Calcium in PDB 4fj7: RB69 Dna Polymerase Ternary Complex with Dgtp/Dt

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

The structure of RB69 Dna Polymerase Ternary Complex with Dgtp/Dt, PDB code: 4fj7 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)	49.17 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.112, 119.544, 130.091, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.3

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dgtp/Dt (pdb code 4fj7). 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/Dt, PDB code: 4fj7:
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/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 Dgtp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:21.1 occ:1.00 O2B A:DGT1001 2.2 20.8 1.0 O1G A:DGT1001 2.3 20.8 1.0 OD2 A:ASP623 2.3 20.7 1.0 OD2 A:ASP411 2.3 26.2 1.0 O A:LEU412 2.3 17.0 1.0 O2A A:DGT1001 2.4 22.8 1.0 PB A:DGT1001 3.4 20.6 1.0 CG A:ASP623 3.4 21.3 1.0 CG A:ASP411 3.5 28.1 1.0 C A:LEU412 3.5 19.6 1.0 PG A:DGT1001 3.6 21.9 1.0 PA A:DGT1001 3.6 22.4 1.0 CA A:CA1003 3.6 53.0 1.0 O3A A:DGT1001 3.7 23.1 1.0 O3B A:DGT1001 3.8 21.5 1.0 OD1 A:ASP623 3.8 18.7 1.0 N A:LEU412 4.0 19.9 1.0 O A:HOH1242 4.0 40.6 1.0 O A:HOH1383 4.0 20.6 0.5 CB A:ASP411 4.1 22.9 1.0 C5' A:DGT1001 4.2 21.3 1.0 O2G A:DGT1001 4.2 22.2 1.0 CA A:LEU412 4.3 19.1 1.0 C A:ASP411 4.4 22.4 1.0 O5' A:DGT1001 4.4 21.8 1.0 OD1 A:ASP411 4.5 28.8 1.0 N A:THR413 4.5 20.3 1.0 N A:SER414 4.6 19.1 1.0 N A:ALA415 4.6 16.6 1.0 CB A:ALA415 4.7 17.2 1.0 CB A:ASP623 4.7 20.1 1.0 CA A:THR413 4.7 22.8 1.0 O1B A:DGT1001 4.7 21.9 1.0 CB A:LEU412 4.7 18.7 1.0 O3G A:DGT1001 4.8 21.4 1.0 O1A A:DGT1001 4.8 21.7 1.0 C A:THR413 4.8 20.9 1.0 O A:ASP411 4.9 23.9 1.0 CA A:ASP411 4.9 21.8 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp/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 Dgtp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:53.0 occ:1.00 O A:HOH1443 2.6 32.6 1.0 OD1 A:ASP623 2.6 18.7 1.0 O2A A:DGT1001 2.7 22.8 1.0 OD2 A:ASP411 3.4 26.2 1.0 CG A:ASP623 3.5 21.3 1.0 OD2 A:ASP623 3.6 20.7 1.0 CG A:ASP411 3.6 28.1 1.0 CA A:CA1002 3.6 21.1 1.0 CB A:ASP411 3.6 22.9 1.0 C3' P:DG115 3.8 24.8 1.0 CB A:SER624 3.9 21.3 1.0 PA A:DGT1001 4.0 22.4 1.0 O P:HOH205 4.2 24.3 1.0 O A:HOH1383 4.2 20.6 0.5 OD1 A:ASP411 4.3 28.8 1.0 O A:HOH1269 4.4 34.8 1.0 OG A:SER624 4.5 23.9 1.0 O5' A:DGT1001 4.5 21.8 1.0 O1A A:DGT1001 4.6 21.7 1.0 C5' A:DGT1001 4.6 21.3 1.0 O A:ASP621 4.7 18.8 1.0 N A:SER624 4.7 19.7 1.0 C A:ASP623 4.7 20.8 1.0 CA A:SER624 4.8 20.4 1.0 O P:HOH203 4.8 26.8 1.0 C5' P:DG115 4.8 28.5 1.0 C4' P:DG115 4.8 26.5 1.0 O5' P:DG115 4.8 29.2 1.0 CB A:ASP623 4.9 20.1 1.0 O A:ASP623 4.9 21.4 1.0 O1G A:DGT1001 4.9 20.8 1.0 C2' P:DG115 4.9 24.8 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp/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 Dgtp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:37.0 occ:1.00 O A:HOH1367 2.2 38.1 1.0 OD1 A:ASN507 2.2 45.0 1.0 O A:LYS531 2.2 42.8 1.0 O A:ASN505 2.3 40.1 1.0 O A:HOH1194 2.4 33.5 1.0 O A:HOH1215 2.6 31.9 1.0 C A:LYS531 3.2 41.2 1.0 CG A:ASN507 3.4 45.9 1.0 C A:ASN505 3.5 42.1 1.0 CA A:LYS531 4.0 37.7 1.0 ND2 A:ASN507 4.0 40.8 1.0 CB A:ASN505 4.1 44.7 1.0 N A:LYS532 4.1 38.5 1.0 N A:ASN507 4.1 44.7 1.0 CA A:LYS532 4.3 41.5 1.0 CA A:PRO506 4.4 42.4 1.0 C A:PRO506 4.4 44.0 1.0 N A:PRO506 4.4 40.3 1.0 CA A:ASN505 4.5 43.3 1.0 CB A:ASN507 4.6 46.7 1.0 O A:HOH1385 4.6 34.7 1.0 O A:LEU533 4.6 33.0 1.0 O A:ALA502 4.6 40.1 1.0 CB A:LYS531 4.6 39.6 1.0 C A:LYS532 4.8 40.5 1.0 CA A:ASN507 4.8 45.8 1.0 N A:LEU533 4.9 36.6 1.0 O A:ILE530 4.9 31.3 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp/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 Dgtp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:39.8 occ:1.00 OE1 A:GLU716 2.4 53.2 1.0 O A:HOH1444 2.5 44.4 1.0 O A:HOH1379 2.5 31.6 1.0 O A:HOH1292 2.5 28.0 1.0 O A:HOH1442 2.5 34.6 1.0 O A:HOH1340 2.9 38.0 1.0 O A:HOH1242 2.9 40.6 1.0 CD A:GLU716 3.5 48.8 1.0 CG A:GLU716 4.1 40.3 1.0 NZ A:LYS486 4.3 33.3 1.0 OG1 A:THR413 4.3 27.6 1.0 CB A:ASP684 4.4 37.4 1.0 OE2 A:GLU716 4.5 48.4 1.0 OD1 A:ASP411 4.5 28.8 1.0 O A:ASP411 4.5 23.9 1.0 O A:HOH1329 4.8 37.8 1.0 O A:ASP684 4.8 23.7 1.0 OD2 A:ASP411 4.8 26.2 1.0 OD2 A:ASP684 5.0 52.9 1.0 O A:ARG685 5.0 23.9 1.0 CG A:ASP411 5.0 28.1 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dgtp/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 Dgtp/Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:62.7 occ:1.00 O A:HOH1312 2.4 34.9 1.0 O A:HOH1159 2.4 33.3 1.0 OE1 A:GLU116 2.7 38.1 1.0 OE2 A:GLU116 2.8 38.4 1.0 CD A:GLU116 3.1 33.4 1.0 OD2 A:ASP114 4.3 39.4 1.0 O A:HOH1336 4.3 36.2 1.0 O A:ILE115 4.6 21.7 1.0 CG A:GLU116 4.6 26.1 1.0 O A:HOH1363 4.8 22.7 0.5 CD1 A:ILE309 4.9 45.2 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