Calcium in PDB 4fjj: RB69 Dna Polymerase Ternary Complex with Dttp/Dc

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

The structure of RB69 Dna Polymerase Ternary Complex with Dttp/Dc, PDB code: 4fjj 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)	49.31 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.196, 119.818, 130.637, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.5

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dttp/Dc (pdb code 4fjj). 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/Dc, PDB code: 4fjj:
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/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 Dttp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:19.9 occ:1.00 O2B A:TTP1001 2.3 19.6 1.0 OD2 A:ASP411 2.3 19.7 1.0 OD1 A:ASP623 2.3 21.6 1.0 O1G A:TTP1001 2.3 17.1 1.0 O A:LEU412 2.3 17.7 1.0 O2A A:TTP1001 2.4 19.9 1.0 PB A:TTP1001 3.4 20.4 1.0 CG A:ASP623 3.4 21.7 1.0 CG A:ASP411 3.4 28.0 1.0 C A:LEU412 3.5 19.4 1.0 PG A:TTP1001 3.6 21.8 1.0 PA A:TTP1001 3.6 20.9 1.0 CA A:CA1003 3.6 49.6 1.0 O3A A:TTP1001 3.8 22.6 1.0 OD2 A:ASP623 3.8 21.3 1.0 O3B A:TTP1001 3.8 23.1 1.0 O A:HOH1119 3.9 30.0 1.0 N A:LEU412 4.0 18.1 1.0 CB A:ASP411 4.0 23.9 1.0 C5' A:TTP1001 4.2 16.2 1.0 CA A:LEU412 4.2 19.9 1.0 O2G A:TTP1001 4.3 20.0 1.0 C A:ASP411 4.3 19.8 1.0 O5' A:TTP1001 4.4 19.9 1.0 OD1 A:ASP411 4.5 28.0 1.0 N A:THR413 4.5 20.7 1.0 N A:SER414 4.6 20.0 1.0 N A:ALA415 4.6 17.9 1.0 CB A:ASP623 4.7 18.7 1.0 CB A:ALA415 4.7 16.5 1.0 CB A:LEU412 4.7 18.0 1.0 O1B A:TTP1001 4.7 23.8 1.0 CA A:THR413 4.8 21.4 1.0 O3G A:TTP1001 4.8 21.5 1.0 O1A A:TTP1001 4.8 20.6 1.0 CA A:ASP411 4.8 23.0 1.0 O A:ASP411 4.8 23.2 1.0 C A:THR413 4.8 20.4 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:49.6 occ:1.00 O A:HOH1460 2.6 37.1 1.0 O2A A:TTP1001 2.7 19.9 1.0 OD2 A:ASP623 2.7 21.3 1.0 OD2 A:ASP411 3.3 19.7 1.0 CG A:ASP623 3.6 21.7 1.0 CG A:ASP411 3.6 28.0 1.0 CA A:CA1002 3.6 19.9 1.0 CB A:ASP411 3.6 23.9 1.0 OD1 A:ASP623 3.7 21.6 1.0 C3' P:DOC115 3.8 25.5 1.0 PA A:TTP1001 3.9 20.9 1.0 CB A:SER624 3.9 21.4 1.0 O A:HOH1183 4.2 25.5 1.0 OD1 A:ASP411 4.4 28.0 1.0 O1A A:TTP1001 4.4 20.6 1.0 O A:HOH1249 4.5 34.8 1.0 O5' A:TTP1001 4.5 19.9 1.0 OG A:SER624 4.6 22.2 1.0 C5' A:TTP1001 4.6 16.2 1.0 O A:ASP621 4.7 18.4 1.0 C5' P:DOC115 4.7 28.5 1.0 O A:HOH1210 4.8 27.2 1.0 C4' P:DOC115 4.8 27.8 1.0 N A:SER624 4.8 20.6 1.0 CA A:SER624 4.8 21.2 1.0 C A:ASP623 4.9 20.5 1.0 O5' P:DOC115 4.9 27.4 1.0 O1G A:TTP1001 4.9 17.1 1.0 C2' P:DOC115 5.0 26.4 1.0 CB A:ASP623 5.0 18.7 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:36.0 occ:1.00 O A:LYS531 2.2 42.5 1.0 O A:HOH1234 2.2 39.1 1.0 OD1 A:ASN507 2.3 42.3 1.0 O A:ASN505 2.3 36.4 1.0 O A:HOH1197 2.5 31.3 1.0 O A:HOH1163 2.6 30.7 1.0 C A:LYS531 3.2 41.9 1.0 CG A:ASN507 3.4 43.5 1.0 C A:ASN505 3.6 38.2 1.0 CA A:LYS531 4.0 40.0 1.0 ND2 A:ASN507 4.1 40.3 1.0 CB A:ASN505 4.1 40.6 1.0 N A:LYS532 4.2 37.6 1.0 N A:ASN507 4.2 38.6 1.0 CA A:LYS532 4.4 40.5 1.0 C A:PRO506 4.4 40.2 1.0 CA A:PRO506 4.4 40.0 1.0 N A:PRO506 4.5 36.7 1.0 CA A:ASN505 4.5 40.6 1.0 O A:LEU533 4.5 32.9 1.0 O A:ALA502 4.5 38.0 1.0 O A:HOH1250 4.6 30.6 1.0 CB A:ASN507 4.6 43.5 1.0 CB A:LYS531 4.7 41.2 1.0 C A:LYS532 4.8 40.3 1.0 N A:LEU533 4.8 38.8 1.0 CA A:ASN507 4.8 40.6 1.0 O A:ILE530 4.9 33.3 1.0 O A:PRO506 5.0 43.6 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:40.6 occ:1.00 O A:HOH1261 2.3 39.1 1.0 OE1 A:GLU716 2.5 44.8 1.0 O A:HOH1154 2.5 25.8 1.0 O A:HOH1262 2.6 27.5 1.0 O A:HOH1313 2.6 25.8 1.0 O A:HOH1458 2.8 39.1 1.0 O A:HOH1119 2.9 30.0 1.0 CD A:GLU716 3.7 38.7 1.0 CG A:GLU716 4.3 36.2 1.0 NZ A:LYS486 4.3 33.0 1.0 OG1 A:THR413 4.4 23.6 1.0 CB A:ASP684 4.4 33.4 1.0 OD1 A:ASP411 4.5 28.0 1.0 O A:ASP411 4.5 23.2 1.0 OE2 A:GLU716 4.6 41.6 1.0 OD2 A:ASP411 4.8 19.7 1.0 O A:HOH1356 4.8 36.6 1.0 O A:ASP684 4.8 21.4 1.0 CG A:ASP411 4.9 28.0 1.0 O1G A:TTP1001 5.0 17.1 1.0 O2G A:TTP1001 5.0 20.0 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:63.2 occ:1.00 O A:HOH1563 2.4 41.8 1.0 OE1 A:GLU116 2.5 30.7 1.0 O A:HOH1388 2.5 31.9 1.0 O A:HOH1142 2.6 30.1 1.0 OE2 A:GLU116 3.0 35.9 1.0 CD A:GLU116 3.1 29.5 1.0 O A:HOH1564 4.3 37.7 1.0 OD2 A:ASP114 4.5 44.5 1.0 CG A:GLU116 4.6 24.1 1.0 O A:ILE115 4.6 21.9 1.0 CD1 A:ILE309 4.6 34.9 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