Magnesium in PDB 3hhn: Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd

The structure of Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd, PDB code: 3hhn was solved by D.M.Shechner, R.A.Grant, S.C.Bagby, D.P.Bartel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.12 / 2.99
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.561, 70.412, 70.906, 100.29, 99.61, 103.89
R / Rfree (%)	20.2 / 23.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd (pdb code 3hhn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 34 binding sites of Magnesium where determined in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd, PDB code: 3hhn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg184 b:0.0 occ:1.00 O B:HOH185 2.1 68.5 1.0 O B:HOH183 2.1 77.7 1.0 O B:HOH188 2.1 74.9 1.0 O B:HOH186 2.1 98.5 1.0 O B:HOH187 2.1 99.4 1.0 O B:HOH189 2.1 79.3 1.0 NZ B:LYS27 3.9 80.6 1.0 CE B:LYS23 4.0 81.5 1.0 NZ B:LYS23 4.2 93.9 1.0 N B:VAL45 4.2 54.5 1.0 O B:ILE43 4.3 63.5 1.0 CD B:LYS27 4.4 64.5 1.0 CD1 B:LEU44 4.4 65.3 1.0 CE B:LYS27 4.4 76.4 1.0 O B:VAL45 4.5 63.3 1.0 CA B:LEU44 4.5 61.0 1.0 C B:LEU44 4.9 57.3 1.0

Magnesium binding site 2 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1019 b:53.1 occ:1.00 O C:HOH1030 2.1 71.9 1.0 O C:HOH1027 2.1 55.4 1.0 O C:HOH1029 2.1 55.8 1.0 O C:HOH1028 2.1 44.8 1.0 OP2 C:A32 2.1 46.4 1.0 OP2 C:A31 2.1 51.3 1.0 P C:A31 3.5 60.0 1.0 P C:A32 3.6 54.9 1.0 N6 C:A33 4.1 44.8 1.0 O3' C:C30 4.2 54.5 1.0 O5' C:A31 4.2 57.1 1.0 O5' C:A32 4.3 43.6 1.0 N7 C:A33 4.4 54.1 1.0 OP1 C:A32 4.4 52.9 1.0 O3' C:A31 4.5 54.6 1.0 N7 C:A32 4.6 41.1 1.0 C3' C:A31 4.6 56.8 1.0 OP1 C:A31 4.6 60.9 1.0 C8 C:A32 4.8 46.6 1.0 C5' C:A31 4.9 52.4 1.0

Magnesium binding site 3 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1020 b:68.6 occ:1.00 O C:HOH1033 2.1 71.8 1.0 O C:HOH1031 2.1 69.6 1.0 O C:HOH1034 2.1 72.3 1.0 O C:HOH1035 2.1 75.1 1.0 O C:HOH1036 2.1 75.5 1.0 O C:HOH1032 2.1 62.6 1.0 N2 C:G1 4.1 62.5 1.0 O2 C:C12 4.2 74.1 1.0 O2' C:C12 4.2 70.1 1.0 O4' C:U13 4.4 77.1 1.0 C1' C:U13 4.9 70.2 1.0 O2' C:U48 4.9 77.2 1.0 C2' C:C12 4.9 73.3 1.0 C6 C:A3 5.0 76.8 1.0

Magnesium binding site 4 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1021 b:94.7 occ:1.00 O C:HOH1039 2.1 86.5 1.0 O C:HOH1040 2.1 0.5 1.0 O C:HOH1038 2.1 84.0 1.0 O C:HOH1037 2.1 0.3 1.0 OP1 C:U106 2.5 66.0 1.0 OP1 C:C70 2.8 95.7 1.0 OP2 C:G72 3.6 79.7 1.0 P C:U106 3.9 69.7 1.0 P C:C70 4.0 0.8 1.0 O5' C:U106 4.1 72.0 1.0 O3' C:G69 4.2 0.1 1.0 O2' C:A71 4.3 71.1 1.0 C5' C:U106 4.4 74.7 1.0 O3' C:A71 4.5 67.0 1.0 P C:G72 4.7 73.0 1.0 C3' C:A71 4.7 71.8 1.0 O3' C:G105 4.8 60.0 1.0 OP2 C:C70 4.8 81.9 1.0 OP2 C:U106 4.9 75.8 1.0 C2' C:A71 5.0 69.9 1.0

Magnesium binding site 5 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1022 b:71.8 occ:1.00 O C:HOH1045 2.1 71.5 1.0 O C:HOH1044 2.1 85.6 1.0 O C:HOH1041 2.1 68.1 1.0 O C:HOH1043 2.1 95.2 1.0 O C:HOH1042 2.1 76.7 1.0 OP1 C:G77 2.5 65.8 1.0 P C:G77 3.7 58.7 1.0 OP2 C:G75 3.8 55.5 1.0 O3' C:U76 4.2 66.0 1.0 OP2 C:G77 4.3 54.3 1.0 C4' C:U76 4.6 57.2 1.0 C3' C:U76 4.7 63.4 1.0 OP1 C:G46 4.8 68.5 1.0 O5' C:G77 4.9 59.2 1.0 OP2 C:G78 5.0 51.2 1.0

