Magnesium in PDB 1yls: Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene

The structure of Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene, PDB code: 1yls 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 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.873, 43.269, 79.928, 90.00, 106.19, 90.00
R / Rfree (%)	20.9 / 23.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene (pdb code 1yls). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene, PDB code: 1yls:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


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 Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg240 b:21.3 occ:1.00 O B:HOH346 2.1 22.5 1.0 O B:HOH349 2.1 24.3 1.0 O B:HOH347 2.2 22.8 1.0 O B:HOH345 2.2 22.1 1.0 O B:HOH348 2.2 21.7 1.0 OP1 B:U234 2.2 16.2 1.0 P B:U234 3.4 15.8 1.0 O5' B:U234 4.0 14.8 1.0 OP2 B:U234 4.1 15.7 1.0 N7 B:G236 4.2 18.7 1.0 N7 B:G237 4.3 20.0 1.0 O6 B:G237 4.3 19.4 1.0 O6 B:G236 4.4 20.0 1.0 C5' B:U234 4.4 16.1 1.0 O3' B:C233 4.6 18.3 1.0 N4 B:C235 4.9 17.2 1.0 C5 B:G236 4.9 18.9 1.0 C6 B:G236 5.0 20.0 1.0 C5 B:C235 5.0 17.3 1.0

Magnesium binding site 2 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


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 Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg241 b:34.8 occ:1.00 O B:HOH352 2.1 35.7 1.0 O B:HOH354 2.1 35.0 1.0 O B:HOH353 2.1 36.5 1.0 O B:HOH351 2.1 36.6 1.0 O B:HOH350 2.2 36.4 1.0 OP2 B:C233 2.2 29.2 1.0 P B:C233 3.7 21.8 1.0 O6 B:G211 4.0 14.3 1.0 C3' B:A232 4.1 21.6 1.0 C2' B:A232 4.1 22.5 1.0 O3' B:A232 4.3 21.9 1.0 N4 B:C210 4.4 26.2 1.0 O2' B:A232 4.4 23.9 1.0 OP1 B:C233 4.4 16.4 1.0 OP2 B:U234 4.5 15.7 1.0 C5' B:C233 4.5 19.4 1.0 O5' B:C233 4.6 20.7 1.0 N4 B:C235 4.8 17.2 1.0 OP2 B:G208 4.9 21.4 1.0

Magnesium binding site 3 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


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 Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg242 b:51.7 occ:1.00 O B:HOH356 2.1 52.0 1.0 O B:HOH359 2.1 53.0 1.0 O B:HOH355 2.1 51.7 1.0 O B:HOH357 2.1 51.6 1.0 O B:HOH358 2.2 51.7 1.0 O B:HOH360 2.2 51.8 1.0 OP2 B:C215 3.6 22.3 1.0 N7 B:G216 3.8 25.6 1.0 O6 B:G217 4.0 16.4 1.0 OP2 B:G216 4.2 25.5 1.0 O6 B:G216 4.4 30.4 1.0 P B:C215 4.6 23.9 1.0 C5 B:G216 4.7 27.8 1.0 C8 B:G216 4.7 27.0 1.0 O5' B:C215 4.8 25.3 1.0 N7 B:G217 4.9 21.0 1.0 C6 B:G216 5.0 29.2 1.0 C6 B:G217 5.0 18.4 1.0

Magnesium binding site 4 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


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 Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg243 b:57.1 occ:1.00 O A:HOH366 2.1 57.2 1.0 O B:HOH363 2.1 56.8 1.0 O B:HOH362 2.1 57.0 1.0 O A:HOH361 2.2 56.8 1.0 O B:HOH364 2.2 56.7 1.0 O B:HOH365 2.2 56.9 1.0 O6 B:G202 3.9 11.6 1.0 O6 B:G203 3.9 20.4 1.0 N7 B:G202 4.2 13.5 1.0 O6 A:G108 4.4 11.3 1.0 C6 B:G202 4.7 13.0 1.0 C5 B:G202 4.8 13.2 1.0

Magnesium binding site 5 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


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 Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg244 b:92.4 occ:1.00 O B:HOH367 2.2 92.3 1.0 O B:HOH368 2.2 92.0 1.0 O B:HOH371 2.2 91.7 1.0 O B:HOH370 2.2 92.5 1.0 O B:HOH372 2.2 91.9 1.0 O B:HOH369 2.2 91.6 1.0 O6 B:G213 4.5 30.6 1.0 N7 B:G213 4.5 32.5 1.0 O4 B:U231 4.6 24.6 1.0 C5 B:U231 4.7 22.4 1.0

