Iodine in PDB 1v3o: Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex

The structure of Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex, PDB code: 1v3o was solved by J.Kondo, S.Umeda, T.Sunami, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.00 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	34.650, 42.490, 64.080, 90.00, 90.00, 90.00
R / Rfree (%)	26.2 / 29.6

The structure of Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Iodine atom in the Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex (pdb code 1v3o). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex, PDB code: 1v3o:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex within 5.0Å range: probe atom residue distance (Å) B Occ A:I2 b:52.1 occ:1.00 I A:C382 0.0 52.1 1.0 C5 A:C382 2.2 23.3 1.0 C6 A:C382 3.1 34.7 1.0 C4 A:C382 3.1 38.4 1.0 N4 A:C382 3.3 30.9 1.0 O A:HOH51 3.4 68.4 1.0 O6 A:DG3 3.5 34.2 1.0 C8 A:DG1 3.8 46.3 1.0 O A:HOH21 3.8 48.4 1.0 N7 A:DG1 3.9 45.1 1.0 C6 A:DG3 3.9 33.0 1.0 N1 A:DG3 4.0 44.4 1.0 O A:HOH26 4.2 45.4 1.0 O A:HOH41 4.3 47.0 1.0 N1 A:C382 4.4 35.7 1.0 N3 A:C382 4.4 29.5 1.0 O A:HOH42 4.4 41.8 1.0 O A:HOH33 4.4 42.6 1.0 N9 A:DG1 4.5 41.6 1.0 C2' A:DG1 4.5 42.2 1.0 O A:HOH20 4.5 35.4 1.0 C5 A:DG1 4.7 42.6 1.0 C2 A:C382 4.9 31.9 1.0 C5 A:DG3 4.9 35.9 1.0 C2 A:DG3 4.9 28.3 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of D(Gcgagagc): the Dna Quadruplex Structure Split From the Octaplex within 5.0Å range: probe atom residue distance (Å) B Occ B:I10 b:39.4 occ:1.00 I B:C3810 0.0 39.4 1.0 C5 B:C3810 2.2 33.4 1.0 C6 B:C3810 3.1 32.4 1.0 C4 B:C3810 3.1 30.4 1.0 N4 B:C3810 3.3 27.4 1.0 O6 B:DG11 3.6 31.2 1.0 C6 B:DG11 3.6 28.4 1.0 C8 B:DG9 3.7 39.2 1.0 N1 B:DG11 3.9 26.1 1.0 C2' B:DG9 4.0 32.1 1.0 O B:HOH18 4.0 43.8 1.0 N7 B:DG9 4.1 37.6 1.0 C5 B:DG11 4.2 33.2 1.0 N9 B:DG9 4.2 33.0 1.0 N1 B:C3810 4.3 33.0 1.0 N3 B:C3810 4.4 33.2 1.0 C2 B:DG11 4.6 28.8 1.0 C1' B:DG9 4.7 38.0 1.0 N7 B:DG11 4.8 30.4 1.0 C5 B:DG9 4.8 36.1 1.0 C4 B:DG11 4.8 29.0 1.0 C2 B:C3810 4.9 34.3 1.0 C4 B:DG9 4.9 26.3 1.0

J.Kondo, W.Adachi, S.Umeda, T.Sunami, A.Takenaka. Crystal Structures of A Dna Octaplex with I-Motif of G-Quartets and Its Splitting Into Two Quadruplexes Suggest A Folding Mechanism of Eight Tandem Repeats Nucleic Acids Res. V. 32 2541 2004.
ISSN: ISSN 0305-1048
PubMed: 15133122
DOI: 10.1093/NAR/GKH575