Magnesium in PDB 4rge: Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme

The structure of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme, PDB code: 4rge was solved by A.Ren, K.R.Rajashankar, D.Simanshu, D.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.49 / 2.89
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.071, 64.071, 578.773, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 22.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme (pdb code 4rge). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme, PDB code: 4rge:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister 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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:75.4 occ:1.00 O A:HOH202 2.1 68.3 1.0 O A:HOH201 2.1 80.0 1.0 OP1 A:A6 2.1 78.5 1.0 O A:HOH203 2.2 65.9 1.0 OP2 A:A7 2.2 82.3 1.0 O4 A:U8 2.3 80.4 1.0 O5' A:A6 2.9 79.2 1.0 P A:A6 3.1 69.6 1.0 C4 A:U8 3.3 75.5 1.0 P A:A7 3.6 91.1 1.0 C5 A:U8 3.8 75.9 1.0 N6 A:A47 3.9 70.3 1.0 C5' A:A6 4.0 72.5 1.0 OP2 A:A6 4.0 79.0 1.0 C3' A:A6 4.0 80.5 1.0 O3' A:A6 4.1 79.6 1.0 C4' A:A6 4.2 83.2 1.0 O3' A:DU5 4.2 83.7 1.0 N2 A:G48 4.4 77.1 1.0 N3 A:U8 4.5 77.4 1.0 O5' A:A7 4.5 79.0 1.0 OP1 A:A7 4.7 88.3 1.0 O6 A:G9 4.9 75.3 1.0 C6 A:A47 5.0 70.5 1.0

Magnesium binding site 2 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister 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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:84.8 occ:1.00 OP2 A:U2 2.3 0.3 1.0 P A:U2 3.6 0.9 1.0 O3' A:U1 3.7 96.2 1.0 OP1 A:U2 4.5 96.9 1.0 O5' A:U2 4.6 0.7 1.0 C5' A:U2 4.7 0.7 1.0

Magnesium binding site 3 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister 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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:0.2 occ:1.00 O A:HOH216 2.7 0.6 1.0 O A:HOH215 2.8 0.6 1.0 OP2 A:G53 3.5 0.5 1.0 P A:G53 4.9 0.5 1.0 N6 A:A54 4.9 1.0 1.0

Magnesium binding site 4 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister 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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:74.8 occ:1.00 O A:HOH205 1.8 62.8 1.0 O A:HOH206 1.9 63.0 1.0 O A:HOH204 2.2 76.8 1.0 O6 A:G27 2.2 92.2 1.0 N7 A:G27 2.7 83.5 1.0 C6 A:G27 2.9 73.5 1.0 C5 A:G27 3.0 72.5 1.0 O6 A:G28 3.5 73.7 1.0 N7 A:G28 4.0 74.2 1.0 C8 A:G27 4.0 75.5 1.0 O A:HOH207 4.0 85.0 1.0 OP2 A:A26 4.1 96.3 1.0 N1 A:G27 4.2 64.3 1.0 C6 A:G28 4.2 73.5 1.0 N4 A:C40 4.3 74.2 1.0 C4 A:G27 4.4 65.1 1.0 C5 A:G28 4.4 73.1 1.0 N7 A:A26 4.7 60.9 1.0 N9 A:G27 4.8 65.0 1.0 N6 A:A26 5.0 75.4 1.0 N4 A:C39 5.0 74.8 1.0 O3' A:G36 5.0 76.9 1.0

Magnesium binding site 5 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister 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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:85.7 occ:1.00 OP2 A:U30 2.2 79.2 1.0 OP1 A:C32 2.4 0.2 1.0 P A:C32 3.5 0.8 1.0 O3' A:C31 3.5 0.6 1.0 P A:U30 3.7 89.0 1.0 C5' A:C32 4.1 82.8 1.0 O5' A:C32 4.2 81.9 1.0 OP1 A:U30 4.3 99.0 1.0 O5' A:G29 4.4 71.9 1.0 OP1 A:G29 4.6 93.9 1.0 O5' A:U30 4.6 80.9 1.0 OP2 A:G29 4.6 91.7 1.0 O3' A:G29 4.7 79.0 1.0 P A:G29 4.8 87.6 1.0 OP2 A:C32 4.8 0.2 1.0 C3' A:C31 4.9 96.3 1.0 C3' A:G29 4.9 75.5 1.0

