24.9 1.0 OD2 A:ASP623 3.6 24.0 1.0 CB A:ASP411 3.6 25.8 1.0 C3' P:DG115 3.8 27.4 1.0 PA A:TTP1001 3.9 23.5 1.0 CB A:SER624 4.0 25.9 1.0 O P:HOH206 4.3 23.8 1.0 O1A A:TTP1001 4.3 22.7 1.0 OD1 A:ASP411 4.4 27.3 1.0 O A:HOH1174 4.4 34.7 1.0 OG A:SER624 4.5 26.6 1.0 O5' A:TTP1001 4.6 23.1 1.0 C5' P:DG115 4.7 29.5 1.0 O P:HOH203 4.7 27.2 1.0 C4' P:DG115 4.8 27.9 1.0 O A:ASP621 4.8 22.1 1.0 N A:SER624 4.8 24.9 1.0 O1G A:TTP1001 4.8 22.9 1.0 C5' A:TTP1001 4.8 22.4 1.0 C A:ASP623 4.8 24.8 1.0 CA A:SER624 4.9 25.4 1.0 CB A:ASP623 4.9 23.6 1.0 C2' P:DG115 5.0 26.7 1.0 O5' P:DG115 5.0 30.4 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:41.2 occ:1.00 O A:HOH1670 2.2 36.6 1.0 O A:LYS531 2.2 43.3 1.0 OD1 A:ASN507 2.2 44.7 1.0 O A:ASN505 2.3 42.8 1.0 O A:HOH1669 2.5 32.2 1.0 O A:HOH1672 2.6 40.3 1.0 C A:LYS531 3.2 42.1 1.0 CG A:ASN507 3.4 46.3 1.0 C A:ASN505 3.6 44.4 1.0 CA A:LYS531 4.0 40.6 1.0 ND2 A:ASN507 4.0 47.3 1.0 N A:ASN507 4.1 45.4 1.0 N A:LYS532 4.1 42.4 1.0 CB A:ASN505 4.2 46.0 1.0 C A:PRO506 4.3 44.2 1.0 CA A:LYS532 4.3 42.9 1.0 CA A:PRO506 4.4 43.2 1.0 N A:PRO506 4.4 42.8 1.0 CA A:ASN505 4.5 45.4 1.0 CB A:ASN507 4.6 46.5 1.0 O A:LEU533 4.6 37.8 1.0 O A:HOH1671 4.6 39.2 1.0 O A:ALA502 4.7 40.8 1.0 CB A:LYS531 4.7 42.2 1.0 C A:LYS532 4.7 42.3 1.0 CA A:ASN507 4.7 46.5 1.0 N A:LEU533 4.8 40.7 1.0 O A:ILE530 4.9 36.0 1.0 O A:PRO506 5.0 46.3 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:43.5 occ:1.00 O A:HOH1658 2.5 39.8 1.0 O A:HOH1661 2.6 37.4 1.0 O A:HOH1660 2.6 35.8 1.0 OE1 A:GLU716 2.7 40.3 1.0 O A:HOH1662 2.7 41.6 1.0 O A:HOH1652 2.9 31.9 1.0 O A:HOH1655 3.2 34.4 1.0 CD A:GLU716 3.7 39.3 1.0 NZ A:LYS486 4.1 32.1 1.0 CG A:GLU716 4.1 36.8 1.0 OG1 A:THR413 4.3 26.8 1.0 CB A:ASP684 4.4 38.6 1.0 OD1 A:ASP411 4.5 27.3 1.0 O A:ASP411 4.6 25.6 1.0 OE2 A:GLU716 4.8 41.5 1.0 OD2 A:ASP411 4.8 26.3 1.0 O A:HOH1659 4.8 44.1 1.0 O A:ASP684 4.8 30.3 1.0 CG A:ASP411 4.9 26.6 1.0 OD2 A:ASP684 4.9 45.7 1.0 O2G A:TTP1001 5.0 23.8 1.0 O1G A:TTP1001 5.0 22.9 1.0 O A:ARG685 5.0 28.1 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:57.0 occ:1.00 O A:HOH1680 2.3 36.8 1.0 O A:HOH1590 2.4 33.9 1.0 OE1 A:GLU116 2.5 33.4 1.0 OE2 A:GLU116 2.8 33.9 1.0 CD A:GLU116 3.0 31.8 1.0 CD1 A:ILE309 4.1 50.9 1.0 O A:HOH1487 4.2 39.3 1.0 OD2 A:ASP114 4.2 38.6 1.0 O A:HOH1410 4.3 43.6 1.0 O A:HOH1431 4.5 49.4 1.0 O A:ILE115 4.5 26.5 1.0 CG A:GLU116 4.5 29.1 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