Calcium in PDB 4fjn: RB69 Dna Polymerase Ternary Complex with Dttp/Da

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

The structure of RB69 Dna Polymerase Ternary Complex with Dttp/Da, PDB code: 4fjn 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)	46.97 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.010, 120.501, 130.847, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24

The binding sites of Calcium atom in the RB69 Dna Polymerase Ternary Complex with Dttp/Da (pdb code 4fjn). 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/Da, PDB code: 4fjn:
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/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 Dttp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:29.9 occ:1.00 OD2 A:ASP411 2.2 31.8 1.0 O2B A:TTP1001 2.3 29.2 1.0 O1G A:TTP1001 2.3 26.1 1.0 OD1 A:ASP623 2.3 29.0 1.0 O A:LEU412 2.3 29.3 1.0 O2A A:TTP1001 2.4 29.5 1.0 PB A:TTP1001 3.4 30.2 1.0 CG A:ASP411 3.4 36.9 1.0 CG A:ASP623 3.5 32.9 1.0 C A:LEU412 3.5 32.1 1.0 PA A:TTP1001 3.6 33.5 1.0 PG A:TTP1001 3.6 31.3 1.0 CA A:CA1003 3.7 58.1 1.0 O3A A:TTP1001 3.7 34.1 1.0 O3B A:TTP1001 3.8 31.3 1.0 OD2 A:ASP623 3.9 30.9 1.0 N A:LEU412 4.0 30.8 1.0 CB A:ASP411 4.0 34.8 1.0 O A:HOH1414 4.0 43.5 1.0 C5' A:TTP1001 4.2 28.3 1.0 O2G A:TTP1001 4.2 29.9 1.0 CA A:LEU412 4.3 31.9 1.0 C A:ASP411 4.3 32.1 1.0 O5' A:TTP1001 4.4 33.6 1.0 OD1 A:ASP411 4.4 34.3 1.0 N A:THR413 4.5 33.2 1.0 N A:SER414 4.6 31.4 1.0 N A:ALA415 4.6 29.2 1.0 O1B A:TTP1001 4.7 32.8 1.0 CB A:ASP623 4.7 28.1 1.0 CB A:LEU412 4.7 28.4 1.0 O3G A:TTP1001 4.7 35.3 1.0 CA A:THR413 4.7 32.0 1.0 CB A:ALA415 4.8 25.2 1.0 O1A A:TTP1001 4.8 34.1 1.0 O A:ASP411 4.8 32.5 1.0 CA A:ASP411 4.8 35.2 1.0 C A:THR413 4.8 29.9 1.0

Calcium binding site 2 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:58.1 occ:1.00 O A:HOH1308 2.4 42.3 1.0 O2A A:TTP1001 2.7 29.5 1.0 OD2 A:ASP623 2.8 30.9 1.0 OD2 A:ASP411 3.4 31.8 1.0 CG A:ASP623 3.6 32.9 1.0 CG A:ASP411 3.6 36.9 1.0 CB A:ASP411 3.6 34.8 1.0 OD1 A:ASP623 3.7 29.0 1.0 CA A:CA1002 3.7 29.9 1.0 C3' P:DOC115 3.9 33.8 1.0 CB A:SER624 3.9 27.5 1.0 PA A:TTP1001 4.0 33.5 1.0 C5' P:DOC115 4.1 36.4 1.0 O A:HOH1253 4.3 35.4 1.0 OD1 A:ASP411 4.4 34.3 1.0 O1A A:TTP1001 4.4 34.1 1.0 O A:HOH1183 4.4 39.5 1.0 C4' P:DOC115 4.4 34.2 1.0 OG A:SER624 4.5 33.8 1.0 O5' A:TTP1001 4.6 33.6 1.0 C5' A:TTP1001 4.6 28.3 1.0 O A:ASP621 4.6 30.5 1.0 N A:SER624 4.7 28.0 1.0 O P:HOH202 4.7 35.3 1.0 CA A:SER624 4.8 28.6 1.0 C A:ASP623 4.8 29.2 1.0 O1G A:TTP1001 5.0 26.1 1.0 CB A:ASP623 5.0 28.1 1.0

Calcium binding site 3 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:50.7 occ:1.00 OD1 A:ASN507 2.2 50.7 1.0 O A:HOH1156 2.2 53.4 1.0 O A:LYS531 2.3 67.9 1.0 O A:ASN505 2.3 51.3 1.0 O A:HOH1201 2.5 51.4 1.0 O A:HOH1403 2.5 47.1 1.0 C A:LYS531 3.2 58.5 1.0 CG A:ASN507 3.4 55.3 1.0 C A:ASN505 3.5 55.9 1.0 CA A:LYS531 3.9 53.9 1.0 ND2 A:ASN507 4.0 46.0 1.0 CB A:ASN505 4.1 55.3 1.0 N A:ASN507 4.1 52.9 1.0 N A:LYS532 4.2 53.0 1.0 C A:PRO506 4.3 53.7 1.0 CA A:PRO506 4.4 56.7 1.0 CA A:LYS532 4.4 54.9 1.0 N A:PRO506 4.5 56.0 1.0 CA A:ASN505 4.5 58.2 1.0 O A:LEU533 4.5 47.6 1.0 CB A:ASN507 4.5 53.1 1.0 CB A:LYS531 4.6 62.7 1.0 O A:ALA502 4.7 55.8 1.0 C A:LYS532 4.7 54.0 1.0 CA A:ASN507 4.8 53.7 1.0 O A:PRO506 4.8 59.7 1.0 N A:LEU533 4.8 52.9 1.0 O A:ILE530 4.8 49.6 1.0

Calcium binding site 4 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:50.3 occ:1.00 OE1 A:GLU716 2.4 56.8 1.0 O A:HOH1140 2.5 42.7 1.0 O A:HOH1108 2.6 26.4 0.5 O A:HOH1188 2.6 50.1 1.0 O A:HOH1414 2.9 43.5 1.0 CD A:GLU716 3.5 52.7 1.0 CB A:ASP684 4.2 49.1 1.0 NZ A:LYS486 4.2 37.5 1.0 CG A:GLU716 4.2 48.5 1.0 OG1 A:THR413 4.4 32.9 1.0 OE2 A:GLU716 4.4 44.1 1.0 OD1 A:ASP411 4.5 34.3 1.0 O A:HOH1108 4.5 27.1 0.5 O A:ASP411 4.5 32.5 1.0 OD2 A:ASP684 4.6 57.3 1.0 O A:ASP684 4.8 32.2 1.0 OD2 A:ASP411 4.9 31.8 1.0 CG A:ASP411 4.9 36.9 1.0 CG A:ASP684 5.0 57.9 1.0

Calcium binding site 5 out of 5 in the RB69 Dna Polymerase Ternary Complex with Dttp/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 Dttp/Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:59.3 occ:1.00 O A:HOH1386 2.3 39.8 1.0 O A:HOH1109 2.4 39.6 1.0 OE1 A:GLU116 2.5 35.1 1.0 O A:HOH1404 2.5 51.9 1.0 OE2 A:GLU116 2.7 45.0 1.0 CD A:GLU116 2.9 44.1 1.0 OD2 A:ASP114 4.2 66.2 1.0 CG A:GLU116 4.5 31.4 1.0 O A:ILE115 4.6 32.6 1.0 CD1 A:ILE309 4.7 55.0 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