Calcium in PDB 3r1h: Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound

The structure of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound, PDB code: 3r1h 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)	30.00 / 3.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.690, 70.011, 71.858, 99.85, 99.74, 103.65
R / Rfree (%)	21.2 / 25.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound (pdb code 3r1h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 26 binding sites of Calcium where determined in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound, PDB code: 3r1h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1019 b:74.5 occ:1.00 OP2 C:A31 2.3 74.2 1.0 O C:HOH1036 2.3 96.9 1.0 O C:HOH1034 2.3 79.5 1.0 O C:HOH1035 2.3 73.4 1.0 O C:HOH1033 2.3 94.9 1.0 OP2 C:A32 2.3 78.7 1.0 P C:A31 3.7 77.8 1.0 P C:A32 3.8 66.3 1.0 N6 C:A33 4.1 61.6 1.0 O3' C:C30 4.2 70.6 1.0 O5' C:A31 4.3 66.5 1.0 C3' C:A31 4.5 69.8 1.0 O5' C:A32 4.5 63.0 1.0 N7 C:A33 4.6 69.0 1.0 O3' C:A31 4.6 64.3 1.0 N7 C:A32 4.6 64.7 1.0 OP1 C:A32 4.7 71.0 1.0 OP1 C:A31 4.8 77.5 1.0 C8 C:A32 4.9 67.1 1.0

Calcium binding site 2 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1020 b:94.8 occ:1.00 O C:HOH1038 2.3 87.2 1.0 O C:HOH1039 2.3 86.8 1.0 O C:HOH1037 2.3 72.0 1.0 OP1 C:C70 2.5 79.2 1.0 OP1 C:U106 2.5 80.8 1.0 OP2 C:G72 2.5 83.5 1.0 O3' C:A71 3.3 70.8 1.0 P C:G72 3.5 68.6 1.0 C3' C:A71 3.6 67.9 1.0 O2' C:A71 3.7 77.2 1.0 P C:C70 3.8 96.9 1.0 P C:U106 3.9 78.6 1.0 C2' C:A71 4.1 71.3 1.0 O3' C:G69 4.1 95.4 1.0 C5' C:U106 4.1 74.3 1.0 O5' C:U106 4.4 75.3 1.0 O5' C:G72 4.5 67.1 1.0 O3' C:G105 4.6 60.4 1.0 C5' C:C70 4.7 87.3 1.0 OP1 C:G72 4.7 58.4 1.0 O5' C:C70 4.7 88.6 1.0 OP2 C:C70 4.9 89.3 1.0

Calcium binding site 3 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1021 b:0.0 occ:1.00 O C:HOH1041 2.3 93.0 1.0 O C:HOH1040 2.3 99.0 1.0 OP2 C:A4 2.6 93.4 1.0 OP2 C:A3 2.7 92.5 1.0 OP2 C:A115 3.3 82.5 1.0 O5' C:A3 3.3 78.1 1.0 O2' C:A114 3.4 76.8 1.0 P C:A3 3.6 84.3 1.0 P C:A4 3.9 90.2 1.0 O3' C:A114 4.2 93.0 1.0 C3' C:A3 4.2 76.0 1.0 P C:A115 4.3 90.2 1.0 C2' C:A114 4.5 78.8 1.0 OP1 C:A4 4.5 94.8 1.0 O3' C:G2 4.6 82.4 1.0 O3' C:A3 4.6 82.7 1.0 C5' C:A3 4.6 84.8 1.0 OP1 C:A3 4.8 85.1 1.0 C3' C:A114 4.9 81.0 1.0 C4' C:A3 5.0 81.7 1.0

