Calcium in PDB 4rzr: Bypass of A Bulky Adduct DG1,8 By DPO4

All present enzymatic activity of Bypass of A Bulky Adduct DG1,8 By DPO4:
2.7.7.7;

The structure of Bypass of A Bulky Adduct DG1,8 By DPO4, PDB code: 4rzr was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.23 / 2.20
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	56.397, 56.397, 288.776, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 25

The structure of Bypass of A Bulky Adduct DG1,8 By DPO4 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Bypass of A Bulky Adduct DG1,8 By DPO4 (pdb code 4rzr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Bypass of A Bulky Adduct DG1,8 By DPO4, PDB code: 4rzr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Bypass of A Bulky Adduct DG1,8 By DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bypass of A Bulky Adduct DG1,8 By DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:77.5 occ:1.00 OE2 A:GLU106 2.4 39.7 1.0 O A:HOH502 2.5 35.0 1.0 O A:HOH503 2.8 43.1 1.0 OD1 A:ASP7 3.0 38.7 1.0 OD2 A:ASP105 3.0 50.8 1.0 CA A:CA402 3.0 69.9 1.0 OD2 A:ASP7 3.1 36.8 1.0 CG A:ASP7 3.4 35.2 1.0 CD A:GLU106 3.4 36.8 1.0 CG A:GLU106 3.6 36.0 1.0 CG A:ASP105 3.6 46.0 1.0 OD1 A:ASP105 3.8 44.2 1.0 NZ A:LYS159 3.9 41.7 1.0 C3' C:DC13 4.1 40.1 1.0 O A:HOH541 4.3 48.7 1.0 O3' C:DC13 4.5 40.3 1.0 O A:HOH574 4.5 51.4 1.0 OE1 A:GLU106 4.6 36.8 1.0 O A:ASP105 4.6 39.2 1.0 C2' C:DC13 4.6 39.2 1.0 CB A:ASP7 4.8 34.6 1.0 O A:HOH501 4.8 35.9 1.0 CB A:ASP105 4.8 43.8 1.0 O5' C:DC13 4.8 39.1 1.0

Calcium binding site 2 out of 4 in the Bypass of A Bulky Adduct DG1,8 By DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bypass of A Bulky Adduct DG1,8 By DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:69.9 occ:1.00 O A:PHE8 2.4 37.1 1.0 O A:HOH574 2.6 51.4 1.0 OD1 A:ASP7 2.6 38.7 1.0 O A:HOH501 3.0 35.9 1.0 OD2 A:ASP105 3.0 50.8 1.0 CA A:CA401 3.0 77.5 1.0 O A:HOH503 3.1 43.1 1.0 C A:PHE8 3.6 38.8 1.0 O A:HOH504 3.6 46.1 1.0 CG A:ASP7 3.7 35.2 1.0 N A:TYR10 4.0 44.1 1.0 CG A:ASP105 4.0 46.0 1.0 OD2 A:ASP7 4.0 36.8 1.0 N A:PHE8 4.2 35.6 1.0 NZ A:LYS159 4.4 41.7 1.0 CA A:ASP9 4.4 42.4 1.0 N A:ASP9 4.4 41.6 1.0 O A:HOH516 4.4 44.2 1.0 C A:ASP9 4.4 44.0 1.0 O A:HOH541 4.4 48.7 1.0 CA A:PHE8 4.5 38.6 1.0 N A:PHE11 4.5 41.1 1.0 CB A:ASP105 4.5 43.8 1.0 C A:ASP7 4.6 34.5 1.0 CA A:TYR10 4.7 44.6 1.0 O A:HOH502 4.8 35.0 1.0 O A:ASP105 4.8 39.2 1.0 CB A:ASP7 4.9 34.6 1.0 O A:ASP7 4.9 35.6 1.0 CB A:PHE11 4.9 40.4 1.0

