Cadmium in PDB 1ykq: Crystal Structure of Diels-Alder Ribozyme

The structure of Crystal Structure of Diels-Alder Ribozyme, PDB code: 1ykq was solved by A.Serganov, S.Keiper, L.Malinina, V.Tereshko, E.Skripkin, C.Hobartner, A.Polonskaia, A.T.Phan, R.Wombacher, R.Micura, Z.Dauter, A.Jaschke, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.690, 44.240, 79.640, 90.00, 107.12, 90.00
R / Rfree (%)	28.6 / 32.4

The structure of Crystal Structure of Diels-Alder Ribozyme also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Cadmium atom in the Crystal Structure of Diels-Alder Ribozyme (pdb code 1ykq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Diels-Alder Ribozyme, PDB code: 1ykq:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd242 b:40.0 occ:0.50 OP2 B:A216 2.5 40.0 1.0 N7 B:A216 3.3 40.0 1.0 O6 B:G217 3.4 40.0 1.0 N7 B:G217 3.5 40.0 1.0 P B:A216 3.7 40.0 1.0 C8 B:A216 3.7 40.0 1.0 O5' B:A216 3.8 40.0 1.0 C6 B:G217 4.1 40.0 1.0 C5 B:G217 4.2 40.0 1.0 C5 B:A216 4.4 40.0 1.0 OP1 B:A216 4.4 40.0 1.0 C8 B:G217 4.7 40.0 1.0 OP2 B:G217 4.8 40.0 1.0 N9 B:A216 4.8 40.0 1.0 OP2 B:C215 4.9 40.0 1.0 C5' B:A216 4.9 40.0 1.0 O3' B:C215 4.9 40.0 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd243 b:40.0 occ:0.50 N7 B:G201 2.7 40.0 1.0 C8 B:G201 3.4 40.0 1.0 C5 B:G201 3.8 40.0 1.0 O6 B:G201 4.2 40.0 1.0 C6 B:G201 4.4 40.0 1.0 O6 B:G202 4.5 40.0 1.0 N9 B:G201 4.6 40.0 1.0 C4 B:G201 4.8 40.0 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd249 b:40.0 occ:0.50 N7 A:G101 2.3 40.0 1.0 O6 A:G101 2.6 40.0 1.0 C5 A:G101 3.0 40.0 1.0 C6 A:G101 3.1 40.0 1.0 C8 A:G101 3.5 40.0 1.0 N3 B:A230 3.8 40.0 1.0 C4 A:G101 4.3 40.0 1.0 N1 A:G101 4.5 40.0 1.0 C2 B:A230 4.5 40.0 1.0 N9 A:G101 4.5 40.0 1.0 O2' B:A230 4.6 40.0 1.0 C1' B:A230 4.8 40.0 1.0 C4 B:A230 4.9 40.0 1.0 C2' B:A230 5.0 40.0 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd342 b:40.0 occ:0.50 OP2 D:A216 2.3 40.0 1.0 P D:A216 3.4 40.0 1.0 O5' D:A216 3.6 40.0 1.0 N7 D:A216 3.7 40.0 1.0 C8 D:A216 3.9 40.0 1.0 OP2 D:C215 4.1 40.0 1.0 N7 D:G217 4.1 40.0 1.0 OP1 D:A216 4.2 40.0 1.0 O6 D:G217 4.3 40.0 1.0 O3' D:C215 4.6 40.0 1.0 C3' D:C215 4.7 40.0 1.0 O5' D:C215 4.8 40.0 1.0 P D:C215 4.9 40.0 1.0 C5 D:G217 4.9 40.0 1.0 C5' D:A216 5.0 40.0 1.0 C5 D:A216 5.0 40.0 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd343 b:40.0 occ:0.50 N7 D:G201 2.7 40.0 1.0 C5 D:G201 3.4 40.0 1.0 C8 D:G201 3.5 40.0 1.0 O6 D:G201 3.8 40.0 1.0 C6 D:G201 3.9 40.0 1.0 O6 D:G202 4.3 40.0 1.0 C4 D:G201 4.5 40.0 1.0 N9 D:G201 4.5 40.0 1.0 N7 D:G202 4.9 40.0 1.0

A.Serganov, S.Keiper, L.Malinina, V.Tereshko, E.Skripkin, C.Hobartner, A.Polonskaia, A.T.Phan, R.Wombacher, R.Micura, Z.Dauter, A.Jaschke, D.J.Patel. Structural Basis For Diels-Alder Ribozyme-Catalyzed Carbon-Carbon Bond Formation. Nat.Struct.Mol.Biol. V. 12 218 2005.
ISSN: ISSN 1545-9993
PubMed: 15723077
DOI: 10.1038/NSMB906