Calcium in PDB 4fj8: RB69 Dna Polymerase Ternary Complex with Dctp/Dt

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

The structure of RB69 Dna Polymerase Ternary Complex with Dctp/Dt, PDB code: 4fj8 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)	38.11 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.023, 120.085, 130.845, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.2

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dctp/Dt (pdb code 4fj8). 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/Dt, PDB code: 4fj8:
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/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 Dctp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:26.7 occ:1.00 O2B A:DCP1001 2.2 25.5 1.0 O A:LEU412 2.3 27.1 1.0 O1G A:DCP1001 2.3 29.0 1.0 OD1 A:ASP623 2.4 27.4 1.0 OD2 A:ASP411 2.4 26.8 1.0 O2A A:DCP1001 2.4 24.7 1.0 PB A:DCP1001 3.3 28.4 1.0 C A:LEU412 3.4 27.1 1.0 CG A:ASP623 3.5 27.3 1.0 PG A:DCP1001 3.5 27.3 1.0 CG A:ASP411 3.5 31.0 1.0 PA A:DCP1001 3.6 31.6 1.0 CA A:CA1003 3.7 64.0 1.0 O3A A:DCP1001 3.8 29.8 1.0 O3B A:DCP1001 3.8 28.3 1.0 O A:HOH1372 3.8 13.9 0.5 OD2 A:ASP623 3.9 25.1 1.0 N A:LEU412 3.9 27.0 1.0 CB A:ASP411 4.1 29.3 1.0 O A:HOH1372 4.1 5.1 0.5 O2G A:DCP1001 4.1 30.1 1.0 C5' A:DCP1001 4.2 26.4 1.0 CA A:LEU412 4.2 26.1 1.0 N A:SER414 4.3 24.3 1.0 C A:ASP411 4.4 26.3 1.0 O5' A:DCP1001 4.4 28.0 1.0 N A:THR413 4.5 25.6 1.0 OD1 A:ASP411 4.6 34.4 1.0 N A:ALA415 4.6 25.1 1.0 CB A:ALA415 4.6 23.8 1.0 O3G A:DCP1001 4.7 28.7 1.0 O1B A:DCP1001 4.7 31.9 1.0 CB A:LEU412 4.7 25.8 1.0 CA A:THR413 4.7 22.8 1.0 CB A:ASP623 4.7 24.4 1.0 O1A A:DCP1001 4.8 35.0 1.0 C A:THR413 4.8 24.7 1.0 CA A:ASP411 4.9 28.0 1.0 O A:ASP411 4.9 24.6 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/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 Dctp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:64.0 occ:1.00 O2A A:DCP1001 2.8 24.7 1.0 OD2 A:ASP623 2.8 25.1 1.0 OD2 A:ASP411 3.4 26.8 1.0 CG A:ASP411 3.6 31.0 1.0 CB A:ASP411 3.6 29.3 1.0 CG A:ASP623 3.7 27.3 1.0 CA A:CA1002 3.7 26.7 1.0 C3' P:DOC115 3.7 29.6 1.0 OD1 A:ASP623 3.8 27.4 1.0 PA A:DCP1001 4.0 31.6 1.0 CB A:SER624 4.0 23.6 1.0 O A:HOH1372 4.2 13.9 0.5 O A:HOH1125 4.2 38.2 1.0 OD1 A:ASP411 4.3 34.4 1.0 O P:HOH201 4.3 21.0 1.0 O1A A:DCP1001 4.4 35.0 1.0 O5' A:DCP1001 4.5 28.0 1.0 O P:HOH202 4.6 24.1 1.0 C5' P:DOC115 4.6 31.8 1.0 OG A:SER624 4.7 25.1 1.0 C5' A:DCP1001 4.7 26.4 1.0 C4' P:DOC115 4.7 31.5 1.0 O5' P:DOC115 4.8 35.3 1.0 O A:ASP621 4.8 24.6 1.0 N A:SER624 4.9 23.4 1.0 O1G A:DCP1001 4.9 29.0 1.0 CA A:SER624 4.9 25.1 1.0 C2' P:DOC115 4.9 32.0 1.0 C A:ASP623 5.0 27.3 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/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 Dctp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:44.1 occ:1.00 O A:HOH1388 2.1 21.0 1.0 OD1 A:ASN507 2.2 53.2 1.0 O A:ASN505 2.3 46.0 1.0 O A:LYS531 2.3 47.1 1.0 O A:HOH1163 2.4 30.3 1.0 O A:HOH1389 2.5 24.7 1.0 C A:LYS531 3.4 46.3 1.0 CG A:ASN507 3.4 52.3 1.0 C A:ASN505 3.5 47.7 1.0 ND2 A:ASN507 4.1 53.2 1.0 CA A:LYS531 4.2 46.6 1.0 CB A:ASN505 4.2 51.5 1.0 N A:ASN507 4.2 50.6 1.0 C A:PRO506 4.3 49.7 1.0 N A:LYS532 4.3 43.5 1.0 CA A:PRO506 4.3 47.5 1.0 N A:PRO506 4.4 47.6 1.0 CA A:LYS532 4.4 44.3 1.0 CA A:ASN505 4.5 50.4 1.0 CB A:ASN507 4.6 52.1 1.0 O A:ALA502 4.7 42.9 1.0 O A:LEU533 4.7 37.8 1.0 O A:PRO506 4.8 51.4 1.0 CA A:ASN507 4.8 51.7 1.0 C A:LYS532 4.8 43.5 1.0 CB A:LYS531 4.9 46.3 1.0 N A:LEU533 4.9 42.2 1.0 O A:ILE530 4.9 43.3 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/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 Dctp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:58.2 occ:1.00 O A:HOH1347 2.6 31.4 1.0 O A:HOH1208 2.7 33.1 1.0 O A:HOH1177 2.7 24.6 1.0 O A:HOH1372 3.0 5.1 0.5 OE1 A:GLU716 3.2 42.8 1.0 CD A:GLU716 4.1 44.6 1.0 NZ A:LYS486 4.3 30.4 1.0 CB A:ASP684 4.3 38.3 1.0 OG1 A:THR413 4.3 28.6 1.0 CG A:GLU716 4.4 41.6 1.0 OD1 A:ASP411 4.6 34.4 1.0 O A:ASP411 4.7 24.6 1.0 OD2 A:ASP411 4.7 26.8 1.0 OD2 A:ASP684 4.8 46.3 1.0 O A:ASP684 4.9 31.8 1.0 O2G A:DCP1001 4.9 30.1 1.0 CG A:ASP411 5.0 31.0 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/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 Dctp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:81.5 occ:1.00 O A:HOH1359 2.3 38.3 1.0 O A:HOH1157 2.4 26.7 1.0 OE2 A:GLU116 2.6 44.3 1.0 OD2 A:ASP114 3.3 46.7 1.0 CD A:GLU116 3.4 38.7 1.0 OE1 A:GLU116 3.6 42.1 1.0 CG A:ASP114 4.2 38.9 1.0 OD1 A:ASP114 4.3 39.5 1.0 O A:HOH1368 4.5 25.1 1.0 CB A:ALA327 4.7 24.9 1.0 O A:ILE115 4.7 28.4 1.0 CG A:GLU116 4.8 34.0 1.0 ND2 A:ASN324 4.9 34.2 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