Calcium in PDB 4fjm: RB69 Dna Polymerase Ternary Complex with Dctp/Da

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

The structure of RB69 Dna Polymerase Ternary Complex with Dctp/Da, PDB code: 4fjm 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)	45.55 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.238, 119.744, 130.297, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.2

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dctp/Da (pdb code 4fjm). 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 Dctp/Da, PDB code: 4fjm:
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 Dctp/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 Dctp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:27.4 occ:1.00 O2B A:DCP1001 2.2 27.4 1.0 O1G A:DCP1001 2.3 27.3 1.0 OD2 A:ASP411 2.3 28.9 1.0 OD1 A:ASP623 2.3 24.6 1.0 O A:LEU412 2.3 25.8 1.0 O2A A:DCP1001 2.4 27.0 1.0 PB A:DCP1001 3.4 26.7 1.0 CG A:ASP623 3.4 26.7 1.0 CG A:ASP411 3.4 30.7 1.0 C A:LEU412 3.5 24.7 1.0 PG A:DCP1001 3.5 27.0 1.0 PA A:DCP1001 3.6 25.2 1.0 CA A:CA1003 3.7 55.5 1.0 O3A A:DCP1001 3.8 27.2 1.0 O3B A:DCP1001 3.8 28.6 1.0 OD2 A:ASP623 3.9 24.2 1.0 O A:HOH1432 3.9 31.3 1.0 CB A:ASP411 4.0 32.1 1.0 N A:LEU412 4.0 23.9 1.0 O2G A:DCP1001 4.2 26.1 1.0 C5' A:DCP1001 4.2 25.0 1.0 CA A:LEU412 4.2 26.4 1.0 C A:ASP411 4.3 28.2 1.0 O5' A:DCP1001 4.4 26.0 1.0 OD1 A:ASP411 4.5 29.6 1.0 N A:THR413 4.5 30.0 1.0 N A:SER414 4.6 26.8 1.0 N A:LEU415 4.6 24.3 1.0 CB A:ASP623 4.7 21.7 1.0 CB A:LEU415 4.7 20.5 1.0 CB A:LEU412 4.7 27.1 1.0 O3G A:DCP1001 4.7 28.7 1.0 CA A:THR413 4.7 28.2 1.0 O1B A:DCP1001 4.8 30.1 1.0 O A:ASP411 4.8 29.5 1.0 O1A A:DCP1001 4.8 27.9 1.0 CA A:ASP411 4.8 29.9 1.0 C A:THR413 4.9 26.8 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/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 Dctp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:55.5 occ:1.00 O A:HOH1307 2.5 34.8 1.0 OD2 A:ASP623 2.6 24.2 1.0 O2A A:DCP1001 2.7 27.0 1.0 OD2 A:ASP411 3.3 28.9 1.0 CG A:ASP623 3.5 26.7 1.0 CG A:ASP411 3.5 30.7 1.0 CB A:ASP411 3.6 32.1 1.0 OD1 A:ASP623 3.6 24.6 1.0 CA A:CA1002 3.7 27.4 1.0 C3' P:DOC115 3.8 28.0 1.0 CB A:SER624 3.9 26.8 1.0 PA A:DCP1001 3.9 25.2 1.0 OD1 A:ASP411 4.2 29.6 1.0 O A:HOH1219 4.3 27.8 1.0 O A:HOH1152 4.3 37.3 1.0 O1A A:DCP1001 4.4 27.9 1.0 O5' A:DCP1001 4.5 26.0 1.0 OG A:SER624 4.5 29.8 1.0 C5' P:DOC115 4.6 34.4 1.0 C4' P:DOC115 4.7 30.0 1.0 O A:ASP621 4.7 25.3 1.0 N A:SER624 4.7 24.9 1.0 C5' A:DCP1001 4.7 25.0 1.0 O A:HOH1161 4.8 33.0 1.0 O5' P:DOC115 4.8 34.8 1.0 C A:ASP623 4.8 25.7 1.0 CA A:SER624 4.8 27.4 1.0 CB A:ASP623 4.9 21.7 1.0 O1G A:DCP1001 4.9 27.3 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/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 Dctp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:44.4 occ:1.00 O A:HOH1462 2.1 47.2 1.0 OD1 A:ASN507 2.2 52.5 1.0 O A:LYS531 2.3 51.3 1.0 O A:ASN505 2.4 46.2 1.0 O A:HOH1236 2.4 41.1 1.0 O A:HOH1137 2.6 40.5 1.0 C A:LYS531 3.3 55.3 1.0 CG A:ASN507 3.4 48.5 1.0 C A:ASN505 3.6 44.8 1.0 CA A:LYS531 4.0 51.0 1.0 CB A:ASN505 4.1 53.9 1.0 N A:ASN507 4.2 46.6 1.0 ND2 A:ASN507 4.2 46.8 1.0 N A:LYS532 4.2 48.7 1.0 C A:PRO506 4.4 44.1 1.0 CA A:LYS532 4.4 50.6 1.0 O A:HOH1463 4.5 39.9 1.0 CA A:PRO506 4.5 45.4 1.0 CA A:ASN505 4.5 48.2 1.0 N A:PRO506 4.6 45.1 1.0 CB A:ASN507 4.6 50.9 1.0 O A:LEU533 4.6 37.7 1.0 O A:ALA502 4.6 45.5 1.0 CB A:LYS531 4.7 51.1 1.0 CA A:ASN507 4.7 48.6 1.0 C A:LYS532 4.7 50.3 1.0 N A:LEU533 4.8 44.9 1.0 O A:ILE530 4.9 42.3 1.0 O A:PRO506 5.0 47.6 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/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 Dctp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:54.3 occ:1.00 OE1 A:GLU716 2.6 58.1 1.0 O A:HOH1176 2.7 38.2 1.0 O A:HOH1341 2.8 38.5 1.0 O A:HOH1432 3.0 31.3 1.0 O A:HOH1340 3.1 54.6 1.0 O A:HOH1292 3.3 42.2 1.0 CD A:GLU716 3.8 54.6 1.0 NZ A:LYS486 4.1 35.8 1.0 CG A:GLU716 4.3 51.4 1.0 OG1 A:THR413 4.4 33.5 1.0 CB A:ASP684 4.4 37.7 1.0 OD1 A:ASP411 4.5 29.6 1.0 O A:ASP411 4.5 29.5 1.0 O A:HOH1434 4.7 44.5 1.0 O A:ASP684 4.7 31.6 1.0 OD2 A:ASP411 4.8 28.9 1.0 OE2 A:GLU716 4.8 53.6 1.0 CG A:ASP411 4.9 30.7 1.0 O1G A:DCP1001 4.9 27.3 1.0 OD2 A:ASP684 5.0 57.2 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dctp/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 Dctp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:61.9 occ:1.00 O A:HOH1455 2.3 32.8 1.0 O A:HOH1456 2.3 51.2 1.0 O A:HOH1106 2.4 30.2 1.0 OE1 A:GLU116 2.6 36.0 1.0 OE2 A:GLU116 2.8 41.6 1.0 CD A:GLU116 3.1 35.5 1.0 CD1 A:ILE309 4.0 75.4 1.0 OD2 A:ASP114 4.3 41.8 1.0 O A:HOH1457 4.5 51.9 1.0 CG A:GLU116 4.6 28.4 1.0 O A:ILE115 4.6 29.1 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