Calcium in PDB 3iay: Ternary Complex of Dna Polymerase Delta

All present enzymatic activity of Ternary Complex of Dna Polymerase Delta:
2.7.7.7;

The structure of Ternary Complex of Dna Polymerase Delta, PDB code: 3iay was solved by M.K.Swan, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.52 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.077, 85.948, 86.872, 90.00, 111.10, 90.00
R / Rfree (%)	19.3 / 23.6

The binding sites of Calcium atom in the Ternary Complex of Dna Polymerase Delta (pdb code 3iay). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Ternary Complex of Dna Polymerase Delta, PDB code: 3iay:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Ternary Complex of Dna Polymerase Delta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ T:Ca17 b:47.4 occ:1.00 O T:HOH463 2.5 35.3 1.0 O T:HOH461 2.5 38.3 1.0 O T:HOH462 2.8 45.0 1.0 O T:HOH51 2.9 24.8 1.0 O P:HOH317 4.1 34.9 1.0 O P:HOH389 4.2 35.2 1.0 O T:HOH82 4.3 38.7 1.0 OP2 T:DG9 4.4 21.9 1.0 C2' T:DG8 4.6 23.8 1.0 N7 T:DG9 4.6 21.4 1.0 O6 T:DG10 4.8 22.6 1.0 N7 T:DG10 5.0 22.8 1.0

Calcium binding site 2 out of 5 in the Ternary Complex of Dna Polymerase Delta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:20.2 occ:1.00 O A:PHE609 2.2 22.7 1.0 OD1 A:ASP764 2.3 25.1 1.0 O2B A:DCP986 2.3 20.3 1.0 O3G A:DCP986 2.3 22.0 1.0 O1A A:DCP986 2.4 20.9 1.0 OD1 A:ASP608 2.4 25.5 1.0 PB A:DCP986 3.3 21.1 1.0 CG A:ASP764 3.4 24.3 1.0 C A:PHE609 3.4 22.8 1.0 PG A:DCP986 3.6 21.9 1.0 CG A:ASP608 3.6 27.1 1.0 PA A:DCP986 3.6 21.9 1.0 CA A:CA2 3.7 43.3 1.0 O3B A:DCP986 3.8 21.9 1.0 O3A A:DCP986 3.8 21.9 1.0 CA A:CA3 3.8 40.6 1.0 OD2 A:ASP764 3.9 24.5 1.0 O A:HOH1272 4.0 37.2 1.0 N A:PHE609 4.0 23.2 1.0 CA A:PHE609 4.2 22.6 1.0 C5' A:DCP986 4.2 18.4 1.0 CB A:ASP608 4.3 25.8 1.0 O2G A:DCP986 4.3 20.2 1.0 N A:ASN610 4.4 21.9 1.0 N A:SER611 4.4 22.4 1.0 O A:HOH1207 4.5 70.8 1.0 O5' A:DCP986 4.5 20.4 1.0 C A:ASP608 4.5 23.3 1.0 CA A:ASN610 4.6 23.0 1.0 OD2 A:ASP608 4.6 30.5 1.0 N A:LEU612 4.6 22.2 1.0 CB A:ASP764 4.6 22.7 1.0 C A:ASN610 4.6 22.9 1.0 O1B A:DCP986 4.7 21.7 1.0 O1G A:DCP986 4.7 20.4 1.0 CB A:PHE609 4.8 22.6 1.0 O2A A:DCP986 4.8 21.1 1.0 CB A:LEU612 4.9 21.4 1.0 CA A:ASP608 5.0 24.1 1.0

