Calcium in PDB 4fjx: RB69 Dna Polymerase Ternary Complex with Datp/Dg

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

The structure of RB69 Dna Polymerase Ternary Complex with Datp/Dg, PDB code: 4fjx 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)	44.15 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.052, 119.860, 130.540, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 22.5

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


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/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:26.1 occ:1.00 OD2 A:ASP411 2.2 27.3 1.0 O1G A:DTP1001 2.3 26.8 1.0 O2B A:DTP1001 2.3 27.1 1.0 O A:LEU412 2.3 24.4 1.0 OD2 A:ASP623 2.3 28.9 1.0 O2A A:DTP1001 2.4 23.5 1.0 PB A:DTP1001 3.4 27.5 1.0 CG A:ASP623 3.4 27.6 1.0 CG A:ASP411 3.4 33.1 1.0 CA A:CA1003 3.5 52.4 1.0 C A:LEU412 3.5 24.1 1.0 PG A:DTP1001 3.6 28.6 1.0 PA A:DTP1001 3.6 26.8 1.0 O A:HOH1606 3.8 42.0 1.0 O3A A:DTP1001 3.8 27.3 1.0 OD1 A:ASP623 3.8 27.0 1.0 O3B A:DTP1001 3.9 28.5 1.0 O A:HOH1605 3.9 41.0 1.0 N A:LEU412 3.9 24.7 1.0 CB A:ASP411 4.0 29.0 1.0 CA A:LEU412 4.2 26.5 1.0 O2G A:DTP1001 4.2 27.9 1.0 C5' A:DTP1001 4.3 24.2 1.0 C A:ASP411 4.3 27.2 1.0 OD1 A:ASP411 4.4 33.3 1.0 O5' A:DTP1001 4.4 27.7 1.0 N A:THR413 4.5 28.2 1.0 N A:SER414 4.6 27.1 1.0 N A:ALA415 4.7 21.4 1.0 CB A:LEU412 4.7 25.8 1.0 CB A:ASP623 4.7 25.9 1.0 O3G A:DTP1001 4.7 32.0 1.0 CB A:ALA415 4.8 21.0 1.0 CA A:THR413 4.8 25.5 1.0 O1B A:DTP1001 4.8 28.7 1.0 O A:ASP411 4.8 28.6 1.0 O1A A:DTP1001 4.8 28.4 1.0 CA A:ASP411 4.8 28.8 1.0 C A:THR413 4.9 28.6 1.0

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


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/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:52.4 occ:1.00 O P:HOH211 2.4 36.4 1.0 O2A A:DTP1001 2.6 23.5 1.0 OD1 A:ASP623 2.7 27.0 1.0 OD2 A:ASP411 3.3 27.3 1.0 CA A:CA1002 3.5 26.1 1.0 CG A:ASP623 3.5 27.6 1.0 CG A:ASP411 3.6 33.1 1.0 OD2 A:ASP623 3.6 28.9 1.0 CB A:ASP411 3.7 29.0 1.0 O A:HOH1606 3.8 42.0 1.0 C3' P:DC115 3.8 27.5 1.0 PA A:DTP1001 3.8 26.8 1.0 CB A:SER624 4.0 26.1 1.0 C5' P:DC115 4.1 30.5 1.0 OD1 A:ASP411 4.3 33.3 1.0 O1A A:DTP1001 4.3 28.4 1.0 O A:HOH1231 4.4 29.8 1.0 C4' P:DC115 4.4 28.7 1.0 O5' A:DTP1001 4.4 27.7 1.0 C5' A:DTP1001 4.6 24.2 1.0 O A:HOH1296 4.6 38.5 1.0 OG A:SER624 4.7 28.8 1.0 O P:HOH206 4.7 29.8 1.0 O1G A:DTP1001 4.7 26.8 1.0 O A:ASP621 4.8 25.1 1.0 C A:ASP623 4.9 29.3 1.0 N A:SER624 4.9 27.4 1.0 CB A:ASP623 4.9 25.9 1.0 CA A:SER624 5.0 27.2 1.0 O A:ASP623 5.0 28.1 1.0

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


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/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:45.7 occ:1.00 O A:HOH1261 2.1 44.3 1.0 OD1 A:ASN507 2.3 54.0 1.0 O A:ASN505 2.3 41.1 1.0 O A:LYS531 2.3 52.4 1.0 O A:HOH1633 2.4 45.0 1.0 C A:LYS531 3.3 52.3 1.0 CG A:ASN507 3.4 58.9 1.0 C A:ASN505 3.5 47.9 1.0 CA A:LYS531 4.0 50.3 1.0 ND2 A:ASN507 4.1 55.8 1.0 CB A:ASN505 4.2 52.4 1.0 N A:LYS532 4.2 48.1 1.0 N A:ASN507 4.3 52.6 1.0 C A:PRO506 4.3 49.0 1.0 CA A:PRO506 4.3 46.8 1.0 N A:PRO506 4.4 44.5 1.0 CA A:LYS532 4.4 51.7 1.0 CA A:ASN505 4.5 53.0 1.0 O A:HOH1379 4.5 44.5 1.0 O A:LEU533 4.5 37.5 1.0 O A:ALA502 4.6 44.5 1.0 CB A:ASN507 4.6 56.9 1.0 CB A:LYS531 4.7 53.0 1.0 O A:PRO506 4.8 50.8 1.0 CA A:ASN507 4.8 52.4 1.0 C A:LYS532 4.8 52.0 1.0 O A:ILE530 4.9 37.4 1.0 N A:LEU533 4.9 50.1 1.0

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


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/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:47.1 occ:1.00 OE1 A:GLU716 2.4 48.4 1.0 O A:HOH1584 2.4 53.2 1.0 O A:HOH1510 2.5 38.9 1.0 O A:HOH1103 2.6 32.4 1.0 O A:HOH1467 2.6 40.7 1.0 O A:HOH1605 2.8 41.0 1.0 CD A:GLU716 3.5 46.0 1.0 CG A:GLU716 4.2 42.4 1.0 NZ A:LYS486 4.2 35.8 1.0 CB A:ASP684 4.2 39.2 1.0 OG1 A:THR413 4.4 28.7 1.0 OE2 A:GLU716 4.4 40.0 1.0 O A:ASP411 4.5 28.6 1.0 OD1 A:ASP411 4.5 33.3 1.0 O A:ASP684 4.7 29.9 1.0 OD2 A:ASP411 4.8 27.3 1.0 O A:HOH1536 4.8 47.2 1.0 OD2 A:ASP684 4.8 59.1 1.0 CG A:ASP411 4.9 33.1 1.0 O A:ARG685 5.0 29.7 1.0

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


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/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:63.0 occ:1.00 O A:HOH1352 2.2 38.0 1.0 O A:HOH1393 2.4 50.8 1.0 O A:HOH1125 2.4 40.5 1.0 OE1 A:GLU116 2.6 37.8 1.0 OE2 A:GLU116 2.8 36.7 1.0 CD A:GLU116 3.1 38.3 1.0 OD2 A:ASP114 4.2 48.2 1.0 CG A:GLU116 4.6 31.1 1.0 O A:ILE115 4.7 31.4 1.0 CD1 A:ILE309 4.9 52.5 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