Magnesium 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:

Cadmium

(Cd)

5 atoms

The binding sites of Magnesium atom in the Crystal Structure of Diels-Alder Ribozyme (pdb code 1ykq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Diels-Alder Ribozyme, PDB code: 1ykq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg240 b:40.0 occ:1.00 OP1 B:U234 1.9 40.0 1.0 P B:U234 3.2 40.0 1.0 N7 B:G236 3.6 40.0 1.0 O5' B:U234 3.8 40.0 1.0 O6 B:G236 3.9 40.0 1.0 C5' B:U234 4.0 40.0 1.0 OP2 B:U234 4.0 40.0 1.0 N4 B:C235 4.3 40.0 1.0 O3' B:C233 4.4 40.0 1.0 C5 B:G236 4.4 40.0 1.0 C6 B:G236 4.5 40.0 1.0 C8 B:G236 4.7 40.0 1.0 C4 B:C235 4.7 40.0 1.0 N7 B:G237 4.8 40.0 1.0 O6 B:G237 4.9 40.0 1.0 C5 B:C235 4.9 40.0 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg241 b:40.0 occ:1.00 OP2 B:C233 2.4 40.0 1.0 P B:C233 3.6 40.0 1.0 OP1 B:C233 4.0 40.0 1.0 N4 B:C210 4.1 40.0 1.0 C3' B:A232 4.2 40.0 1.0 C2' B:A232 4.3 40.0 1.0 O3' B:A232 4.4 40.0 1.0 OP2 B:U234 4.5 40.0 1.0 OP2 B:G208 4.6 40.0 1.0 O2' B:A232 4.7 40.0 1.0 O5' B:C233 4.8 40.0 1.0 OP1 B:A232 4.8 40.0 1.0 O6 B:G211 4.9 40.0 1.0 N4 B:C235 5.0 40.0 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg246 b:40.0 occ:1.00 OP1 B:G213 2.1 40.0 1.0 OP1 D:G213 2.3 40.0 1.0 P B:G213 3.4 40.0 1.0 O5' B:G213 3.8 40.0 1.0 P D:G213 3.8 40.0 1.0 C5' B:G213 4.0 40.0 1.0 OP2 B:G213 4.2 40.0 1.0 O3' D:U212 4.5 40.0 1.0 O3' B:U212 4.6 40.0 1.0 O5' D:G213 4.7 40.0 1.0 C5' D:G213 4.7 40.0 1.0 OP2 D:G213 4.7 40.0 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg340 b:40.0 occ:1.00 OP1 D:U234 2.7 40.0 1.0 N7 D:G236 3.7 40.0 1.0 P D:U234 3.9 40.0 1.0 N7 D:G237 4.1 40.0 1.0 O6 D:G237 4.1 40.0 1.0 C5' D:U234 4.1 40.0 1.0 O6 D:G236 4.3 40.0 1.0 C5 D:C235 4.4 40.0 1.0 O5' D:U234 4.5 40.0 1.0 OP2 D:U234 4.5 40.0 1.0 N4 D:C235 4.5 40.0 1.0 C5 D:G236 4.5 40.0 1.0 C4 D:C235 4.5 40.0 1.0 C8 D:G236 4.6 40.0 1.0 C6 D:G236 4.7 40.0 1.0 C6 D:G237 4.9 40.0 1.0 C5 D:G237 4.9 40.0 1.0 OP2 D:G236 5.0 40.0 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg341 b:40.0 occ:1.00 OP2 D:C233 2.4 40.0 1.0 P D:C233 3.4 40.0 1.0 OP1 D:C233 3.6 40.0 1.0 C3' D:A232 4.3 40.0 1.0 N4 D:C210 4.3 40.0 1.0 OP2 D:U234 4.3 40.0 1.0 O3' D:A232 4.4 40.0 1.0 C2' D:A232 4.5 40.0 1.0 O6 D:G211 4.6 40.0 1.0 O2' D:A232 4.7 40.0 1.0 O5' D:C233 4.7 40.0 1.0 N4 D:C235 4.8 40.0 1.0 C5' D:C233 4.9 40.0 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg348 b:40.0 occ:0.50 N7 D:G225 2.4 40.0 1.0 O6 D:G225 3.2 40.0 1.0 C5 D:G225 3.3 40.0 1.0 C8 D:G225 3.4 40.0 1.0 C6 D:G225 3.6 40.0 1.0 C4 D:G225 4.5 40.0 1.0 N9 D:G225 4.6 40.0 1.0 OP2 D:G225 4.6 40.0 1.0 N7 D:A226 5.0 40.0 1.0 N1 D:G225 5.0 40.0 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Diels-Alder Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Diels-Alder Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg349 b:40.0 occ:0.50 N7 C:G101 2.2 40.0 1.0 O6 C:G101 2.6 40.0 1.0 C5 C:G101 2.8 40.0 1.0 C6 C:G101 3.0 40.0 1.0 C8 C:G101 3.3 40.0 1.0 N3 D:A230 3.9 40.0 1.0 C4 C:G101 4.1 40.0 1.0 N1 C:G101 4.3 40.0 1.0 N9 C:G101 4.3 40.0 1.0 C2 D:A230 4.5 40.0 1.0 O2' D:A230 4.6 40.0 1.0 C1' D:A230 4.8 40.0 1.0 C4 D:A230 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