Iodine in PDB 3cgp: X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions

The structure of X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions, PDB code: 3cgp was solved by Y.Lin, C.L.Kielkopf, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.300, 40.790, 32.550, 90.00, 94.93, 90.00
R / Rfree (%)	20.1 / 22.8

The binding sites of Iodine atom in the X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions (pdb code 3cgp). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions, PDB code: 3cgp:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:I14 b:27.1 occ:1.00 O B:HOH38 3.0 31.2 1.0 O A:HOH46 3.2 32.7 1.0 C1' B:A21 3.9 15.0 1.0 C1' A:G8 4.0 15.5 1.0 O4' A:G8 4.1 16.3 1.0 O B:HOH62 4.3 39.0 1.0 O4' B:A21 4.4 12.8 1.0 N3 B:A21 4.4 15.6 1.0 N9 B:A21 4.4 13.2 1.0 C2 A:A7 4.4 15.4 1.0 N3 A:A7 4.5 17.9 1.0 O2' A:G8 4.6 15.8 1.0 C4 B:A21 4.6 14.0 1.0 O2 B:U19 4.7 15.3 1.0 N9 A:G8 4.9 15.3 1.0 O2' B:A21 4.9 18.1 1.0 C2' A:G8 5.0 14.7 1.0

Iodine binding site 2 out of 3 in the X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:I15 b:42.5 occ:1.00 O B:HOH76 3.3 34.7 1.0 O A:HOH50 3.4 28.5 1.0 O A:HOH26 3.6 20.1 1.0 N2 A:G3 3.6 15.4 1.0 O B:HOH91 3.9 27.8 1.0 O B:HOH116 4.0 42.5 1.0 C1' A:C4 4.1 12.2 1.0 O4' A:C4 4.3 14.8 1.0 C1' B:G25 4.4 17.8 1.0 O4' B:G25 4.5 19.5 1.0 O2' A:C4 4.6 16.5 1.0 C2 A:G3 4.6 11.7 1.0 N3 A:G3 4.7 16.4 1.0 O2 A:C4 4.8 12.3 1.0 O2' B:G25 4.9 22.8 1.0 O2 B:C24 4.9 12.9 1.0 N1 A:C4 5.0 13.1 1.0

Iodine binding site 3 out of 3 in the X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of X-Ray Structure of A Pseudouridine-Containing Yeast Spliceosomal U2 Snrna-Intron Branch Site Duplex Bound to Iodide Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:I2 b:32.9 occ:1.00 C4' B:A20 3.9 11.4 1.0 O4' B:A20 3.9 16.5 1.0 C5' B:A20 4.1 14.5 1.0 O B:HOH103 4.2 33.8 1.0 O B:HOH46 4.4 28.8 1.0 O B:HOH83 4.5 40.7 1.0 C1' B:A20 5.0 14.2 1.0

Y.Lin, C.L.Kielkopf. X-Ray Structures of U2 Snrna-Branchpoint Duplexes Containing Conserved Pseudouridines. Biochemistry V. 47 5503 2008.
ISSN: ISSN 0006-2960
PubMed: 18435545
DOI: 10.1021/BI7022392