Calcium in PDB 5uuh: Bacillus Cereus Dna Glycosylase Alkd Bound to A Yatakemycin-Adenine Nucleobase Adduct and Dna Containing A Fluorinated Abasic Site (9-Mer Product Complex)

The structure of Bacillus Cereus Dna Glycosylase Alkd Bound to A Yatakemycin-Adenine Nucleobase Adduct and Dna Containing A Fluorinated Abasic Site (9-Mer Product Complex), PDB code: 5uuh was solved by E.A.Mullins, B.F.Eichman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.42 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.396, 55.748, 48.124, 90.00, 111.18, 90.00
R / Rfree (%)	14.1 / 17.3

The structure of Bacillus Cereus Dna Glycosylase Alkd Bound to A Yatakemycin-Adenine Nucleobase Adduct and Dna Containing A Fluorinated Abasic Site (9-Mer Product Complex) also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Calcium atom in the Bacillus Cereus Dna Glycosylase Alkd Bound to A Yatakemycin-Adenine Nucleobase Adduct and Dna Containing A Fluorinated Abasic Site (9-Mer Product Complex) (pdb code 5uuh). 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 Bacillus Cereus Dna Glycosylase Alkd Bound to A Yatakemycin-Adenine Nucleobase Adduct and Dna Containing A Fluorinated Abasic Site (9-Mer Product Complex), PDB code: 5uuh:

Calcium binding site 1 out of 1 in the Bacillus Cereus Dna Glycosylase Alkd Bound to A Yatakemycin-Adenine Nucleobase Adduct and Dna Containing A Fluorinated Abasic Site (9-Mer Product Complex)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacillus Cereus Dna Glycosylase Alkd Bound to A Yatakemycin-Adenine Nucleobase Adduct and Dna Containing A Fluorinated Abasic Site (9-Mer Product Complex) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:23.0 occ:1.00 O B:HOH230 2.4 25.4 1.0 O C:HOH121 2.4 29.1 1.0 O A:HOH444 2.4 26.5 1.0 O A:HOH471 2.5 20.2 1.0 O B:HOH210 2.5 17.7 1.0 O B:HOH217 2.5 25.3 1.0 O B:HOH205 2.6 20.4 1.0 HZ3 A:LYS183 3.5 20.6 1.0 O C:HOH102 3.5 32.8 1.0 HZ3 A:LYS219 3.7 49.1 1.0 HZ1 A:LYS183 3.8 20.6 1.0 H62 B:DA7 3.8 23.4 1.0 OE2 A:GLU216 4.0 18.3 1.0 NZ A:LYS183 4.0 17.2 1.0 HE3 A:LYS183 4.1 18.7 1.0 H41 C:DC3 4.3 24.3 1.0 O C:HOH128 4.4 35.0 1.0 OP3 B:RF56 4.4 22.2 1.0 O B:HOH214 4.5 31.6 1.0 NZ A:LYS219 4.5 40.9 1.0 N7 B:DA7 4.5 16.1 1.0 H42 C:DC3 4.6 24.3 1.0 HZ2 A:LYS219 4.6 49.1 1.0 CE A:LYS183 4.6 15.6 1.0 OE1 A:GLU216 4.6 18.0 1.0 N6 B:DA7 4.6 19.5 1.0 CD A:GLU216 4.6 17.2 1.0 O6 B:DG8 4.7 19.7 1.0 HZ1 A:LYS219 4.7 49.1 1.0 N4 C:DC3 4.8 20.2 1.0 HZ2 A:LYS183 4.8 20.6 1.0 O6 C:DG2 4.9 19.2 1.0 HH21 A:ARG215 4.9 30.2 1.0 O C:HOH127 5.0 31.5 1.0

E.A.Mullins, R.Shi, B.F.Eichman. Toxicity and Repair of Dna Adducts Produced By the Natural Product Yatakemycin. Nat. Chem. Biol. V. 13 1002 2017.
ISSN: ESSN 1552-4469
PubMed: 28759018
DOI: 10.1038/NCHEMBIO.2439