Magnesium binding site 6 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


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 Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg245 b:72.7 occ:1.00 O B:HOH377 2.1 72.1 1.0 O B:HOH373 2.1 72.0 1.0 O B:HOH376 2.2 72.2 1.0 O B:HOH378 2.2 73.0 1.0 O B:HOH375 2.2 72.0 1.0 O B:HOH374 2.2 73.1 1.0 OP2 B:A206 3.7 24.9 1.0 N7 B:A206 3.7 17.4 1.0 C8 B:A206 4.3 19.3 1.0 OP2 B:G205 4.3 34.8 1.0 N7 B:G207 4.6 21.1 1.0 C5 B:A206 4.8 18.1 1.0 P B:A206 5.0 26.5 1.0

Magnesium binding site 7 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


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 Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg246 b:42.0 occ:1.00 OP1 D:G213 2.0 23.2 1.0 OP1 B:G213 2.0 27.8 1.0 O B:HOH382 2.1 41.4 1.0 O B:HOH381 2.1 41.2 1.0 O D:HOH380 2.1 40.4 1.0 O D:HOH379 2.2 42.9 1.0 P B:G213 3.4 24.8 1.0 P D:G213 3.4 23.7 1.0 OP2 B:G213 4.2 25.2 1.0 O3' B:U212 4.2 25.3 1.0 C5' D:G213 4.2 24.1 1.0 O5' D:G213 4.3 24.3 1.0 OP2 D:G213 4.3 25.2 1.0 O3' D:U212 4.3 25.3 1.0 O5' B:G213 4.4 24.6 1.0 C5' B:G213 4.5 25.0 1.0

Magnesium binding site 8 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg247 b:37.1 occ:1.00 O B:HOH388 2.1 37.2 1.0 O B:HOH385 2.1 36.8 1.0 O B:HOH384 2.1 37.0 1.0 O D:HOH383 2.2 36.8 1.0 O B:HOH386 2.2 36.7 1.0 O B:HOH387 2.2 36.9 1.0 OP1 D:C235 4.2 21.1 1.0 OP1 D:G236 4.6 23.1 1.0 OP2 D:G236 4.7 14.7 1.0 OP1 B:C235 4.7 21.1 1.0 O3' D:C235 4.7 21.9 1.0 P D:G236 4.9 21.0 1.0 OP1 B:G236 4.9 20.3 1.0 P D:C235 5.0 20.9 1.0

Magnesium binding site 9 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg340 b:28.3 occ:1.00 OP1 D:U234 2.1 25.5 1.0 O D:HOH393 2.1 29.2 1.0 O D:HOH391 2.1 29.7 1.0 O D:HOH389 2.1 28.6 1.0 O D:HOH390 2.2 29.4 1.0 O D:HOH392 2.2 28.1 1.0 P D:U234 3.4 24.0 1.0 O5' D:U234 4.0 24.9 1.0 OP2 D:U234 4.3 25.8 1.0 C5' D:U234 4.3 22.6 1.0 N7 D:G236 4.3 20.7 1.0 O6 D:G237 4.4 18.8 1.0 N7 D:G237 4.5 21.6 1.0 O3' D:C233 4.5 19.8 1.0 O6 D:G236 4.6 18.9 1.0 N4 D:C235 4.7 27.3 1.0

Magnesium binding site 10 out of 13 in the Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Selenium-Modified Diels-Alder Ribozyme Complexed with the Product of the Reaction Between N-Pentylmaleimide and Covalently Attached 9-Hydroxymethylanthracene within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg341 b:25.4 occ:1.00 OP2 D:C233 2.0 17.0 1.0 O D:HOH398 2.2 26.2 1.0 O D:HOH397 2.2 25.4 1.0 O D:HOH396 2.2 24.0 1.0 O D:HOH395 2.2 26.9 1.0 O D:HOH394 2.2 26.1 1.0 P D:C233 3.4 21.0 1.0 O5' D:C233 4.0 21.5 1.0 C2' D:A232 4.2 24.2 1.0 C3' D:A232 4.3 23.2 1.0 C5' D:C233 4.3 23.3 1.0 O2' D:A232 4.3 25.4 1.0 O3' D:A232 4.3 22.3 1.0 O6 D:G211 4.4 18.7 1.0 OP2 D:G208 4.4 23.5 1.0 OP2 D:U234 4.4 25.8 1.0 OP1 D:C233 4.5 19.9 1.0 N4 D:C210 4.7 23.6 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