Bromine in PDB 3zd5: The 2.2 A Structure of A Full-Length Catalytically Active Hammerhead Ribozyme

The structure of The 2.2 A Structure of A Full-Length Catalytically Active Hammerhead Ribozyme, PDB code: 3zd5 was solved by M.Martick, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.22 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	49.886, 69.210, 60.076, 90.00, 111.83, 90.00
R / Rfree (%)	17.7 / 21.2

The binding sites of Bromine atom in the The 2.2 A Structure of A Full-Length Catalytically Active Hammerhead Ribozyme (pdb code 3zd5). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the The 2.2 A Structure of A Full-Length Catalytically Active Hammerhead Ribozyme, PDB code: 3zd5:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the The 2.2 A Structure of A Full-Length Catalytically Active Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of The 2.2 A Structure of A Full-Length Catalytically Active Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Br11 b:57.8 occ:1.00 BR B:5BU11 0.0 57.8 1.0 C5 B:5BU11 1.9 41.4 1.0 C6 B:5BU11 2.9 39.3 1.0 C4 B:5BU11 3.0 42.8 1.0 O4 B:5BU11 3.1 42.7 1.0 O B:HOH2006 3.2 44.6 1.0 O B:HOH2008 3.5 47.1 1.0 N7 B:G10 3.6 45.1 1.0 O B:HOH2011 3.6 36.5 1.0 C8 B:G10 3.6 41.0 1.0 C5 B:G10 3.6 43.9 1.0 O B:HOH2007 3.7 49.3 1.0 N9 B:G10 3.8 40.5 1.0 OP2 B:5BU11 3.8 42.5 1.0 C4 B:G10 3.8 39.3 1.0 C3' B:G10 4.1 37.3 1.0 N1 B:5BU11 4.1 46.2 1.0 N3 B:5BU11 4.2 40.7 1.0 C6 B:G10 4.3 42.8 1.0 C2' B:G10 4.4 43.5 1.0 N3 B:G10 4.5 39.5 1.0 O5' B:5BU11 4.5 42.5 1.0 C1' B:G10 4.6 46.3 1.0 C2 B:5BU11 4.7 48.8 1.0 P B:5BU11 4.7 40.8 1.0 C5' B:G10 4.8 46.5 1.0 N7 B:A12 4.8 44.6 1.0 N1 B:G10 4.8 38.3 1.0 O6 B:G10 4.8 36.3 1.0 C4' B:G10 4.9 44.6 1.0 C2 B:G10 4.9 38.6 1.0 O3' B:G10 4.9 33.6 1.0 O4' B:G10 5.0 42.9 1.0

Bromine binding site 2 out of 2 in the The 2.2 A Structure of A Full-Length Catalytically Active Hammerhead Ribozyme


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of The 2.2 A Structure of A Full-Length Catalytically Active Hammerhead Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Br18 b:58.0 occ:1.00 BR B:5BU18 0.0 58.0 1.0 C5 B:5BU18 1.9 38.6 1.0 C6 B:5BU18 2.9 31.4 1.0 C4 B:5BU18 2.9 34.0 1.0 O4 B:5BU18 3.0 39.5 1.0 O B:HOH2015 3.4 45.1 1.0 N7 B:A17 3.5 39.8 1.0 C8 B:A17 3.5 40.5 1.0 OP2 B:5BU18 3.7 45.6 1.0 C5 B:A17 3.9 40.6 1.0 O5' B:A17 4.0 50.6 1.0 N9 B:A17 4.0 41.6 1.0 C3' B:A17 4.1 34.1 1.0 N1 B:5BU18 4.1 36.2 1.0 N3 B:5BU18 4.2 35.8 1.0 OP2 B:A17 4.3 59.4 1.0 C4 B:A17 4.3 38.8 1.0 O B:HOH2012 4.4 46.3 1.0 O5' B:5BU18 4.4 42.6 1.0 P B:5BU18 4.6 44.4 1.0 C2' B:A17 4.6 39.0 1.0 C2 B:5BU18 4.6 40.2 1.0 C6 B:A17 4.7 35.8 1.0 N4 B:C19 4.8 34.6 1.0 C1' B:A17 4.8 37.0 1.0 O3' B:A17 4.8 34.1 1.0 P B:A17 4.8 52.4 1.0 C5' B:A17 4.9 37.9 1.0 C4' B:A17 4.9 35.1 1.0 C5 B:C19 4.9 38.1 1.0

M.Martick, W.G.Scott. Tertiary Contacts Distant From the Active Site Prime A Ribozyme For Catalysis. Cell V. 126 309 2006.
ISSN: ISSN 0092-8674
PubMed: 16859740
DOI: 10.1016/J.CELL.2006.06.036