Calcium binding site 3 out of 5 in the Ternary Complex of Dna Polymerase Delta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Complex of Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:43.3 occ:1.00 O A:HOH1270 2.3 32.6 1.0 OD2 A:ASP764 2.5 24.5 1.0 O1A A:DCP986 2.7 20.9 1.0 O A:HOH1071 2.9 41.1 1.0 CG A:ASP764 3.4 24.3 1.0 OD1 A:ASP764 3.5 25.1 1.0 OD1 A:ASP608 3.5 25.5 1.0 C3' P:DOC12 3.5 14.2 1.0 CA A:CA1 3.7 20.2 1.0 PA A:DCP986 3.8 21.9 1.0 C5' P:DOC12 3.9 16.6 1.0 CG A:ASP608 3.9 27.1 1.0 CB A:ASP608 4.0 25.8 1.0 C4' P:DOC12 4.2 15.3 1.0 O2A A:DCP986 4.2 21.1 1.0 O A:HOH1207 4.3 70.8 1.0 O5' A:DCP986 4.3 20.4 1.0 CB A:SER765 4.3 23.5 1.0 O A:HOH998 4.3 17.9 1.0 C5' A:DCP986 4.5 18.4 1.0 OG A:SER765 4.6 24.0 1.0 O A:ASP762 4.6 21.2 1.0 O P:HOH113 4.7 24.9 1.0 OD2 A:ASP608 4.7 30.5 1.0 O A:HOH1269 4.8 44.2 1.0 CB A:ASP764 4.8 22.7 1.0 C A:ASP764 4.9 22.5 1.0 C2' P:DOC12 4.9 13.4 1.0 O3G A:DCP986 4.9 22.0 1.0 O5' P:DOC12 5.0 17.0 1.0 N A:SER765 5.0 22.3 1.0

Calcium binding site 4 out of 5 in the Ternary Complex of Dna Polymerase Delta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Complex of Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:40.6 occ:1.00 O A:HOH1272 2.1 37.2 1.0 O A:HOH1271 2.4 56.7 1.0 OD1 A:ASP608 2.6 25.5 1.0 OD2 A:ASP608 2.7 30.5 1.0 O A:HOH1378 2.7 44.2 1.0 O3G A:DCP986 2.7 22.0 1.0 OE2 A:GLU802 2.8 39.0 1.0 CG A:ASP608 2.9 27.1 1.0 O A:HOH1207 3.2 70.8 1.0 CD A:GLU802 3.6 35.8 1.0 PG A:DCP986 3.8 21.9 1.0 CA A:CA1 3.8 20.2 1.0 O1G A:DCP986 4.1 20.4 1.0 OE1 A:GLU800 4.2 41.1 1.0 OE1 A:GLU802 4.3 35.9 1.0 O2G A:DCP986 4.3 20.2 1.0 CG A:GLU802 4.4 30.2 1.0 CB A:ASP608 4.4 25.8 1.0 O A:PHE609 4.5 22.7 1.0 O A:ASP608 4.7 22.4 1.0 O A:HOH1133 4.8 29.8 1.0 O1A A:DCP986 4.9 20.9 1.0 C A:ASP608 4.9 23.3 1.0 OD1 A:ASN610 4.9 33.0 1.0

Calcium binding site 5 out of 5 in the Ternary Complex of Dna Polymerase Delta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ternary Complex of Dna Polymerase Delta within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:55.0 occ:1.00 O A:HOH1290 2.3 31.8 1.0 O A:HOH1314 2.4 34.4 1.0 O A:HOH1291 2.5 44.5 1.0 OD1 A:ASP321 2.5 34.3 1.0 O A:HOH1289 2.7 54.4 1.0 CG A:ASP321 3.5 31.8 1.0 OD2 A:ASP321 3.8 36.3 1.0 O A:HOH1069 4.4 26.8 1.0 O A:TYR401 4.4 25.7 1.0 OD1 A:ASP407 4.4 29.2 1.0 O A:ILE322 4.4 29.7 1.0 OD2 A:ASP407 4.4 26.2 1.0 O A:HOH1111 4.7 34.1 1.0 OD2 A:ASP520 4.8 33.0 1.0 CB A:ASP321 4.8 29.4 1.0 CG A:ASP407 4.9 28.5 1.0

M.K.Swan, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Structural Basis of High-Fidelity Dna Synthesis By Yeast Dna Polymerase Delta Nat.Struct.Mol.Biol. V. 16 979 2009.
ISSN: ISSN 1545-9993
PubMed: 19718023
DOI: 10.1038/NSMB.1663