Magnesium binding site 6 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister 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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:82.6 occ:1.00 O A:HOH212 1.9 87.2 1.0 O A:HOH210 2.0 68.3 1.0 OP2 A:A43 2.3 82.0 1.0 O A:HOH211 2.4 86.6 1.0 OP2 A:A42 2.7 0.5 1.0 N7 A:A43 3.0 88.9 1.0 O3' A:U41 3.5 99.8 1.0 C8 A:A43 3.6 84.7 1.0 P A:A42 3.6 98.5 1.0 P A:A43 3.8 87.2 1.0 O5' A:A42 3.9 64.9 1.0 C3' A:A42 4.1 61.9 1.0 O2' A:U41 4.2 83.2 1.0 C5 A:A43 4.3 85.1 1.0 C5' A:A42 4.4 64.1 1.0 O5' A:A43 4.5 68.7 1.0 O3' A:A42 4.5 57.8 1.0 OP2 A:C39 4.6 97.3 1.0 C3' A:U41 4.7 86.9 1.0 OP2 A:C40 4.7 73.7 1.0 N6 A:A43 4.7 83.1 1.0 C8 A:A42 4.8 75.7 1.0 OP1 A:A43 4.8 90.2 1.0 C4' A:A42 4.8 65.7 1.0 N9 A:A43 4.9 82.8 1.0 C2' A:U41 5.0 81.6 1.0

Magnesium binding site 7 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister 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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:96.5 occ:1.00 O4 A:U30 2.5 86.8 1.0 O A:HOH222 2.8 92.2 1.0 O A:HOH208 3.1 88.4 1.0 OP2 A:A35 3.3 0.2 1.0 C4 A:U30 3.6 78.3 1.0 N7 A:G29 3.8 71.0 1.0 C5 A:U30 4.1 77.3 1.0 C8 A:G29 4.6 81.3 1.0 O6 A:G29 4.7 73.0 1.0 C5 A:G29 4.8 71.1 1.0 N3 A:U30 4.8 71.9 1.0 P A:A35 4.8 87.9 1.0 O A:HOH204 4.8 76.8 1.0 O A:HOH207 4.9 85.0 1.0

Magnesium binding site 8 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme


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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:72.6 occ:1.00 O A:HOH219 1.7 70.1 1.0 O A:HOH218 1.9 82.7 1.0 OP2 A:G19 2.3 94.1 1.0 O A:HOH217 2.7 81.9 1.0 P A:G19 3.6 89.3 1.0 OP1 A:G19 4.0 84.8 1.0 O3' A:G18 4.5 92.8 1.0 O5' A:G19 4.7 87.1 1.0

Magnesium binding site 9 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme


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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:94.8 occ:1.00 OP1 A:A7 2.4 88.3 1.0 OP2 A:U8 2.7 0.3 1.0 P A:A7 3.8 91.1 1.0 P A:U8 4.1 97.5 1.0 OP1 A:G36 4.3 81.4 1.0 OP2 A:A7 4.4 82.3 1.0 O5' A:A7 4.6 79.0 1.0 O3' A:A7 4.6 87.1 1.0 C5' A:A7 4.6 78.4 1.0 O3' A:A6 4.8 79.6 1.0 OP1 A:U8 4.9 97.3 1.0 O A:HOH203 4.9 65.9 1.0

Magnesium binding site 10 out of 27 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme


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 the in-Line Aligned ENV22 Twister Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg110 b:0.1 occ:1.00 O A:HOH226 2.0 91.9 1.0 O A:HOH225 2.6 79.2 1.0 O A:HOH224 2.8 0.4 1.0 O A:HOH223 3.1 93.4 1.0 N7 A:G51 4.1 1.0 1.0 O6 A:G51 4.2 0.8 1.0 O4 A:U1 4.5 76.6 1.0 C4 A:U1 4.5 77.8 1.0 O6 A:G52 4.7 0.5 1.0 N7 A:A50 4.7 0.2 1.0 N3 A:U1 4.7 77.9 1.0 N7 A:G52 4.8 0.4 1.0 C5 A:G51 4.9 0.4 1.0 C6 A:G51 5.0 0.4 1.0 C5 A:U1 5.0 86.6 1.0

A.Ren, M.Kosutic, K.R.Rajashankar, M.Frener, T.Santner, E.Westhof, R.Micura, D.J.Patel. In-Line Alignment and Mg(2+) Coordination at the Cleavage Site of the ENV22 Twister Ribozyme. Nat Commun V. 5 5534 2014.
ISSN: ESSN 2041-1723
PubMed: 25410397
DOI: 10.1038/NCOMMS6534