Calcium binding site 3 out of 4 in the Bypass of A Bulky Adduct DG1,8 By DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bypass of A Bulky Adduct DG1,8 By DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:25.2 occ:1.00 O1A D:DCP401 2.2 30.9 1.0 OD1 D:ASP7 2.2 28.2 1.0 OD2 D:ASP105 2.3 26.3 1.0 O2G D:DCP401 2.3 30.8 1.0 O1B D:DCP401 2.3 25.9 1.0 O D:PHE8 2.3 26.2 1.0 CG D:ASP7 3.3 28.1 1.0 PB D:DCP401 3.4 29.1 1.0 CG D:ASP105 3.4 28.3 1.0 CA D:CA403 3.5 44.5 1.0 C D:PHE8 3.5 25.3 1.0 PA D:DCP401 3.5 32.2 1.0 PG D:DCP401 3.5 31.0 1.0 O3A D:DCP401 3.7 31.1 1.0 OD2 D:ASP7 3.8 30.6 1.0 O3B D:DCP401 3.8 27.9 1.0 O D:HOH504 3.8 54.8 1.0 N D:PHE8 3.9 23.6 1.0 NZ D:LYS159 3.9 34.4 1.0 OD1 D:ASP105 3.9 29.4 1.0 C5' D:DCP401 4.1 30.9 1.0 O1G D:DCP401 4.2 27.9 1.0 O D:HOH502 4.2 40.1 1.0 C D:ASP7 4.3 24.5 1.0 CA D:PHE8 4.3 25.1 1.0 O5' D:DCP401 4.3 30.0 1.0 N D:ASP9 4.4 25.5 1.0 CB D:ASP7 4.5 25.8 1.0 N D:TYR10 4.5 24.7 1.0 CA D:ASP9 4.5 25.2 1.0 CB D:ASP105 4.6 27.4 1.0 O2B D:DCP401 4.7 28.1 1.0 C D:ASP9 4.7 25.4 1.0 O2A D:DCP401 4.7 30.9 1.0 O D:ASP7 4.8 24.7 1.0 O3G D:DCP401 4.8 29.5 1.0 CA D:ASP7 4.8 24.3 1.0 N D:PHE11 4.9 25.1 1.0 CE D:LYS159 4.9 34.3 1.0 O D:ASP105 4.9 27.1 1.0 CB D:PHE8 5.0 25.9 1.0

Calcium binding site 4 out of 4 in the Bypass of A Bulky Adduct DG1,8 By DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bypass of A Bulky Adduct DG1,8 By DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca403 b:44.5 occ:1.00 O D:HOH502 2.0 40.1 1.0 O D:HOH503 2.3 42.6 1.0 OE1 D:GLU106 2.4 34.9 1.0 O1A D:DCP401 2.5 30.9 1.0 OD1 D:ASP105 2.5 29.4 1.0 OD1 D:ASP7 2.9 28.2 1.0 OD2 D:ASP7 3.1 30.6 1.0 CG D:ASP7 3.3 28.1 1.0 CG D:ASP105 3.3 28.3 1.0 OD2 D:ASP105 3.3 26.3 1.0 CA D:CA402 3.5 25.2 1.0 PA D:DCP401 3.5 32.2 1.0 CD D:GLU106 3.6 33.0 1.0 O2A D:DCP401 4.0 30.9 1.0 O5' D:DCP401 4.0 30.0 1.0 C5' D:DCP401 4.1 30.9 1.0 CB D:GLU106 4.1 29.4 1.0 CG D:GLU106 4.3 31.4 1.0 NZ D:LYS159 4.5 34.4 1.0 OE2 D:GLU106 4.5 34.2 1.0 OG D:SER103 4.6 33.5 1.0 CB D:ASP7 4.6 25.8 1.0 O D:ASP105 4.6 27.1 1.0 O2G D:DCP401 4.7 30.8 1.0 C D:ASP105 4.8 27.9 1.0 CB D:ASP105 4.8 27.4 1.0 NZ D:LYS152 4.9 33.1 1.0 O3A D:DCP401 4.9 31.1 1.0 O1B D:DCP401 5.0 25.9 1.0

R.Vyas, G.Efthimiopoulos, E.J.Tokarsky, C.K.Malik, A.K.Basu, Z.Suo. Mechanistic Basis For the Bypass of A Bulky Dna Adduct Catalyzed By A Y-Family Dna Polymerase. J.Am.Chem.Soc. V. 137 12131 2015.
ISSN: ISSN 0002-7863
PubMed: 26327169
DOI: 10.1021/JACS.5B08027