Magnesium binding site 6 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1023 b:78.3 occ:1.00 O C:HOH1048 2.1 0.3 1.0 O C:HOH1047 2.1 90.1 1.0 O C:HOH1050 2.1 78.7 1.0 O C:HOH1049 2.1 81.3 1.0 O C:HOH1046 2.1 88.1 1.0 OP2 C:A115 2.6 76.4 1.0 OP2 C:A4 3.7 75.5 1.0 OP2 C:A3 3.7 66.6 1.0 P C:A115 3.8 85.9 1.0 O3' C:A114 3.9 76.2 1.0 O2' C:A114 4.0 65.2 1.0 N7 C:A115 4.6 76.8 1.0 OP1 C:A115 4.7 74.5 1.0 C2' C:A114 4.8 69.8 1.0 O5' C:A3 4.8 51.8 1.0 P C:A3 4.9 66.8 1.0 O5' C:A115 4.9 83.0 1.0 C3' C:A114 4.9 73.9 1.0

Magnesium binding site 7 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg60 b:54.0 occ:1.00 O C:HOH61 2.1 81.7 1.0 O C:HOH65 2.1 70.3 1.0 O C:HOH59 2.1 62.7 1.0 O C:HOH62 2.1 80.3 1.0 O C:HOH63 2.1 79.3 1.0 O C:HOH64 2.1 74.8 1.0 O6 C:G81 4.2 60.8 1.0 N6 C:A80 4.3 56.8 1.0 O6 C:G75 4.4 52.9 1.0 N7 C:A80 4.4 50.1 1.0 N7 C:G81 4.6 50.7 1.0

Magnesium binding site 8 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1024 b:78.8 occ:1.00 O C:HOH1051 2.1 62.1 1.0 O C:HOH1053 2.1 64.4 1.0 O C:HOH1052 2.1 74.3 1.0 O C:HOH1055 2.1 69.6 1.0 O C:HOH1054 2.1 85.0 1.0 O C:HOH1056 2.1 48.0 1.0 N7 C:G105 4.1 48.5 1.0 O6 C:G72 4.2 43.9 1.0 O6 C:G105 4.6 37.9 1.0 C5 C:G105 4.8 42.4 1.0 N6 C:A73 4.9 44.6 1.0 C8 C:G105 4.9 48.4 1.0 N7 C:G72 5.0 42.6 1.0 C6 C:G105 5.0 41.4 1.0

Magnesium binding site 9 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1025 b:75.8 occ:1.00 O C:HOH1061 2.1 37.0 1.0 O C:HOH1058 2.1 70.5 1.0 O C:HOH1057 2.1 37.1 1.0 O C:HOH1059 2.1 69.4 1.0 O C:HOH1060 2.1 78.9 1.0 O C:HOH1062 2.1 44.4 1.0 O6 C:G88 3.9 55.2 1.0 O6 C:G87 4.0 46.2 1.0 N7 C:G87 4.2 33.5 1.0 N6 C:A102 4.6 55.2 1.0 C6 C:G87 4.7 42.2 1.0 C5 C:G87 4.8 37.6 1.0 O4 C:U89 5.0 67.7 1.0

Magnesium binding site 10 out of 34 in the Crystal Structure of Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd


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 Class I Ligase Ribozyme Self-Ligation Product, in Complex with U1A Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1026 b:85.6 occ:1.00 O C:HOH1063 2.1 45.3 1.0 O C:HOH1065 2.1 63.1 1.0 O C:HOH1067 2.1 77.1 1.0 O C:HOH1068 2.1 87.2 1.0 O C:HOH1064 2.1 80.5 1.0 O C:HOH1066 2.1 66.0 1.0 O C:HOH205 3.9 59.1 1.0 O6 C:G37 4.4 55.5 1.0 O6 C:G78 4.6 56.3 1.0 O6 C:G77 4.7 56.6 1.0 O4 C:U36 4.9 58.0 1.0 OP1 C:U76 5.0 51.9 1.0

D.M.Shechner, R.A.Grant, S.C.Bagby, Y.Koldobskaya, J.A.Piccirilli, D.P.Bartel. Crystal Structure of the Catalytic Core of An Rna-Polymerase Ribozyme. Science V. 326 1271 2009.
ISSN: ISSN 0036-8075
PubMed: 19965478
DOI: 10.1126/SCIENCE.1174676