Magnesium in PDB 3r1l: Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound

The structure of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound, PDB code: 3r1l was solved by D.M.Shechner, D.P.Bartel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.91 / 3.13
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.190, 70.237, 71.214, 99.86, 99.34, 103.81
R / Rfree (%)	19.7 / 24

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 46;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound (pdb code 3r1l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 46 binding sites of Magnesium where determined in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound, PDB code: 3r1l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1019 b:52.4 occ:1.00 O C:HOH1047 2.1 48.2 1.0 OP2 C:A31 2.1 48.4 1.0 O C:HOH1044 2.1 53.0 1.0 O C:HOH1045 2.1 51.8 1.0 O C:HOH1046 2.1 58.9 1.0 OP2 C:A32 2.2 55.9 1.0 P C:A31 3.4 52.0 1.0 P C:A32 3.6 50.9 1.0 N6 C:A33 3.9 48.9 1.0 O5' C:A31 4.0 51.3 1.0 N7 C:A32 4.1 48.9 1.0 O3' C:C30 4.1 53.9 1.0 O5' C:A32 4.2 46.0 1.0 N7 C:A33 4.2 50.6 1.0 C3' C:A31 4.3 54.8 1.0 C8 C:A32 4.4 52.3 1.0 O3' C:A31 4.4 53.5 1.0 OP1 C:A31 4.6 61.0 1.0 OP1 C:A32 4.6 50.2 1.0 C6 C:A33 4.7 43.5 1.0 C5' C:A31 4.7 48.5 1.0 C5 C:A33 4.8 51.2 1.0

Magnesium binding site 2 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1020 b:0.9 occ:1.00 O C:HOH1051 2.1 91.0 1.0 O C:HOH1049 2.1 0.0 1.0 O C:HOH1048 2.1 0.4 1.0 O C:HOH1050 2.1 98.9 1.0 O6 C:G2 2.3 90.3 1.0 O3G C:GTP1 2.7 91.1 1.0 O2G C:GTP1 3.3 98.8 1.0 C6 C:G2 3.4 85.6 1.0 PG C:GTP1 3.5 0.5 1.0 O1G C:GTP1 3.9 91.5 1.0 OP2 C:A9 4.1 98.2 1.0 N1 C:G2 4.2 85.0 1.0 C5 C:G2 4.4 82.7 1.0 N7 C:GTP1 4.4 80.1 1.0 N7 C:G2 4.7 84.8 1.0 O3B C:GTP1 4.9 0.0 1.0 O6 C:GTP1 5.0 83.1 1.0

Magnesium binding site 3 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1021 b:75.2 occ:1.00 O C:HOH1054 2.1 81.8 1.0 O C:HOH1052 2.1 74.3 1.0 O C:HOH1053 2.1 79.5 1.0 OP1 C:U106 2.5 61.3 1.0 OP1 C:C70 2.6 79.8 1.0 OP2 C:G72 2.6 68.3 1.0 O C:HOH1071 3.1 56.9 1.0 P C:U106 3.8 64.5 1.0 P C:G72 3.8 63.1 1.0 O3' C:A71 3.8 58.4 1.0 P C:C70 3.9 89.7 1.0 O2' C:A71 4.0 74.6 1.0 C5' C:U106 4.0 60.3 1.0 C3' C:A71 4.1 63.6 1.0 O3' C:G69 4.1 82.9 1.0 O5' C:U106 4.2 58.1 1.0 O3' C:G105 4.5 52.7 1.0 C2' C:A71 4.5 68.8 1.0 O5' C:G72 4.8 53.0 1.0 OP2 C:C70 4.8 72.1 1.0 C5' C:C70 4.9 80.4 1.0 O5' C:C70 4.9 81.1 1.0 OP1 C:G72 4.9 57.0 1.0

Magnesium binding site 4 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1022 b:53.0 occ:1.00 O6 C:G87 3.9 54.9 1.0 O6 C:G88 4.3 59.2 1.0 N7 C:G87 4.3 47.2 1.0 C6 C:G87 4.6 52.1 1.0 N6 C:A102 4.7 56.8 1.0 C5 C:G87 4.8 47.7 1.0

