Calcium in PDB 6l84: Complex of Dna Polymerase IV and D-Dna Duplex

All present enzymatic activity of Complex of Dna Polymerase IV and D-Dna Duplex:
2.7.7.7;

The structure of Complex of Dna Polymerase IV and D-Dna Duplex, PDB code: 6l84 was solved by H.S.Chung, J.An, D.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.87 / 2.60
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.763, 98.664, 100.769, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.6

The binding sites of Calcium atom in the Complex of Dna Polymerase IV and D-Dna Duplex (pdb code 6l84). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Complex of Dna Polymerase IV and D-Dna Duplex, PDB code: 6l84:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Complex of Dna Polymerase IV and D-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Dna Polymerase IV and D-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:35.4 occ:1.00 OP1 P:DC14 2.4 39.8 1.0 OD2 A:ASP7 2.5 38.2 1.0 OE1 A:GLU106 2.5 39.7 1.0 O A:HOH535 2.5 15.4 1.0 O A:HOH521 2.7 25.4 1.0 OD1 A:ASP105 2.7 27.4 1.0 OD2 A:ASP105 2.8 25.8 1.0 CG A:ASP105 2.9 25.3 1.0 CG A:ASP7 3.3 36.0 1.0 OD1 A:ASP7 3.4 36.3 1.0 P P:DC14 3.7 42.9 1.0 CD A:GLU106 3.7 39.4 1.0 CA A:CA403 3.8 73.0 1.0 O5' P:DC14 4.0 41.1 1.0 C5' P:DC14 4.2 32.5 1.0 CB A:GLU106 4.2 27.7 1.0 O A:ASP105 4.2 26.8 1.0 CB A:ASP105 4.2 23.4 1.0 OG A:SER103 4.4 30.0 1.0 CG A:GLU106 4.4 34.7 1.0 OP2 P:DC14 4.5 40.7 1.0 C A:ASP105 4.5 25.8 1.0 OE2 A:GLU106 4.6 42.2 1.0 CB A:ASP7 4.7 30.4 1.0 O3' P:DC13 4.8 45.7 1.0 CA A:ASP105 4.9 22.8 1.0 N A:GLU106 4.9 22.7 1.0 O A:HOH555 5.0 26.3 1.0

Calcium binding site 2 out of 3 in the Complex of Dna Polymerase IV and D-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Dna Polymerase IV and D-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:49.9 occ:1.00 O A:ALA181 2.4 42.3 1.0 O A:ILE186 2.5 38.4 1.0 O A:HOH534 2.6 41.3 1.0 O A:HOH528 2.7 40.5 1.0 O A:HOH558 2.8 28.7 1.0 C A:ALA181 3.6 40.1 1.0 C A:ILE186 3.7 35.1 1.0 CA A:GLY187 4.3 38.8 1.0 CA A:ASP182 4.5 40.2 1.0 N A:GLY187 4.5 36.2 1.0 N A:ASP182 4.5 41.6 1.0 C A:GLY187 4.5 42.7 1.0 OP2 P:DC13 4.5 37.3 1.0 CA A:ALA181 4.6 35.9 1.0 O A:GLY187 4.6 40.7 1.0 O A:VAL183 4.7 29.4 1.0 CA A:ILE186 4.8 33.3 1.0 CB A:ALA181 4.8 27.2 1.0 CB A:ILE186 4.9 29.3 1.0 OD1 A:ASP182 5.0 58.5 1.0 OD1 A:ASN188 5.0 67.4 1.0

Calcium binding site 3 out of 3 in the Complex of Dna Polymerase IV and D-Dna Duplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Dna Polymerase IV and D-Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:73.0 occ:1.00 OD2 A:ASP105 2.5 25.8 1.0 O A:PHE8 2.7 24.8 1.0 O A:HOH535 2.8 15.4 1.0 CG A:ASP105 3.5 25.3 1.0 N A:PHE11 3.6 17.0 1.0 OD1 A:ASP7 3.6 36.3 1.0 N A:TYR10 3.7 26.7 1.0 CA A:CA401 3.8 35.4 1.0 C A:PHE8 3.9 21.7 1.0 CB A:ASP105 3.9 23.4 1.0 CA A:TYR10 4.0 27.1 1.0 CB A:PHE11 4.2 12.0 1.0 O3' P:DC14 4.2 29.3 1.0 C A:ASP9 4.2 25.4 1.0 O P:HOH102 4.2 25.5 1.0 O A:HOH555 4.3 26.3 1.0 C A:TYR10 4.3 21.0 1.0 OD1 A:ASP105 4.5 27.4 1.0 CA A:PHE11 4.5 15.6 1.0 CA A:ASP9 4.5 26.0 1.0 CG A:ASP7 4.6 36.0 1.0 N A:ASP9 4.7 22.2 1.0 C3' P:DC14 4.9 29.2 1.0 OD2 A:ASP7 4.9 38.2 1.0 CA A:PHE8 5.0 19.4 1.0 O A:ASP9 5.0 23.4 1.0

J.An, J.Choi, D.Hwang, J.Park, C.W.Pemble 4Th, T.H.M.Duong, K.R.Kim, H.Ahn, H.S.Chung, D.R.Ahn. The Crystal Structure of A Natural Dna Polymerase Complexed with Mirror Dna. Chem.Commun.(Camb.) V. 56 2186 2020.
ISSN: ESSN 1364-548X
PubMed: 31971182
DOI: 10.1039/C9CC09351F