Calcium in PDB 4fjg: RB69 Dna Polymerase Ternary Complex with Datp/Dc

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

The structure of RB69 Dna Polymerase Ternary Complex with Datp/Dc, PDB code: 4fjg 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 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.090, 119.933, 130.592, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 26.4

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Datp/Dc (pdb code 4fjg). 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/Dc, PDB code: 4fjg:
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/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 Datp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:22.7 occ:1.00 O1G A:DTP1001 2.2 22.3 1.0 O A:LEU412 2.2 22.1 1.0 OD2 A:ASP411 2.3 24.2 1.0 O2B A:DTP1001 2.3 22.1 1.0 OD1 A:ASP623 2.3 22.5 1.0 O2A A:DTP1001 2.4 22.1 1.0 PB A:DTP1001 3.4 21.4 1.0 C A:LEU412 3.4 23.9 1.0 CG A:ASP411 3.5 28.5 1.0 CG A:ASP623 3.5 24.8 1.0 PG A:DTP1001 3.5 24.2 1.0 PA A:DTP1001 3.7 22.2 1.0 CA A:CA1003 3.7 54.6 1.0 O3A A:DTP1001 3.8 22.7 1.0 O3B A:DTP1001 3.9 23.0 1.0 O A:HOH1108 3.9 29.5 1.0 OD2 A:ASP623 3.9 25.3 1.0 CB A:ASP411 4.0 25.6 1.0 N A:LEU412 4.0 20.8 1.0 O2G A:DTP1001 4.1 27.7 1.0 C5' A:DTP1001 4.2 21.6 1.0 CA A:LEU412 4.2 21.6 1.0 C A:ASP411 4.3 23.4 1.0 O5' A:DTP1001 4.4 21.7 1.0 N A:SER414 4.5 25.5 1.0 N A:THR413 4.5 26.9 1.0 OD1 A:ASP411 4.5 24.8 1.0 CB A:LEU412 4.6 21.1 1.0 N A:ALA415 4.7 19.1 1.0 CA A:THR413 4.7 25.9 1.0 CB A:ALA415 4.7 17.4 1.0 CB A:ASP623 4.7 22.2 1.0 O3G A:DTP1001 4.7 22.2 1.0 O A:ASP411 4.8 25.1 1.0 O1B A:DTP1001 4.8 22.8 1.0 C A:THR413 4.8 26.7 1.0 CA A:ASP411 4.8 25.4 1.0 O1A A:DTP1001 4.9 26.0 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp/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 Datp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:54.6 occ:1.00 O A:HOH1275 2.4 34.9 1.0 OD2 A:ASP623 2.7 25.3 1.0 O2A A:DTP1001 2.8 22.1 1.0 OD2 A:ASP411 3.3 24.2 1.0 CG A:ASP623 3.5 24.8 1.0 CG A:ASP411 3.5 28.5 1.0 CB A:ASP411 3.6 25.6 1.0 OD1 A:ASP623 3.6 22.5 1.0 CA A:CA1002 3.7 22.7 1.0 CB A:SER624 3.8 23.5 1.0 C3' P:DOC115 3.9 27.7 1.0 PA A:DTP1001 4.0 22.2 1.0 O P:HOH210 4.2 25.2 1.0 OD1 A:ASP411 4.3 24.8 1.0 OG A:SER624 4.4 30.3 1.0 O1A A:DTP1001 4.5 26.0 1.0 C5' P:DOC115 4.5 32.9 1.0 O5' A:DTP1001 4.5 21.7 1.0 C4' P:DOC115 4.7 27.9 1.0 C5' A:DTP1001 4.7 21.6 1.0 O A:ASP621 4.8 25.3 1.0 O A:HOH1154 4.8 23.4 1.0 CA A:SER624 4.8 24.6 1.0 C A:ASP623 4.8 23.1 1.0 N A:SER624 4.8 20.8 1.0 O1G A:DTP1001 4.9 22.3 1.0 O A:ASP623 4.9 23.0 1.0 CB A:ASP623 4.9 22.2 1.0 O5' P:DOC115 5.0 30.3 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp/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 Datp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:38.8 occ:1.00 O A:HOH1362 1.9 35.6 1.0 O A:ASN505 2.2 37.5 1.0 O A:LYS531 2.3 41.6 1.0 OD1 A:ASN507 2.3 41.2 1.0 O A:HOH1168 2.5 32.8 1.0 O A:HOH1136 2.5 27.6 1.0 C A:LYS531 3.3 43.1 1.0 CG A:ASN507 3.5 47.2 1.0 C A:ASN505 3.5 42.4 1.0 CA A:LYS531 3.9 38.8 1.0 ND2 A:ASN507 4.1 41.3 1.0 N A:ASN507 4.1 43.6 1.0 CB A:ASN505 4.2 41.2 1.0 N A:LYS532 4.2 39.7 1.0 CA A:PRO506 4.2 40.2 1.0 C A:PRO506 4.3 42.2 1.0 N A:PRO506 4.3 40.1 1.0 CA A:ASN505 4.5 42.9 1.0 CA A:LYS532 4.5 44.0 1.0 O A:LEU533 4.5 35.6 1.0 O A:ALA502 4.5 39.5 1.0 CB A:LYS531 4.5 41.9 1.0 O A:HOH1397 4.6 35.9 1.0 CB A:ASN507 4.6 44.0 1.0 C A:LYS532 4.8 42.5 1.0 CA A:ASN507 4.8 43.3 1.0 N A:LEU533 4.8 39.8 1.0 O A:ILE530 4.9 36.6 1.0 O A:PRO506 5.0 38.9 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp/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 Datp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:54.5 occ:1.00 O A:HOH1386 2.4 42.2 1.0 OE1 A:GLU716 2.6 47.9 1.0 O A:HOH1163 2.6 41.4 1.0 O A:HOH1171 2.7 25.7 1.0 O A:HOH1384 2.9 39.4 1.0 O A:HOH1108 3.2 29.5 1.0 O A:HOH1424 3.5 34.7 1.0 CD A:GLU716 3.5 40.2 1.0 NZ A:LYS486 4.1 24.7 1.0 CG A:GLU716 4.2 37.7 1.0 CB A:ASP684 4.3 33.5 1.0 OG1 A:THR413 4.3 27.2 1.0 OE2 A:GLU716 4.4 39.9 1.0 OD1 A:ASP411 4.5 24.8 1.0 O A:ASP411 4.5 25.1 1.0 O A:ASP684 4.8 27.3 1.0 OD2 A:ASP411 4.8 24.2 1.0 OD2 A:ASP684 4.9 50.2 1.0 O A:HOH1385 4.9 38.0 1.0 CG A:ASP411 4.9 28.5 1.0 O A:ARG685 5.0 25.7 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Datp/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 Datp/Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:63.0 occ:1.00 O A:HOH1412 2.3 32.1 1.0 O A:HOH1114 2.5 27.5 1.0 OE1 A:GLU116 2.7 36.1 1.0 OE2 A:GLU116 3.0 47.8 1.0 CD A:GLU116 3.2 38.0 1.0 CD1 A:ILE309 3.9 64.0 1.0 OD2 A:ASP114 4.3 37.8 1.0 O A:HOH1311 4.3 37.0 1.0 O A:ILE115 4.7 28.4 1.0 CG A:GLU116 4.7 32.2 1.0 O A:HOH1413 4.8 52.6 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