Calcium in PDB 4fbt: DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion

All present enzymatic activity of DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion:
2.7.7.7;

The structure of DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion, PDB code: 4fbt was solved by K.Kirouac, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.98 / 2.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	56.226, 56.226, 290.602, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 22.6

The binding sites of Calcium atom in the DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion (pdb code 4fbt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion, PDB code: 4fbt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:17.9 occ:1.00 OD2 A:ASP105 2.3 21.1 1.0 O A:PHE8 2.3 15.4 1.0 O1B A:DGT401 2.4 21.0 1.0 OD1 A:ASP7 2.4 17.1 1.0 O1A A:DGT401 2.5 31.7 1.0 O2G A:DGT401 2.7 31.2 1.0 PB A:DGT401 3.4 26.6 1.0 CG A:ASP105 3.5 20.4 1.0 PA A:DGT401 3.5 40.1 1.0 C A:PHE8 3.5 18.3 1.0 CG A:ASP7 3.5 23.7 1.0 CA A:CA403 3.5 42.5 1.0 O3A A:DGT401 3.8 39.2 1.0 PG A:DGT401 3.8 40.0 1.0 O5' A:DGT401 3.8 45.5 1.0 N A:PHE8 4.0 14.3 1.0 O A:HOH550 4.0 21.6 1.0 O3B A:DGT401 4.0 28.5 1.0 OD2 A:ASP7 4.0 27.8 1.0 NZ A:LYS159 4.2 26.7 1.0 OD1 A:ASP105 4.2 19.1 1.0 CA A:PHE8 4.3 15.3 1.0 C A:ASP7 4.3 15.8 1.0 N A:TYR10 4.4 19.4 1.0 N A:ASP9 4.4 15.6 1.0 CB A:ASP105 4.4 18.3 1.0 CA A:ASP9 4.5 16.6 1.0 O1G A:DGT401 4.5 22.5 1.0 O A:HOH849 4.5 26.3 1.0 C5' A:DGT401 4.6 36.5 1.0 CB A:ASP7 4.7 18.1 1.0 O2B A:DGT401 4.7 24.6 1.0 O A:ASP105 4.7 16.2 1.0 C A:ASP9 4.7 20.4 1.0 N A:PHE11 4.7 18.6 1.0 O A:ASP7 4.8 14.6 1.0 O2A A:DGT401 4.8 39.3 1.0 CA A:ASP7 4.9 14.2 1.0 CB A:PHE11 4.9 19.0 1.0 CB A:PHE8 4.9 15.8 1.0 C4' A:DGT401 5.0 38.6 1.0

Calcium binding site 2 out of 3 in the DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:42.5 occ:1.00 O A:HOH849 2.4 26.3 1.0 O1A A:DGT401 2.6 31.7 1.0 OE2 A:GLU106 2.7 43.6 1.0 O A:HOH869 2.8 36.4 1.0 OD1 A:ASP7 2.9 17.1 1.0 OD2 A:ASP7 2.9 27.8 1.0 CG A:GLU106 3.1 26.5 1.0 CD A:GLU106 3.1 26.6 1.0 CG A:ASP7 3.2 23.7 1.0 OD1 A:ASP105 3.3 19.1 1.0 OD2 A:ASP105 3.4 21.1 1.0 PA A:DGT401 3.5 40.1 1.0 CA A:CA402 3.5 17.9 1.0 O5' A:DGT401 3.5 45.5 1.0 O A:HOH779 3.6 39.7 1.0 CG A:ASP105 3.7 20.4 1.0 O2A A:DGT401 4.0 39.3 1.0 OE1 A:GLU106 4.1 27.2 1.0 O A:HOH656 4.1 41.5 1.0 NZ A:LYS159 4.3 26.7 1.0 O A:HOH592 4.4 29.0 1.0 NZ A:LYS152 4.5 28.2 1.0 CB A:GLU106 4.6 18.8 1.0 CB A:ASP7 4.6 18.1 1.0 O A:ASP105 4.7 16.2 1.0 O2G A:DGT401 4.8 31.2 1.0 C5' A:DGT401 4.9 36.5 1.0 O3A A:DGT401 4.9 39.2 1.0 OG A:SER103 5.0 22.0 1.0 O A:HOH593 5.0 43.0 1.0

Calcium binding site 3 out of 3 in the DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DPO4 Post-Insertion Complex with the N-(Deoxyguanosin-8-Yl)-1- Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:27.4 occ:1.00 O A:ALA181 2.3 16.5 1.0 O A:HOH727 2.4 28.4 1.0 O P:HOH113 2.5 36.0 1.0 O P:HOH104 2.6 20.4 1.0 O P:HOH126 2.6 29.3 1.0 O A:ILE186 2.6 19.4 1.0 C A:ALA181 3.5 19.1 1.0 C A:ILE186 3.8 18.6 1.0 CA A:GLY187 4.3 18.0 1.0 CA A:ALA181 4.3 20.1 1.0 N A:ASP182 4.5 15.1 1.0 CA A:ASP182 4.5 15.6 1.0 N A:GLY187 4.5 17.5 1.0 OP2 P:DC12 4.5 25.0 1.0 CB A:ALA181 4.5 18.8 1.0 C A:GLY187 4.6 21.1 1.0 OP1 P:DC12 4.7 23.0 1.0 O A:VAL183 4.7 15.9 1.0 CA A:ILE186 4.9 15.5 1.0 ND2 A:ASN188 4.9 38.3 1.0 C A:ASP182 4.9 17.4 1.0 O A:GLY187 5.0 17.9 1.0 CB A:ILE186 5.0 19.4 1.0

K.N.Kirouac, A.K.Basu, H.Ling. Structural Mechanism of Replication Stalling on A Bulky Amino-Polycyclic Aromatic Hydrocarbon Dna Adduct By A Y Family Dna Polymerase. J.Mol.Biol. V. 425 4167 2013.
ISSN: ISSN 0022-2836
PubMed: 23876706
DOI: 10.1016/J.JMB.2013.07.020