Iodine in PDB 1v3p: Crystal Structure of D(Gcgagagc): the Dna Octaplex Structure with I-Motif of G-Quartet

The structure of Crystal Structure of D(Gcgagagc): the Dna Octaplex Structure with I-Motif of G-Quartet, PDB code: 1v3p 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 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	36.180, 36.380, 63.120, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 26.5

The structure of Crystal Structure of D(Gcgagagc): the Dna Octaplex Structure with I-Motif of G-Quartet also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Iodine atom in the Crystal Structure of D(Gcgagagc): the Dna Octaplex Structure with I-Motif of G-Quartet (pdb code 1v3p). 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 Octaplex Structure with I-Motif of G-Quartet, PDB code: 1v3p:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of D(Gcgagagc): the Dna Octaplex Structure with I-Motif of G-Quartet


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 Octaplex Structure with I-Motif of G-Quartet within 5.0Å range: probe atom residue distance (Å) B Occ A:I2 b:26.1 occ:1.00 I A:C382 0.0 26.1 1.0 C5 A:C382 2.2 27.6 1.0 C6 A:C382 3.1 27.3 1.0 C4 A:C382 3.1 28.7 1.0 N4 A:C382 3.3 30.6 1.0 O A:HOH94 3.4 29.1 1.0 O6 A:DG3 3.4 19.5 1.0 C6 A:DG3 3.5 21.0 1.0 O A:HOH90 3.8 19.4 1.0 C5 A:DG3 4.0 19.4 1.0 N1 A:DG3 4.0 20.6 1.0 C8 A:DG1 4.1 23.3 1.0 O A:HOH23 4.2 20.3 1.0 N7 A:DG1 4.3 25.9 1.0 N1 A:C382 4.4 27.3 1.0 N7 A:DG3 4.4 20.8 1.0 N3 A:C382 4.4 28.0 1.0 O A:HOH42 4.4 27.4 1.0 C2' A:DG1 4.4 26.5 1.0 N9 A:DG1 4.6 23.8 1.0 C4 A:DG3 4.7 23.8 1.0 O A:HOH19 4.7 26.3 1.0 C2 A:DG3 4.7 22.1 1.0 C5 A:DG1 4.9 22.4 1.0 C2 A:C382 4.9 25.0 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of D(Gcgagagc): the Dna Octaplex Structure with I-Motif of G-Quartet


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 Octaplex Structure with I-Motif of G-Quartet within 5.0Å range: probe atom residue distance (Å) B Occ B:I10 b:24.1 occ:1.00 I B:C3810 0.0 24.1 1.0 C5 B:C3810 2.2 19.0 1.0 C6 B:C3810 3.1 15.2 1.0 C4 B:C3810 3.1 18.4 1.0 N4 B:C3810 3.3 12.2 1.0 O6 B:DG11 3.6 26.6 1.0 C6 B:DG11 3.7 27.3 1.0 N1 B:DG11 3.7 27.0 1.0 C2' B:DG9 3.9 19.6 1.0 C8 B:DG9 4.0 16.1 1.0 N1 B:C3810 4.4 16.9 1.0 N3 B:C3810 4.4 12.0 1.0 N7 B:DG9 4.4 17.4 1.0 N9 B:DG9 4.5 16.4 1.0 C2 B:DG11 4.5 27.4 1.0 C5 B:DG11 4.6 27.6 1.0 C1' B:DG9 4.8 16.6 1.0 C2 B:C3810 4.9 15.8 1.0 O1P B:C3810 5.0 25.4 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