Magnesium binding site 5 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1023 b:64.8 occ:1.00 O C:HOH1072 2.8 65.3 1.0 OP2 C:A96 3.2 58.6 1.0 OP2 C:A95 3.5 49.1 1.0 P C:A96 4.1 58.9 1.0 C5' C:A95 4.2 61.5 1.0 C6 C:U94 4.2 56.5 1.0 OP1 C:A96 4.2 49.3 1.0 O5' C:A95 4.3 66.2 1.0 C3' C:U94 4.3 64.1 1.0 C5 C:U94 4.3 53.5 1.0 C5' C:U94 4.4 54.1 1.0 P C:A95 4.4 60.0 1.0 O3' C:A95 4.4 62.2 1.0 OP2 C:U94 4.5 57.9 1.0 O3' C:U94 4.8 65.2 1.0 N1 C:U94 5.0 55.5 1.0 C3' C:A95 5.0 58.8 1.0 C4' C:U94 5.0 58.3 1.0

Magnesium binding site 6 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1024 b:78.1 occ:1.00 OP1 C:A97 3.7 70.6 1.0 C5' C:A97 4.1 80.9 1.0 OP2 C:A97 4.1 68.2 1.0 P C:A97 4.3 83.1 1.0 O4 C:U93 4.4 72.6 1.0 O6 C:G92 4.6 73.1 1.0 O5' C:A97 4.6 75.7 1.0 MG C:MG1040 4.6 76.5 1.0 OP2 C:A98 4.8 96.0 1.0

Magnesium binding site 7 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1025 b:55.2 occ:1.00 O6 C:G72 3.9 45.0 1.0 N7 C:G105 4.1 47.3 1.0 O6 C:G105 4.4 52.5 1.0 N7 C:G72 4.4 39.7 1.0 C5 C:G105 4.6 42.2 1.0 C6 C:G105 4.7 47.8 1.0 C6 C:G72 4.8 39.4 1.0 C8 C:G105 4.8 45.0 1.0 N6 C:A73 4.9 41.4 1.0

Magnesium binding site 8 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1026 b:46.0 occ:1.00 O6 C:G75 4.3 45.7 1.0 O6 C:G81 4.3 60.5 1.0 N7 C:G81 4.6 60.9 1.0 N7 C:A80 4.6 56.0 1.0 N6 C:A80 4.9 63.0 1.0

Magnesium binding site 9 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1027 b:92.5 occ:1.00 O C:HOH1056 2.1 68.6 1.0 O C:HOH1057 2.1 76.0 1.0 O C:HOH1055 2.1 79.6 1.0 O C:HOH1060 2.1 68.4 1.0 O C:HOH1059 2.1 63.3 1.0 O C:HOH1058 2.1 77.0 1.0 O6 C:G37 3.7 64.5 1.0 O4 C:U36 4.3 63.5 1.0 O6 C:G78 4.4 64.3 1.0 N4 C:C38 4.5 68.7 1.0 O6 C:G77 4.7 59.6 1.0 C6 C:G37 4.9 66.0 1.0

Magnesium binding site 10 out of 46 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound


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 Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, MG2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1028 b:52.9 occ:1.00 O4 C:U68 3.0 71.0 1.0 C4 C:U68 4.1 65.7 1.0 O6 C:G69 4.5 62.6 1.0 C5 C:U68 4.6 62.3 1.0 N7 C:A67 4.7 63.5 1.0 N6 C:A67 4.8 66.9 1.0 N6 C:A56 5.0 62.2 1.0

D.M.Shechner, D.P.Bartel. The Structural Basis of Rna-Catalyzed Rna Polymerization. Nat.Struct.Mol.Biol. V. 18 1036 2011.
ISSN: ISSN 1545-9993
PubMed: 21857665
DOI: 10.1038/NSMB.2107