Calcium in PDB 4fjh: RB69 Dna Polymerase Ternary Complex with Dgtp/Dc

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

The structure of RB69 Dna Polymerase Ternary Complex with Dgtp/Dc, PDB code: 4fjh 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)	38.09 / 2.11
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.020, 120.074, 130.675, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.3

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


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/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:18.4 occ:1.00 O2B A:DGT1001 2.2 18.8 1.0 OD2 A:ASP411 2.3 22.8 1.0 O1G A:DGT1001 2.3 18.6 1.0 OD2 A:ASP623 2.3 20.3 1.0 O A:LEU412 2.3 15.8 1.0 O2A A:DGT1001 2.4 19.8 1.0 PB A:DGT1001 3.4 19.3 1.0 CG A:ASP411 3.4 23.7 1.0 CG A:ASP623 3.4 20.5 1.0 CA A:CA1003 3.5 49.8 1.0 C A:LEU412 3.5 18.1 1.0 PG A:DGT1001 3.6 20.0 1.0 PA A:DGT1001 3.6 21.5 1.0 O3A A:DGT1001 3.8 21.3 1.0 OD1 A:ASP623 3.9 19.2 1.0 O3B A:DGT1001 3.9 20.7 1.0 O A:HOH1118 3.9 36.1 1.0 N A:LEU412 4.0 17.1 1.0 CB A:ASP411 4.0 19.9 1.0 C5' A:DGT1001 4.2 20.0 1.0 O2G A:DGT1001 4.2 20.4 1.0 CA A:LEU412 4.2 17.5 1.0 C A:ASP411 4.3 19.4 1.0 O5' A:DGT1001 4.4 20.6 1.0 OD1 A:ASP411 4.5 23.6 1.0 N A:THR413 4.5 17.8 1.0 N A:SER414 4.5 18.8 1.0 N A:ALA415 4.7 16.5 1.0 CB A:ASP623 4.7 18.7 1.0 CB A:ALA415 4.7 14.7 1.0 CB A:LEU412 4.7 16.0 1.0 CA A:THR413 4.7 17.3 1.0 O1B A:DGT1001 4.8 20.1 1.0 O A:ASP411 4.8 18.6 1.0 O3G A:DGT1001 4.8 21.4 1.0 CA A:ASP411 4.8 20.1 1.0 O1A A:DGT1001 4.8 21.9 1.0 C A:THR413 4.9 18.8 1.0

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


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/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:49.8 occ:1.00 O A:HOH1383 2.5 29.8 1.0 O2A A:DGT1001 2.6 19.8 1.0 OD1 A:ASP623 2.7 19.2 1.0 OD2 A:ASP411 3.4 22.8 1.0 CG A:ASP623 3.5 20.5 1.0 CA A:CA1002 3.5 18.4 1.0 OD2 A:ASP623 3.5 20.3 1.0 CG A:ASP411 3.6 23.7 1.0 CB A:ASP411 3.6 19.9 1.0 C3' P:DT115 3.7 21.4 1.0 PA A:DGT1001 3.8 21.5 1.0 CB A:SER624 4.0 18.5 1.0 OD1 A:ASP411 4.3 23.6 1.0 O A:HOH1171 4.3 20.6 1.0 O1A A:DGT1001 4.4 21.9 1.0 O A:HOH1200 4.4 25.8 1.0 O5' A:DGT1001 4.5 20.6 1.0 C5' A:DGT1001 4.5 20.0 1.0 OG A:SER624 4.6 24.2 1.0 O A:HOH1187 4.7 21.6 1.0 O1G A:DGT1001 4.8 18.6 1.0 N A:SER624 4.8 19.2 1.0 C2' P:DT115 4.8 21.4 1.0 O A:ASP621 4.8 16.2 1.0 C A:ASP623 4.8 19.6 1.0 C4' P:DT115 4.9 21.0 1.0 O5' P:DT115 4.9 22.9 1.0 CA A:SER624 4.9 19.7 1.0 CB A:ASP623 4.9 18.7 1.0 C5' P:DT115 5.0 22.3 1.0

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


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/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:36.4 occ:1.00 O A:HOH1273 2.1 35.4 1.0 O A:LYS531 2.3 41.2 1.0 OD1 A:ASN507 2.3 43.6 1.0 O A:ASN505 2.3 34.5 1.0 O A:HOH1354 2.5 35.2 1.0 O A:HOH1218 2.5 33.5 1.0 C A:LYS531 3.3 39.1 1.0 CG A:ASN507 3.5 45.2 1.0 C A:ASN505 3.6 38.2 1.0 CA A:LYS531 4.0 38.6 1.0 ND2 A:ASN507 4.0 43.5 1.0 CB A:ASN505 4.2 43.0 1.0 N A:LYS532 4.2 37.1 1.0 N A:ASN507 4.2 41.4 1.0 CA A:PRO506 4.4 38.0 1.0 C A:PRO506 4.4 39.3 1.0 CA A:LYS532 4.5 38.9 1.0 N A:PRO506 4.5 36.7 1.0 CA A:ASN505 4.5 41.8 1.0 O A:HOH1264 4.5 34.7 1.0 O A:ALA502 4.6 38.5 1.0 CB A:LYS531 4.6 42.9 1.0 O A:LEU533 4.6 33.0 1.0 CB A:ASN507 4.7 45.1 1.0 C A:LYS532 4.8 38.6 1.0 CA A:ASN507 4.9 43.1 1.0 O A:ILE530 4.9 29.0 1.0 N A:LEU533 5.0 37.3 1.0

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


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/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:39.7 occ:1.00 O A:HOH1299 2.4 41.1 1.0 O A:HOH1380 2.5 34.3 1.0 O A:HOH1118 2.6 36.1 1.0 OE1 A:GLU716 2.6 42.8 1.0 O A:HOH1128 2.6 22.1 1.0 O A:HOH1219 2.7 26.2 1.0 O A:HOH1650 3.5 33.0 1.0 CD A:GLU716 3.6 40.9 1.0 NZ A:LYS486 4.2 28.5 1.0 CG A:GLU716 4.3 35.8 1.0 OG1 A:THR413 4.3 19.9 1.0 CB A:ASP684 4.3 28.5 1.0 O A:HOH1531 4.4 49.1 1.0 OE2 A:GLU716 4.4 37.5 1.0 O A:ASP411 4.5 18.6 1.0 OD1 A:ASP411 4.5 23.6 1.0 OD2 A:ASP411 4.7 22.8 1.0 O A:HOH1492 4.7 31.9 1.0 O A:ASP684 4.7 20.1 1.0 OD2 A:ASP684 4.8 44.9 1.0 CG A:ASP411 4.9 23.7 1.0

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


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/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:58.3 occ:1.00 O A:HOH1429 2.3 34.2 1.0 O A:HOH1496 2.4 40.5 1.0 O A:HOH1119 2.4 29.5 1.0 OE1 A:GLU116 2.6 29.5 1.0 OE2 A:GLU116 3.0 31.8 1.0 CD A:GLU116 3.1 29.5 1.0 O A:HOH1670 4.3 34.8 1.0 OD2 A:ASP114 4.3 36.2 1.0 O A:HOH1444 4.3 49.0 1.0 O A:HOH1610 4.5 42.7 1.0 CG A:GLU116 4.6 23.9 1.0 O A:ILE115 4.6 23.4 1.0 O A:HOH1501 4.8 57.1 1.0 CD1 A:ILE309 4.8 44.4 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