Calcium binding site 4 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1022 b:90.9 occ:1.00 OP2 C:U47 2.7 88.7 1.0 OP1 C:G74 2.7 64.5 1.0 OP1 C:G46 2.7 97.7 1.0 P C:G74 4.0 56.5 1.0 P C:U47 4.1 95.6 1.0 P C:G46 4.1 84.9 1.0 OP2 C:G75 4.4 63.6 1.0 O5' C:G74 4.5 55.1 1.0 C5' C:G74 4.5 57.1 1.0 O3' C:G45 4.6 86.8 1.0 O5' C:U47 4.7 76.8 1.0 O5' C:G46 4.8 88.7 1.0 C3' C:G46 4.8 89.0 1.0 C5' C:U47 4.8 83.6 1.0 C5' C:G46 4.8 89.1 1.0 OP2 C:G74 4.8 63.3 1.0 N3 C:C30 4.9 70.1 1.0 O3' C:G46 4.9 96.8 1.0

Calcium binding site 5 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1023 b:97.3 occ:1.00 O6 C:G88 4.0 65.6 1.0 O6 C:G87 4.6 51.2 1.0 N7 C:G87 4.9 51.6 1.0 N6 C:A102 4.9 61.3 1.0

Calcium binding site 6 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1024 b:0.6 occ:1.00 OP2 C:C104 3.4 80.8 1.0 OP1 C:A103 4.2 97.7 1.0 P C:C104 4.4 91.6 1.0 OP1 C:C104 4.5 95.2 1.0 O5' C:A103 4.5 87.8 1.0 P C:A103 4.8 0.8 1.0 C5' C:A103 5.0 86.5 1.0

Calcium binding site 7 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1025 b:0.4 occ:1.00 O4 C:U68 2.5 74.2 1.0 C4 C:U68 3.6 67.5 1.0 O6 C:G69 3.9 65.9 1.0 C5 C:U68 4.3 73.5 1.0 N6 C:A56 4.5 67.6 1.0 N6 C:A67 4.6 70.2 1.0 N7 C:A67 4.7 67.7 1.0 N4 C:C55 4.7 67.0 1.0 N3 C:U68 4.7 60.0 1.0 C6 C:G69 5.0 67.4 1.0

Calcium binding site 8 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1026 b:0.7 occ:1.00 O6 C:G1017 3.7 75.1 1.0 O6 C:G1016 4.7 76.2 1.0 N7 C:G1017 4.7 72.6 1.0 C6 C:G1017 4.8 73.4 1.0 N7 C:G1016 4.8 69.0 1.0

Calcium binding site 9 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1027 b:0.6 occ:1.00 OP2 C:C110 3.1 82.2 1.0 OP1 C:C110 3.8 90.0 1.0 P C:C110 3.9 91.6 1.0 O5' C:C110 4.6 89.1 1.0

Calcium binding site 10 out of 26 in the Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Class I Ligase Ribozyme-Substrate Preligation Complex, C47U Mutant, CA2+ Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1028 b:0.3 occ:1.00 O6 C:G2 1.9 0.8 1.0 O C:HOH1046 2.3 0.3 1.0 O C:HOH1043 2.3 0.4 1.0 O C:HOH1044 2.3 0.0 1.0 O C:HOH1045 2.3 0.7 1.0 O C:HOH1042 2.3 98.7 1.0 C6 C:G2 3.0 0.1 1.0 OP2 C:A9 3.7 0.2 1.0 O2G C:GTP1 3.8 0.8 1.0 C5 C:G2 3.9 99.5 1.0 N1 C:G2 4.0 0.9 1.0 O C:HOH1050 4.0 0.9 1.0 N7 C:G2 4.2 98.8 1.0 N7 C:GTP1 4.5 0.9 1.0 OP1 C:U8 4.5 0.4 1.0 O2A C:GTP1 4.6 0.9 1.0 P C:A9 4.8 0.3 1.0 OP2 C:U8 4.9 0.8 1.0 O3G C:GTP1 4.9 0.1 1.0 PG C:GTP1 4.9 0.6 1.0 C8 C:GTP1 4.9 0.1 1.0 P C:U8 5.0 99.2 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