Magnesium in PDB 3ajl: Crystal Structure of D(CGCGGATF5UCGCG): 5-Formyluridine:Guanosine Base-Pair in B-Dna with Dapi

The structure of Crystal Structure of D(CGCGGATF5UCGCG): 5-Formyluridine:Guanosine Base-Pair in B-Dna with Dapi, PDB code: 3ajl was solved by M.Tsunoda, T.Sakaue, Y.Ueno, A.Matsuda, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.86 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.003, 40.501, 66.773, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 28.1

The binding sites of Magnesium atom in the Crystal Structure of D(CGCGGATF5UCGCG): 5-Formyluridine:Guanosine Base-Pair in B-Dna with Dapi (pdb code 3ajl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of D(CGCGGATF5UCGCG): 5-Formyluridine:Guanosine Base-Pair in B-Dna with Dapi, PDB code: 3ajl:

Magnesium binding site 1 out of 1 in the Crystal Structure of D(CGCGGATF5UCGCG): 5-Formyluridine:Guanosine Base-Pair in B-Dna with Dapi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of D(CGCGGATF5UCGCG): 5-Formyluridine:Guanosine Base-Pair in B-Dna with Dapi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg26 b:44.5 occ:1.00 O A:HOH143 2.2 33.7 1.0 O A:HOH140 2.6 32.9 1.0 O A:HOH162 3.7 32.1 1.0 O5' A:DA6 3.7 48.9 1.0 O A:HOH121 3.9 22.6 1.0 OP2 A:DT7 4.0 38.8 1.0 C3' A:DA6 4.1 36.5 1.0 C5' A:DA6 4.3 42.6 1.0 OP2 A:DA6 4.4 51.3 1.0 P A:DA6 4.6 51.9 1.0 O3' A:DA6 4.7 35.9 1.0 C4' A:DA6 4.8 38.8 1.0 P A:DT7 4.9 37.8 1.0 C2' A:DA6 4.9 34.3 1.0

M.Tsunoda, T.Sakaue, S.Naito, T.Sunami, N.Abe, Y.Ueno, A.Matsuda, A.Takenaka. Insights Into the Structures of Dna Damaged By Hydroxyl Radical: Crystal Structures of Dna Duplexes Containing 5-Formyluracil J Nucleic Acids V.2010 10728 2010.
ISSN: ISSN 2090-0201
PubMed: 20976303
DOI: 10.4061/2010/107289