Calcium in PDB 4fk2: RB69 Dna Polymerase Ternary Complex with Dttp/Dg

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

The structure of RB69 Dna Polymerase Ternary Complex with Dttp/Dg, PDB code: 4fk2 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)	38.07 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.007, 120.261, 130.301, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.5

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dttp/Dg (pdb code 4fk2). 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 Dttp/Dg, PDB code: 4fk2:
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 Dttp/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 Dttp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:20.5 occ:1.00 OD1 A:ASP623 2.3 23.1 1.0 O A:LEU412 2.3 19.6 1.0 O1G A:TTP1001 2.3 19.3 1.0 OD2 A:ASP411 2.3 24.2 1.0 O2B A:TTP1001 2.3 19.7 1.0 O2A A:TTP1001 2.3 19.2 1.0 CG A:ASP623 3.4 21.6 1.0 PB A:TTP1001 3.4 22.5 1.0 CG A:ASP411 3.4 26.7 1.0 C A:LEU412 3.4 21.3 1.0 PA A:TTP1001 3.5 21.6 1.0 PG A:TTP1001 3.6 23.6 1.0 CA A:CA1003 3.7 51.6 1.0 O3A A:TTP1001 3.7 22.3 1.0 OD2 A:ASP623 3.8 21.0 1.0 O3B A:TTP1001 3.9 23.6 1.0 N A:LEU412 3.9 20.0 1.0 CB A:ASP411 3.9 25.2 1.0 O A:HOH1107 4.0 32.6 1.0 CA A:LEU412 4.2 20.2 1.0 C5' A:TTP1001 4.2 18.8 1.0 O2G A:TTP1001 4.2 22.8 1.0 C A:ASP411 4.3 21.6 1.0 O5' A:TTP1001 4.4 21.7 1.0 N A:SER414 4.5 23.6 1.0 OD1 A:ASP411 4.5 28.9 1.0 N A:THR413 4.5 21.4 1.0 N A:ALA415 4.6 20.2 1.0 CB A:ALA415 4.6 17.3 1.0 CB A:ASP623 4.7 20.8 1.0 CB A:LEU412 4.7 19.3 1.0 CA A:THR413 4.7 21.9 1.0 O3G A:TTP1001 4.7 22.6 1.0 O1A A:TTP1001 4.8 21.5 1.0 CA A:ASP411 4.8 24.5 1.0 O1B A:TTP1001 4.8 22.7 1.0 O A:ASP411 4.8 23.8 1.0 C A:THR413 4.8 22.4 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:51.6 occ:1.00 O A:HOH1336 2.5 34.7 1.0 OD2 A:ASP623 2.5 21.0 1.0 O2A A:TTP1001 2.8 19.2 1.0 CG A:ASP623 3.4 21.6 1.0 OD2 A:ASP411 3.5 24.2 1.0 CB A:ASP411 3.5 25.2 1.0 CG A:ASP411 3.5 26.7 1.0 OD1 A:ASP623 3.6 23.1 1.0 CA A:CA1002 3.7 20.5 1.0 CB A:SER624 3.8 24.3 1.0 C3' P:DOC115 3.9 28.3 1.0 PA A:TTP1001 4.0 21.6 1.0 OD1 A:ASP411 4.2 28.9 1.0 O A:HOH1191 4.3 34.7 1.0 O A:HOH1205 4.3 24.0 1.0 OG A:SER624 4.3 24.6 1.0 O1A A:TTP1001 4.5 21.5 1.0 O5' A:TTP1001 4.5 21.7 1.0 N A:SER624 4.6 25.0 1.0 O A:ASP621 4.6 18.7 1.0 C5' A:TTP1001 4.6 18.8 1.0 CA A:SER624 4.7 23.8 1.0 C A:ASP623 4.7 22.4 1.0 O A:HOH1148 4.7 28.6 1.0 CB A:ASP623 4.8 20.8 1.0 C4' P:DOC115 4.9 28.3 1.0 O A:ASP623 4.9 20.3 1.0 O5' P:DOC115 5.0 30.1 1.0 C5' P:DOC115 5.0 29.4 1.0 C2' P:DOC115 5.0 28.3 1.0 CA A:ASP411 5.0 24.5 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:39.7 occ:1.00 O A:HOH1547 2.2 39.9 1.0 OD1 A:ASN507 2.3 46.2 1.0 O A:LYS531 2.3 46.9 1.0 O A:ASN505 2.3 40.8 1.0 O A:HOH1179 2.4 35.6 1.0 O A:HOH1325 2.4 41.3 1.0 C A:LYS531 3.2 44.7 1.0 CG A:ASN507 3.4 46.5 1.0 C A:ASN505 3.6 43.9 1.0 CA A:LYS531 4.0 45.7 1.0 ND2 A:ASN507 4.0 40.4 1.0 N A:ASN507 4.1 44.4 1.0 N A:LYS532 4.1 41.4 1.0 CB A:ASN505 4.2 45.6 1.0 CA A:LYS532 4.3 45.1 1.0 C A:PRO506 4.4 43.1 1.0 CA A:PRO506 4.4 41.6 1.0 N A:PRO506 4.5 42.4 1.0 CA A:ASN505 4.5 47.8 1.0 O A:LEU533 4.5 37.0 1.0 O A:HOH1548 4.6 40.6 1.0 CB A:ASN507 4.6 48.7 1.0 C A:LYS532 4.7 43.7 1.0 O A:ALA502 4.7 38.0 1.0 CB A:LYS531 4.7 45.6 1.0 O A:ILE530 4.8 39.0 1.0 CA A:ASN507 4.8 44.9 1.0 N A:LEU533 4.8 43.3 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:40.4 occ:1.00 OE1 A:GLU716 2.5 46.6 1.0 O A:HOH1525 2.5 38.5 1.0 O A:HOH1524 2.6 25.5 1.0 O A:HOH1107 2.6 32.6 1.0 O A:HOH1303 2.6 35.2 1.0 O A:HOH1185 2.7 31.2 1.0 O A:HOH1526 2.9 36.0 1.0 CD A:GLU716 3.5 42.2 1.0 NZ A:LYS486 4.1 34.1 1.0 CG A:GLU716 4.3 34.2 1.0 OE2 A:GLU716 4.3 38.8 1.0 CB A:ASP684 4.5 33.1 1.0 OG1 A:THR413 4.5 22.3 1.0 OD1 A:ASP411 4.5 28.9 1.0 O A:ASP411 4.6 23.8 1.0 OD2 A:ASP411 4.7 24.2 1.0 O A:HOH1387 4.7 37.9 1.0 O A:ASP684 4.8 23.3 1.0 CG A:ASP411 4.9 26.7 1.0 O2G A:TTP1001 4.9 22.8 1.0 O1G A:TTP1001 5.0 19.3 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:53.6 occ:1.00 O A:HOH1443 2.3 40.0 1.0 O A:HOH1111 2.4 28.3 1.0 O A:HOH1341 2.5 38.4 1.0 OE1 A:GLU116 2.5 32.7 1.0 OE2 A:GLU116 2.9 37.3 1.0 CD A:GLU116 3.1 33.7 1.0 O A:HOH1511 4.2 62.5 1.0 O A:HOH1498 4.3 37.7 1.0 OD2 A:ASP114 4.3 40.4 1.0 O A:HOH1541 4.5 40.3 1.0 CG A:GLU116 4.6 28.1 1.0 O A:ILE115 4.6 26.7 1.0 CD1 A:ILE309 4.8 42.9 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