Iodine in PDB 1m5k: Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation

The structure of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation, PDB code: 1m5k was solved by P.B.Rupert, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.07 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	256.300, 44.100, 102.400, 90.00, 109.00, 90.00
R / Rfree (%)	22.9 / 28.4

The structure of Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	33 atoms

The binding sites of Iodine atom in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation (pdb code 1m5k). 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 A Hairpin Ribozyme in the Catalytically-Active Conformation, PDB code: 1m5k:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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 A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:I17 b:96.4 occ:0.70 I5 A:IU17 0.0 96.4 0.7 C5 A:IU17 1.6 96.5 1.0 C6 A:IU17 2.6 97.9 1.0 C4 A:IU17 2.7 97.7 1.0 O4 A:IU17 3.0 0.7 1.0 O A:HOH225 3.2 59.7 1.0 O A:HOH219 3.4 52.4 1.0 C5 A:C16 3.6 78.3 1.0 C4 A:C16 3.8 81.2 1.0 C6 A:C16 3.8 83.8 1.0 N1 A:IU17 3.9 95.6 1.0 N3 A:IU17 3.9 94.6 1.0 OP2 A:IU17 4.0 68.1 1.0 N3 A:C16 4.1 81.5 1.0 N1 A:C16 4.1 88.8 1.0 N4 A:C16 4.3 76.4 1.0 C2 A:C16 4.3 87.2 1.0 C2 A:IU17 4.5 96.7 1.0 C2' A:C16 4.6 90.5 1.0 C3' A:C16 4.6 98.3 1.0 N4 A:C18 4.9 83.7 1.0 O4' A:IU17 4.9 91.0 1.0 C1' A:C16 5.0 87.1 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation


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 A Hairpin Ribozyme in the Catalytically-Active Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:I17 b:76.3 occ:0.60 I5 D:IU17 0.0 76.3 0.6 C5 D:IU17 1.6 89.4 1.0 C6 D:IU17 2.6 87.8 1.0 C4 D:IU17 2.6 90.8 1.0 O4 D:IU17 3.0 96.6 1.0 O D:HOH228 3.0 54.2 1.0 OP2 D:IU17 3.4 86.9 1.0 C6 D:C16 3.6 81.1 1.0 C5 D:C16 3.6 73.8 1.0 C3' D:C16 3.8 70.1 1.0 N3 D:IU17 3.9 91.5 1.0 N1 D:IU17 3.9 90.4 1.0 N1 D:C16 3.9 82.4 1.0 C4 D:C16 4.1 79.8 1.0 C2 D:C16 4.3 85.1 1.0 C5' D:C16 4.3 81.8 1.0 N3 D:C16 4.4 83.0 1.0 C2' D:C16 4.4 82.5 1.0 C2 D:IU17 4.4 89.2 1.0 OP2 D:C16 4.5 59.6 1.0 P D:IU17 4.5 82.8 1.0 C4' D:C16 4.6 79.6 1.0 C1' D:C16 4.6 78.4 1.0 O3' D:C16 4.7 76.1 1.0 O D:HOH224 4.7 48.2 1.0 O4' D:C16 4.7 87.0 1.0 N4 D:C16 4.8 55.6 1.0 O5' D:IU17 4.8 81.7 1.0 N4 D:C18 4.9 80.1 1.0

P.B.Rupert, A.P.Massey, S.T.Sigurdsson, A.R.Ferre-D'amare. Transition State Stabilization By A Catalytic Rna Science V. 298 1421 2002.
ISSN: ISSN 0036-8075
PubMed: 11298439
DOI: 10.1126/SCIENCE.1076093