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

Protein crystallography data

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

Other elements in 2yg9:

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

Nickel Binding Sites:

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 2yg9

Go back to Nickel Binding Sites List in 2yg9
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 2yg9

Go back to Nickel Binding Sites List in 2yg9
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

Reference:

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
Page generated: Wed Dec 16 01:20:46 2020

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