Chlorine 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:

Iodine	(I)	2 atoms
Calcium	(Ca)	33 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of A Hairpin Ribozyme in the Catalytically-Active Conformation, PDB code: 1m5k:
Jump to Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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 F:Cl103 b:65.5 occ:1.00 N F:VAL45 3.2 40.3 1.0 O F:VAL45 3.4 41.9 1.0 NZ F:LYS27 3.5 89.7 1.0 CA F:LEU44 3.6 31.7 1.0 CE F:LYS23 3.6 56.4 1.0 NZ F:LYS23 3.9 59.8 1.0 C F:LEU44 3.9 28.0 1.0 O F:ILE43 4.0 32.4 1.0 CE F:LYS27 4.1 74.9 1.0 C F:VAL45 4.2 34.8 1.0 CB F:LEU44 4.2 33.0 1.0 CA F:VAL45 4.3 34.3 1.0 CD1 F:LEU44 4.4 60.3 1.0 CD F:LYS27 4.6 66.7 1.0 N F:LEU44 4.7 30.3 1.0 C F:ILE43 4.7 39.8 1.0 CB F:VAL45 4.9 38.9 1.0 CG F:LEU44 5.0 40.5 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 F:Cl104 b:62.6 occ:1.00 O F:HOH285 3.0 46.7 1.0 N F:LYS23 3.2 51.6 1.0 NE F:ARG47 3.3 48.8 1.0 CB F:LYS23 3.6 42.4 1.0 NH2 F:ARG47 3.7 66.0 1.0 CA F:LYS22 3.8 45.9 1.0 CZ F:ARG47 3.9 60.5 1.0 CD F:LYS22 4.0 77.2 1.0 C F:LYS22 4.0 39.0 1.0 CA F:LYS23 4.0 42.7 1.0 CB F:LYS22 4.1 49.0 1.0 CD F:ARG47 4.3 57.0 1.0 CG F:ARG47 4.6 36.7 1.0 CG F:LYS22 4.6 58.5 1.0 OD1 F:ASP24 4.7 0.8 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