Nickel in PDB 2yg9: Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans

The structure of Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans, PDB code: 2yg9 was solved by E.Moe, D.R.Hall, I.Leiros, V.Talstad, J.Timmins, S.Mcsweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.68 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.311, 51.372, 90.039, 90.00, 99.71, 90.00
R / Rfree (%)	17 / 23.1

The structure of Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Nickel atom in the Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans (pdb code 2yg9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans, PDB code: 2yg9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1229 b:19.4 occ:0.50 O A:HOH2324 2.2 19.8 1.0 O A:HOH2049 2.4 25.6 1.0 O A:HOH2290 2.5 16.6 1.0 O A:HOH2325 2.5 20.1 1.0 ND1 A:HIS35 2.5 20.4 1.0 O A:HOH2050 3.0 42.6 1.0 NI B:NI1228 3.2 22.5 0.5 CE1 A:HIS35 3.4 21.4 1.0 CG A:HIS35 3.4 13.6 1.0 CB A:HIS35 3.7 10.1 1.0 O B:HOH2048 4.2 25.3 1.0 CE2 A:TYR203 4.4 10.9 1.0 NE2 A:HIS35 4.5 17.5 1.0 CD2 A:HIS35 4.5 14.7 1.0 CA A:HIS35 4.6 9.8 1.0 O A:HOH2042 4.7 24.2 1.0 O B:HOH2260 4.9 15.7 1.0

Nickel binding site 2 out of 2 in the Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1228 b:22.5 occ:0.50 O A:HOH2325 2.2 20.1 1.0 O B:HOH2260 2.3 15.7 1.0 O B:HOH2048 2.7 25.3 1.0 O A:HOH2324 2.7 19.8 1.0 ND1 B:HIS35 2.7 19.5 1.0 NI A:NI1229 3.2 19.4 0.5 O A:HOH2050 3.3 42.6 1.0 CE1 B:HIS35 3.6 21.6 1.0 CG B:HIS35 3.6 12.7 1.0 CB B:HIS35 3.9 10.6 1.0 O B:HOH2042 4.2 23.1 1.0 CE2 B:TYR203 4.3 6.9 1.0 O A:HOH2049 4.4 25.6 1.0 O B:HOH2039 4.5 26.6 1.0 NE2 B:HIS35 4.7 16.6 1.0 CD2 B:HIS35 4.7 14.6 1.0 CA B:HIS35 4.8 9.3 1.0 O A:HOH2290 4.9 16.6 1.0 CD B:PRO202 4.9 5.1 1.0 OH B:TYR203 5.0 13.4 1.0

E.Moe, D.R.Hall, I.Leiros, V.T.Monsen, J.Timmins, S.Mcsweeney. Structure-Function Studies of An Unusual 3-Methyladenine Dna Glycosylase II (Alka) From Deinococcus Radiodurans. Acta Crystallogr. D Biol. V. 68 703 2012CRYSTALLOGR..
ISSN: ESSN 1399-0047
PubMed: 22683793
DOI: 10.1107/S090744491200947X