Calcium in PDB 4fjk: RB69 Dna Polymerase Ternary Complex with Datp/Da

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

The structure of RB69 Dna Polymerase Ternary Complex with Datp/Da, PDB code: 4fjk 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)	37.61 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.700, 120.202, 130.606, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.6

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:23.0 occ:1.00 O A:LEU412 2.2 20.1 1.0 O1G A:DTP1001 2.3 22.8 1.0 O2B A:DTP1001 2.3 21.8 1.0 OD1 A:ASP623 2.3 20.0 1.0 OD2 A:ASP411 2.3 25.2 1.0 O2A A:DTP1001 2.4 22.0 1.0 C A:LEU412 3.4 20.7 1.0 PB A:DTP1001 3.4 21.5 1.0 CG A:ASP623 3.4 19.9 1.0 CG A:ASP411 3.5 26.6 1.0 CA A:CA1003 3.5 50.6 1.0 PG A:DTP1001 3.6 22.0 1.0 PA A:DTP1001 3.6 25.4 1.0 O3A A:DTP1001 3.8 24.3 1.0 OD2 A:ASP623 3.9 18.9 1.0 O3B A:DTP1001 3.9 24.5 1.0 O A:HOH1516 3.9 36.6 1.0 N A:LEU412 3.9 20.7 1.0 CB A:ASP411 4.0 25.7 1.0 O A:HOH1635 4.0 36.8 1.0 CA A:LEU412 4.2 21.7 1.0 O2G A:DTP1001 4.2 21.9 1.0 C5' A:DTP1001 4.3 20.2 1.0 C A:ASP411 4.3 23.3 1.0 O5' A:DTP1001 4.5 22.3 1.0 N A:THR413 4.5 22.8 1.0 N A:SER414 4.5 20.7 1.0 OD1 A:ASP411 4.5 29.4 1.0 N A:ALA415 4.6 21.3 1.0 CB A:LEU412 4.6 19.8 1.0 CB A:ALA415 4.7 17.5 1.0 CB A:ASP623 4.7 17.9 1.0 CA A:THR413 4.7 21.2 1.0 O A:ASP411 4.7 22.5 1.0 O3G A:DTP1001 4.8 25.4 1.0 C A:THR413 4.8 21.9 1.0 O1B A:DTP1001 4.8 25.8 1.0 CA A:ASP411 4.8 25.4 1.0 O1A A:DTP1001 4.8 23.1 1.0

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:50.6 occ:1.00 O2A A:DTP1001 2.6 22.0 1.0 O A:HOH1302 2.7 31.2 1.0 OD2 A:ASP623 2.7 18.9 1.0 OD2 A:ASP411 3.5 25.2 1.0 CG A:ASP623 3.5 19.9 1.0 CA A:CA1002 3.5 23.0 1.0 OD1 A:ASP623 3.6 20.0 1.0 CG A:ASP411 3.6 26.6 1.0 CB A:ASP411 3.6 25.7 1.0 C3' P:DC115 3.8 24.7 1.0 PA A:DTP1001 3.8 25.4 1.0 CB A:SER624 4.0 23.2 1.0 O A:HOH1635 4.0 36.8 1.0 C5' P:DC115 4.1 29.9 1.0 O A:HOH1207 4.4 23.8 1.0 OD1 A:ASP411 4.4 29.4 1.0 C4' P:DC115 4.4 26.6 1.0 O1A A:DTP1001 4.4 23.1 1.0 O5' A:DTP1001 4.4 22.3 1.0 O A:HOH1157 4.6 27.5 1.0 C5' A:DTP1001 4.6 20.2 1.0 OG A:SER624 4.6 24.0 1.0 O A:ASP621 4.7 22.5 1.0 O P:HOH206 4.7 25.5 1.0 O1G A:DTP1001 4.8 22.8 1.0 N A:SER624 4.8 22.0 1.0 C A:ASP623 4.8 23.5 1.0 CA A:SER624 4.9 23.0 1.0 CB A:ASP623 4.9 17.9 1.0 O A:ASP623 5.0 24.6 1.0

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:44.0 occ:1.00 O A:HOH1370 2.2 41.4 1.0 OD1 A:ASN507 2.2 51.2 1.0 O A:LYS531 2.2 57.2 1.0 O A:ASN505 2.3 47.4 1.0 O A:HOH1342 2.5 40.7 1.0 O A:HOH1535 2.6 40.2 1.0 C A:LYS531 3.2 55.0 1.0 CG A:ASN507 3.4 52.7 1.0 C A:ASN505 3.5 51.0 1.0 CA A:LYS531 4.0 56.9 1.0 ND2 A:ASN507 4.0 48.5 1.0 CB A:ASN505 4.1 49.5 1.0 N A:ASN507 4.1 49.4 1.0 N A:LYS532 4.1 47.0 1.0 C A:PRO506 4.3 52.9 1.0 CA A:PRO506 4.4 47.8 1.0 CA A:LYS532 4.4 46.4 1.0 N A:PRO506 4.4 49.9 1.0 CA A:ASN505 4.4 50.5 1.0 CB A:ASN507 4.6 52.0 1.0 O A:LEU533 4.6 42.2 1.0 CB A:LYS531 4.7 55.8 1.0 CA A:ASN507 4.7 52.6 1.0 O A:ALA502 4.7 43.4 1.0 C A:LYS532 4.8 46.2 1.0 O A:ILE530 4.8 41.5 1.0 N A:LEU533 4.8 43.0 1.0 O A:PRO506 5.0 50.9 1.0

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:43.0 occ:1.00 O A:HOH1527 2.4 53.6 1.0 O A:HOH1174 2.5 32.3 1.0 O A:HOH1260 2.6 37.5 1.0 OE1 A:GLU716 2.6 38.3 1.0 O A:HOH1501 2.7 35.1 1.0 O A:HOH1516 3.0 36.6 1.0 O A:HOH1394 3.6 36.0 1.0 CD A:GLU716 3.8 38.0 1.0 NZ A:LYS486 4.2 36.6 1.0 CG A:GLU716 4.3 36.9 1.0 OG1 A:THR413 4.4 25.1 1.0 CB A:ASP684 4.4 35.8 1.0 OD1 A:ASP411 4.5 29.4 1.0 O A:ASP411 4.5 22.5 1.0 OD2 A:ASP411 4.7 25.2 1.0 OE2 A:GLU716 4.8 43.0 1.0 O A:ASP684 4.8 27.1 1.0 O A:HOH1508 4.9 38.1 1.0 OD2 A:ASP684 4.9 48.9 1.0 CG A:ASP411 4.9 26.6 1.0

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


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/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:46.7 occ:1.00 O A:HOH1523 2.2 32.1 1.0 O A:HOH1107 2.4 27.1 1.0 OE1 A:GLU116 2.4 27.5 1.0 O A:HOH1522 2.5 41.3 1.0 OE2 A:GLU116 2.6 31.7 1.0 CD A:GLU116 2.9 29.3 1.0 O A:HOH1555 3.6 64.7 1.0 OD2 A:ASP114 4.2 51.5 1.0 CD1 A:ILE309 4.3 58.9 1.0 O A:HOH1521 4.3 37.2 1.0 CG A:GLU116 4.4 20.1 1.0 O A:HOH1520 4.5 37.8 1.0 O A:ILE115 4.6 29.8 1.0 O A:HOH1524 4.7 59.2 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