Calcium in PDB 1n56: Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion

The structure of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion, PDB code: 1n56 was solved by H.Ling, F.Boudsocq, R.Woodgate, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.90 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.016, 102.358, 105.660, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.3

The structure of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion (pdb code 1n56). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion, PDB code: 1n56:

Calcium binding site 1 out of 1 in the Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Y-Family Dna Polymerase DPO4 in Complex with Dna Containing Abasic Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:62.0 occ:1.00 O1A B:ATP1804 2.2 59.3 1.0 OE1 B:GLU106 2.3 56.7 1.0 OP1 E:DA1814 2.4 79.8 1.0 O B:HOH915 2.4 44.1 1.0 OD1 B:ASP7 2.5 53.9 1.0 OD1 B:ASP105 2.7 43.2 1.0 CD B:GLU106 3.0 50.5 1.0 CG B:GLU106 3.0 47.8 1.0 OD2 B:ASP105 3.0 44.5 1.0 O E:HOH649 3.1 75.6 1.0 P E:DA1814 3.2 80.7 1.0 OP2 E:DA1814 3.2 81.7 1.0 CG B:ASP105 3.2 43.0 1.0 O B:HOH799 3.4 68.9 1.0 CG B:ASP7 3.4 50.4 1.0 MG B:MG404 3.4 33.2 1.0 PA B:ATP1804 3.6 64.1 1.0 OD2 B:ASP7 3.9 56.3 1.0 O5' B:ATP1804 4.1 62.3 1.0 OE2 B:GLU106 4.2 52.6 1.0 C5' B:ATP1804 4.2 58.0 1.0 O5' E:DA1814 4.2 78.9 1.0 O3A B:ATP1804 4.4 67.7 1.0 CB B:GLU106 4.5 42.5 1.0 O B:ASP105 4.5 39.9 1.0 O3' E:DA1813 4.5 81.0 1.0 O2A B:ATP1804 4.5 64.3 1.0 CB B:ASP7 4.5 47.5 1.0 O B:HOH934 4.5 94.4 1.0 OG B:SER103 4.6 40.3 1.0 O1G B:ATP1804 4.7 76.5 1.0 OP2 E:DA1813 4.7 77.1 1.0 CB B:ASP105 4.8 38.1 1.0 O B:HOH812 4.8 0.6 1.0 C5' E:DA1814 4.8 76.7 1.0 C B:ASP105 4.8 38.0 1.0 O E:HOH524 5.0 56.2 1.0

H.Ling, F.Boudsocq, R.Woodgate, W.Yang. A Y-Family Polymerase Complexed with Abasic Lesions: Catching Dna with A Loaded Nucleoside Triphosphate To Be Published.