Calcium in PDB 4fjl: RB69 Dna Polymerase Ternary Complex with Dgtp/Da

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

The structure of RB69 Dna Polymerase Ternary Complex with Dgtp/Da, PDB code: 4fjl 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)	49.26 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.884, 120.511, 130.788, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22.3

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:18.6 occ:1.00 OD1 A:ASP623 2.3 20.9 1.0 O1G A:DGT1001 2.3 18.7 1.0 OD2 A:ASP411 2.3 22.8 1.0 O2B A:DGT1001 2.3 20.0 1.0 O A:LEU412 2.4 16.5 1.0 O2A A:DGT1001 2.4 20.4 1.0 CG A:ASP623 3.4 20.1 1.0 PB A:DGT1001 3.4 19.7 1.0 CG A:ASP411 3.5 25.8 1.0 CA A:CA1003 3.5 49.2 1.0 C A:LEU412 3.5 20.1 1.0 PG A:DGT1001 3.6 21.2 1.0 PA A:DGT1001 3.6 22.3 1.0 O3A A:DGT1001 3.8 21.4 1.0 OD2 A:ASP623 3.8 19.4 1.0 O3B A:DGT1001 3.9 22.6 1.0 O A:HOH1659 3.9 34.7 1.0 N A:LEU412 3.9 18.6 1.0 O A:HOH1658 4.0 34.3 1.0 CB A:ASP411 4.0 21.1 1.0 CA A:LEU412 4.2 19.6 1.0 O2G A:DGT1001 4.3 22.0 1.0 C5' A:DGT1001 4.3 17.8 1.0 C A:ASP411 4.3 20.9 1.0 O5' A:DGT1001 4.5 21.1 1.0 OD1 A:ASP411 4.5 23.5 1.0 N A:THR413 4.6 19.3 1.0 N A:SER414 4.6 18.2 1.0 N A:ALA415 4.6 17.9 1.0 CB A:ASP623 4.7 18.6 1.0 CB A:LEU412 4.7 19.6 1.0 CB A:ALA415 4.7 18.8 1.0 O3G A:DGT1001 4.8 22.0 1.0 O1B A:DGT1001 4.8 20.7 1.0 O A:ASP411 4.8 20.0 1.0 CA A:THR413 4.8 18.8 1.0 O1A A:DGT1001 4.8 21.1 1.0 CA A:ASP411 4.8 19.7 1.0 C A:THR413 4.9 18.5 1.0

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:49.2 occ:1.00 O A:HOH1231 2.5 23.8 1.0 O2A A:DGT1001 2.6 20.4 1.0 OD2 A:ASP623 2.7 19.4 1.0 OD2 A:ASP411 3.4 22.8 1.0 CG A:ASP623 3.5 20.1 1.0 CA A:CA1002 3.5 18.6 1.0 OD1 A:ASP623 3.5 20.9 1.0 CG A:ASP411 3.6 25.8 1.0 CB A:ASP411 3.6 21.1 1.0 O A:HOH1659 3.7 34.7 1.0 C3' P:DC115 3.8 22.3 1.0 PA A:DGT1001 3.9 22.3 1.0 CB A:SER624 4.0 18.7 1.0 C5' P:DC115 4.1 25.2 1.0 OD1 A:ASP411 4.3 23.5 1.0 O A:HOH1202 4.3 22.1 1.0 C4' P:DC115 4.4 23.5 1.0 O1A A:DGT1001 4.4 21.1 1.0 O A:HOH1661 4.4 25.9 1.0 O5' A:DGT1001 4.5 21.1 1.0 OG A:SER624 4.6 21.9 1.0 O A:ASP621 4.6 20.9 1.0 C5' A:DGT1001 4.7 17.8 1.0 O P:HOH201 4.7 22.2 1.0 N A:SER624 4.8 19.0 1.0 O1G A:DGT1001 4.8 18.7 1.0 C A:ASP623 4.8 21.4 1.0 CA A:SER624 4.8 21.0 1.0 CB A:ASP623 4.9 18.6 1.0 O A:ASP623 5.0 22.7 1.0

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:44.4 occ:1.00 OD1 A:ASN507 2.2 48.5 1.0 O A:HOH1382 2.2 39.3 1.0 O A:ASN505 2.3 41.7 1.0 O A:LYS531 2.3 50.2 1.0 O A:HOH1347 2.4 38.9 1.0 C A:LYS531 3.3 46.4 1.0 CG A:ASN507 3.4 50.9 1.0 C A:ASN505 3.5 49.1 1.0 ND2 A:ASN507 4.0 47.8 1.0 CA A:LYS531 4.0 44.9 1.0 N A:ASN507 4.1 53.0 1.0 CB A:ASN505 4.1 51.2 1.0 N A:LYS532 4.2 48.1 1.0 C A:PRO506 4.3 51.8 1.0 CA A:PRO506 4.3 46.2 1.0 CA A:LYS532 4.4 46.9 1.0 N A:PRO506 4.4 43.8 1.0 O A:HOH1635 4.4 45.5 1.0 CA A:ASN505 4.5 52.4 1.0 O A:LEU533 4.5 40.6 1.0 CB A:ASN507 4.6 48.8 1.0 O A:ALA502 4.6 45.1 1.0 CB A:LYS531 4.7 51.6 1.0 C A:LYS532 4.8 49.6 1.0 CA A:ASN507 4.8 55.0 1.0 O A:ILE530 4.8 36.4 1.0 N A:LEU533 4.9 47.3 1.0 O A:PRO506 5.0 54.5 1.0

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:35.6 occ:1.00 O A:HOH1173 2.5 26.5 1.0 O A:HOH1282 2.6 30.3 1.0 O A:HOH1199 2.6 32.0 1.0 O A:HOH1707 2.7 42.6 1.0 O A:HOH1658 3.0 34.3 1.0 O A:HOH1447 3.4 39.2 1.0 OE1 A:GLU716 3.9 34.4 1.0 OG1 A:THR413 4.4 20.8 1.0 CB A:ASP684 4.4 29.4 1.0 NZ A:LYS486 4.4 28.1 1.0 O A:HOH1715 4.4 44.4 1.0 O A:ASP411 4.5 20.0 1.0 OD1 A:ASP411 4.6 23.5 1.0 O A:ASP684 4.7 23.0 1.0 O A:HOH1303 4.7 36.5 1.0 CG A:GLU716 4.8 33.4 1.0 CD A:GLU716 4.8 38.8 1.0 OD2 A:ASP411 4.8 22.8 1.0 OD2 A:ASP684 5.0 45.7 1.0 O A:ARG685 5.0 22.3 1.0 CG A:ASP411 5.0 25.8 1.0

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:41.8 occ:1.00 O A:HOH1686 2.3 30.7 1.0 O A:HOH1494 2.5 60.7 1.0 OE1 A:GLU116 2.5 26.4 1.0 O A:HOH1102 2.5 24.5 1.0 O A:HOH1351 2.5 35.4 1.0 OE2 A:GLU116 2.6 30.0 1.0 CD A:GLU116 2.9 27.0 1.0 CD1 A:ILE309 4.1 62.5 1.0 O A:HOH1700 4.2 32.2 1.0 OD2 A:ASP114 4.3 46.3 1.0 O A:HOH1485 4.4 34.5 1.0 CG A:GLU116 4.4 20.8 1.0 O A:ILE115 4.6 21.1 1.0 O A:HOH1402 4.7 60.3 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