Magnesium in PDB 4o5w: O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine

The structure of O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine, PDB code: 4o5w was solved by F.Zhang, M.Tsunoda, K.Suzuki, Y.Kikuchi, O.Wilkinson, C.L.Millington, G.P.Margison, D.M.Williams, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.29 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.863, 40.293, 65.266, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 25.5

The structure of O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine also contains other interesting chemical elements:

Strontium

(Sr)

1 atom

The binding sites of Magnesium atom in the O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine (pdb code 4o5w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine, PDB code: 4o5w:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:30.0 occ:1.00 O B:HOH257 2.3 33.5 1.0 O4 A:DT9 2.7 38.6 1.0 O A:HOH225 2.7 40.1 1.0 O B:HOH256 3.7 32.9 1.0 C4 A:DT9 3.9 36.2 1.0 O A:HOH228 4.6 40.0 1.0 O B:HOH226 4.6 37.4 1.0 O7 B:C6G16 4.6 30.2 1.0 O A:HOH216 4.6 43.0 1.0 C7 A:DT9 4.7 34.3 1.0 N3 A:DT9 4.7 28.9 1.0 C5 A:DT9 4.8 34.6 1.0

Magnesium binding site 2 out of 2 in the O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of O6-Carboxymethylguanine in Dna Forms A Sequence Context Dependent Wobble Base Pair Structure with Thymine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:31.8 occ:0.70 O B:HOH223 2.0 25.9 1.0 O A:HOH247 2.1 29.1 1.0 O A:HOH209 2.2 28.2 1.0 O B:HOH222 2.2 35.3 1.0 O A:HOH221 2.3 32.9 1.0 O A:HOH248 2.5 33.5 1.0 SR B:SR101 3.1 27.5 0.4 O B:HOH210 3.9 34.0 1.0 O6 B:DG22 4.2 22.0 1.0 O A:HOH211 4.5 43.1 1.0 O4 B:DT21 4.5 34.5 1.0 O6 A:DG2 4.5 20.0 1.0 N7 A:DG2 4.6 21.1 1.0 O A:HOH207 4.6 34.3 1.0 O A:HOH205 4.6 35.5 1.0 C5 A:DC1 4.7 23.6 1.0 O A:HOH246 4.8 38.4 1.0 N4 A:DC3 4.9 20.1 1.0 C6 A:DC1 4.9 24.0 1.0

F.Zhang, M.Tsunoda, Y.Kikuchi, O.Wilkinson, C.L.Millington, G.P.Margison, D.M.Williams, A.Takenaka. O(6)-Carboxymethylguanine in Dna Forms A Sequence Context-Dependent Wobble Base-Pair Structure with Thymine Acta Crystallogr.,Sect.D V. 70 1669 2014.
ISSN: ISSN 0907-4449
PubMed: 24914978
DOI: 10.1107/S1399004714006178